Starting phenix.real_space_refine
on Wed Mar 12 18:43:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ioc_35615/03_2025/8ioc_35615.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ioc_35615/03_2025/8ioc_35615.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ioc_35615/03_2025/8ioc_35615.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ioc_35615/03_2025/8ioc_35615.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ioc_35615/03_2025/8ioc_35615.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ioc_35615/03_2025/8ioc_35615.cif"
  }
  resolution = 2.86
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      67      5.16       5
     C    5219      2.51       5
     N    1422      2.21       5
     O    1514      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8223
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1950
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2616
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
    Chain: "R"
      Number of atoms: 2158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 272, 2158
          Classifications: {'peptide': 272}
          Link IDs: {'PTRANS': 8, 'TRANS': 263}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "L"
      Number of atoms: 107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 107
          Classifications: {'peptide': 11}
          Link IDs: {'TRANS': 10}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "R"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.36, per 1000 atoms: 0.65
  Number of scatterers: 8223
  At special positions: 0
  Unit cell: (84.609, 98.532, 128.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      67     16.00
     O    1514      8.00
     N    1422      7.00
     C    5219      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  35 " - pdb=" SG  CYS R 276 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 268 " - pdb=" SG  CYS R 274 " distance=2.02
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.10
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 10 sheets defined
      40.4% alpha, 19.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.867A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 3.802A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.674A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.587A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.558A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 35
      removed outlier: 3.613A  pdb=" N   THR B  34 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ASN B  35 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 31 through 35'
    Processing helix  chain 'R' and resid 41 through 65
      removed outlier: 4.148A  pdb=" N   PHE R  45 " --> pdb=" O   LYS R  41 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 71 through 103
      removed outlier: 3.702A  pdb=" N   PHE R  75 " --> pdb=" O   SER R  71 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   PHE R  76 " --> pdb=" O   PRO R  72 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LEU R  77 " --> pdb=" O   MET R  73 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 109 through 148
      removed outlier: 3.730A  pdb=" N   ILE R 113 " --> pdb=" O   GLU R 109 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   GLN R 114 " --> pdb=" O   ASP R 110 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   HIS R 115 " --> pdb=" O   GLN R 111 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ILE R 119 " --> pdb=" O   HIS R 115 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   PHE R 120 " --> pdb=" O   MET R 116 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 151 through 155
    Processing helix  chain 'R' and resid 157 through 182
      removed outlier: 3.505A  pdb=" N   TYR R 182 " --> pdb=" O   VAL R 178 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 185 through 223
      removed outlier: 4.473A  pdb=" N   ILE R 189 " --> pdb=" O   SER R 185 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL R 190 " --> pdb=" O   LYS R 186 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   MET R 203 " --> pdb=" O   MET R 199 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA R 223 " --> pdb=" O   LYS R 219 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 235 through 268
      removed outlier: 3.932A  pdb=" N   PHE R 251 " --> pdb=" O   LEU R 247 " (cutoff:3.500A)
      Proline residue:  R 257  - end of helix
    Processing helix  chain 'R' and resid 271 through 279
      removed outlier: 4.120A  pdb=" N   CYS R 276 " --> pdb=" O   PRO R 272 " (cutoff:3.500A)
      removed outlier: 5.275A  pdb=" N   TYR R 277 " --> pdb=" O   TYR R 273 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 280 through 299
      removed outlier: 3.889A  pdb=" N   TYR R 284 " --> pdb=" O   HIS R 280 " (cutoff:3.500A)
      Proline residue:  R 296  - end of helix
    Processing helix  chain 'R' and resid 303 through 313
    Processing helix  chain 'G' and resid 9 through 23
      removed outlier: 3.771A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLU G  22 " --> pdb=" O   GLN G  18 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA G  23 " --> pdb=" O   LEU G  19 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 34
    Processing helix  chain 'G' and resid 39 through 45
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.523A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.828A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.422A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 3.601A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.810A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.817A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.912A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.877A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.911A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.054A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.030A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6
      removed outlier: 3.927A  pdb=" N   THR N  78 " --> pdb=" O   ASP N  73 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ASP N  73 " --> pdb=" O   THR N  78 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 3.695A  pdb=" N   SER N  49 " --> pdb=" O   TRP N  36 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)

    408 hydrogen bonds defined for protein.
    1167 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: 2.33

  Time building geometry restraints manager: 2.52 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1413
        1.32 -     1.45: 2263
        1.45 -     1.57: 4616
        1.57 -     1.69: 0
        1.69 -     1.82: 97
  Bond restraints: 8389
  Sorted by residual:
  bond pdb=" CA  ARG L   7 "
       pdb=" C   ARG L   7 "
    ideal  model  delta    sigma   weight residual
    1.523  1.477  0.046 1.24e-02 6.50e+03 1.40e+01
  bond pdb=" C   HIS L   5 "
       pdb=" O   HIS L   5 "
    ideal  model  delta    sigma   weight residual
    1.236  1.197  0.039 1.17e-02 7.31e+03 1.08e+01
  bond pdb=" N   ARG L   7 "
       pdb=" CA  ARG L   7 "
    ideal  model  delta    sigma   weight residual
    1.455  1.419  0.036 1.32e-02 5.74e+03 7.51e+00
  bond pdb=" CA  HIS L   5 "
       pdb=" CB  HIS L   5 "
    ideal  model  delta    sigma   weight residual
    1.527  1.493  0.034 1.44e-02 4.82e+03 5.45e+00
  bond pdb=" C   HIS L   5 "
       pdb=" N   PHE L   6 "
    ideal  model  delta    sigma   weight residual
    1.327  1.303  0.024 1.06e-02 8.90e+03 5.04e+00
  ... (remaining 8384 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 11138
        2.17 -     4.34: 190
        4.34 -     6.51: 25
        6.51 -     8.67: 5
        8.67 -    10.84: 2
  Bond angle restraints: 11360
  Sorted by residual:
  angle pdb=" C   PHE L   6 "
        pdb=" CA  PHE L   6 "
        pdb=" CB  PHE L   6 "
      ideal   model   delta    sigma   weight residual
     116.34  110.74    5.60 1.40e+00 5.10e-01 1.60e+01
  angle pdb=" N   ARG L   7 "
        pdb=" CA  ARG L   7 "
        pdb=" C   ARG L   7 "
      ideal   model   delta    sigma   weight residual
     108.74  113.59   -4.85 1.38e+00 5.25e-01 1.23e+01
  angle pdb=" N   ASN G  24 "
        pdb=" CA  ASN G  24 "
        pdb=" C   ASN G  24 "
      ideal   model   delta    sigma   weight residual
     114.56  110.57    3.99 1.27e+00 6.20e-01 9.85e+00
  angle pdb=" C   LYS N  33 "
        pdb=" N   MET N  34 "
        pdb=" CA  MET N  34 "
      ideal   model   delta    sigma   weight residual
     122.59  118.15    4.44 1.57e+00 4.06e-01 8.00e+00
  angle pdb=" CB  MET R  97 "
        pdb=" CG  MET R  97 "
        pdb=" SD  MET R  97 "
      ideal   model   delta    sigma   weight residual
     112.70  104.34    8.36 3.00e+00 1.11e-01 7.77e+00
  ... (remaining 11355 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.49: 4498
       17.49 -    34.97: 413
       34.97 -    52.46: 79
       52.46 -    69.94: 12
       69.94 -    87.42: 8
  Dihedral angle restraints: 5010
    sinusoidal: 1972
      harmonic: 3038
  Sorted by residual:
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   58.72   34.28     1      1.00e+01 1.00e-02 1.67e+01
  dihedral pdb=" CA  ASP G  36 "
           pdb=" C   ASP G  36 "
           pdb=" N   LEU G  37 "
           pdb=" CA  LEU G  37 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.20   19.80     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  TYR R 182 "
           pdb=" C   TYR R 182 "
           pdb=" N   SER R 183 "
           pdb=" CA  SER R 183 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.57  -19.43     0      5.00e+00 4.00e-02 1.51e+01
  ... (remaining 5007 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 754
       0.037 -    0.074: 378
       0.074 -    0.111: 116
       0.111 -    0.148: 38
       0.148 -    0.185: 5
  Chirality restraints: 1291
  Sorted by residual:
  chirality pdb=" CA  HIS L   5 "
            pdb=" N   HIS L   5 "
            pdb=" C   HIS L   5 "
            pdb=" CB  HIS L   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.19 2.00e-01 2.50e+01 8.58e-01
  chirality pdb=" CA  ILE B 273 "
            pdb=" N   ILE B 273 "
            pdb=" C   ILE B 273 "
            pdb=" CB  ILE B 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.46e-01
  chirality pdb=" CA  VAL L   2 "
            pdb=" N   VAL L   2 "
            pdb=" C   VAL L   2 "
            pdb=" CB  VAL L   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.40e-01
  ... (remaining 1288 not shown)

  Planarity restraints: 1444
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 281 "    0.019 2.00e-02 2.50e+03   1.37e-02 4.69e+00
        pdb=" CG  TRP A 281 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 281 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 281 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 281 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 281 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 281 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 281 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 281 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 281 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA R 256 "    0.033 5.00e-02 4.00e+02   4.93e-02 3.89e+00
        pdb=" N   PRO R 257 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO R 257 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO R 257 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN N  13 "   -0.030 5.00e-02 4.00e+02   4.58e-02 3.35e+00
        pdb=" N   PRO N  14 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO N  14 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO N  14 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1441 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 907
        2.74 -     3.28: 7965
        3.28 -     3.82: 13555
        3.82 -     4.36: 16080
        4.36 -     4.90: 28045
  Nonbonded interactions: 66552
  Sorted by model distance:
  nonbonded pdb=" NE1 TRP R 255 "
            pdb=" OD1 ASN R 291 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" NH1 ARG A 232 "
            pdb=" OD2 ASP N 109 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" O   MET B 325 "
            pdb=" ND2 ASN B 340 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" OE2 GLU R  94 "
            pdb="CA    CA R 501 "
     model   vdw
     2.243 2.510
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.244 3.040
  ... (remaining 66547 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:             1.170
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     22.970
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   8389  Z= 0.486
  Angle     :  0.728  10.843  11360  Z= 0.406
  Chirality :  0.049   0.185   1291
  Planarity :  0.005   0.049   1444
  Dihedral  : 14.043  87.425   3030
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.55 %
    Favored  : 99.33 %
  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: -0.98 (0.25), residues: 1025
  helix:  0.31 (0.26), residues: 401
  sheet: -0.75 (0.32), residues: 234
  loop : -1.50 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP A 281 
 HIS   0.008   0.002   HIS L   5 
 PHE   0.030   0.002   PHE B 235 
 TYR   0.027   0.002   TYR B  59 
 ARG   0.009   0.001   ARG R 151 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 239
  time to evaluate  : 1.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 240
  average time/residue: 1.2311
  time to fit residues: 313.7762
Evaluate side-chains
  157 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 156
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 77 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 92 optimal weight:    5.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
B  75 GLN
B  91 HIS
B 155 ASN
B 259 GLN
** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  18 GLN
G  44 HIS
L   5 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.125749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.088247 restraints weight = 15843.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 3.93
r_work: 0.3111 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8389  Z= 0.264
  Angle     :  0.673  13.356  11360  Z= 0.344
  Chirality :  0.043   0.136   1291
  Planarity :  0.004   0.049   1444
  Dihedral  :  5.003  47.759   1137
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 13.65 %
    Favored  : 83.35 %
  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: -0.27 (0.26), residues: 1025
  helix:  1.01 (0.26), residues: 398
  sheet: -0.33 (0.34), residues: 219
  loop : -1.22 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 234 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.014   0.002   PHE R 259 
 TYR   0.017   0.002   TYR R 277 
 ARG   0.008   0.001   ARG A 280 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 168
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ASP cc_start: 0.8438 (t0) cc_final: 0.7822 (t0)
REVERT: A  279 ASN cc_start: 0.9123 (t0) cc_final: 0.8873 (t0)
REVERT: B  172 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8929 (tp30)
REVERT: B  175 GLN cc_start: 0.8791 (mp10) cc_final: 0.8563 (mp10)
REVERT: B  260 GLU cc_start: 0.8627 (pp20) cc_final: 0.8343 (tm-30)
REVERT: B  280 LYS cc_start: 0.9018 (tptp) cc_final: 0.8555 (tptp)
REVERT: B  292 PHE cc_start: 0.8988 (m-10) cc_final: 0.8767 (m-10)
REVERT: B  325 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8924 (mpp)
REVERT: R   41 LYS cc_start: 0.8720 (ttpt) cc_final: 0.8281 (tmmt)
REVERT: R  277 TYR cc_start: 0.8783 (t80) cc_final: 0.8399 (t80)
REVERT: R  281 PHE cc_start: 0.8299 (t80) cc_final: 0.8087 (t80)
REVERT: G   21 MET cc_start: 0.8035 (tpt) cc_final: 0.7699 (tpt)
REVERT: G   24 ASN cc_start: 0.9184 (t0) cc_final: 0.8508 (m110)
REVERT: G   28 ILE cc_start: 0.8810 (mp) cc_final: 0.8585 (mp)
REVERT: G   47 GLU cc_start: 0.8105 (pm20) cc_final: 0.7719 (pm20)
  outliers start: 27
  outliers final: 12
  residues processed: 178
  average time/residue: 1.4929
  time to fit residues: 281.7561
Evaluate side-chains
  154 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 141
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain R residue   73 MET
Chi-restraints excluded: chain R residue   86 LEU
Chi-restraints excluded: chain R residue   96 ILE
Chi-restraints excluded: chain R residue  102 HIS
Chi-restraints excluded: chain R residue  117 ASP
Chi-restraints excluded: chain R residue  293 VAL
Chi-restraints excluded: chain G residue   19 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 87 optimal weight:    5.9990
   chunk 86 optimal weight:    9.9990
   chunk 28 optimal weight:    4.9990
   chunk 57 optimal weight:    8.9990
   chunk 13 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 95 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 291 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.126585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.089482 restraints weight = 16162.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 4.00
r_work: 0.3131 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.3157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8389  Z= 0.203
  Angle     :  0.631  13.318  11360  Z= 0.318
  Chirality :  0.042   0.137   1291
  Planarity :  0.004   0.043   1444
  Dihedral  :  4.737  48.088   1135
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 15.21 %
    Favored  : 81.58 %
  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:  0.14 (0.26), residues: 1025
  helix:  1.51 (0.27), residues: 394
  sheet: -0.28 (0.33), residues: 239
  loop : -1.08 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 234 
 HIS   0.007   0.001   HIS R 261 
 PHE   0.012   0.001   PHE R 310 
 TYR   0.013   0.001   TYR N  60 
 ARG   0.008   0.001   ARG L   7 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 162
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLN cc_start: 0.8649 (tt0) cc_final: 0.8383 (tt0)
REVERT: A  209 GLU cc_start: 0.8310 (tt0) cc_final: 0.7913 (tm-30)
REVERT: A  229 ASP cc_start: 0.8445 (t0) cc_final: 0.7823 (t0)
REVERT: A  279 ASN cc_start: 0.9110 (t0) cc_final: 0.8862 (t0)
REVERT: A  302 LEU cc_start: 0.9726 (mm) cc_final: 0.9457 (mm)
REVERT: A  349 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.8867 (p)
REVERT: B  172 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8998 (tp30)
REVERT: B  175 GLN cc_start: 0.8803 (mp10) cc_final: 0.8552 (mp10)
REVERT: B  227 SER cc_start: 0.8934 (t) cc_final: 0.8680 (p)
REVERT: B  280 LYS cc_start: 0.8937 (tptp) cc_final: 0.8270 (tptp)
REVERT: B  292 PHE cc_start: 0.9094 (m-10) cc_final: 0.8826 (m-10)
REVERT: R   41 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8148 (tmmt)
REVERT: R   65 ARG cc_start: 0.8590 (ttp-170) cc_final: 0.8092 (ttm170)
REVERT: R  111 GLN cc_start: 0.8766 (tp-100) cc_final: 0.8221 (tp-100)
REVERT: R  115 HIS cc_start: 0.7848 (m90) cc_final: 0.7114 (m90)
REVERT: R  116 MET cc_start: 0.8615 (tmm) cc_final: 0.8011 (mpt)
REVERT: R  277 TYR cc_start: 0.8845 (t80) cc_final: 0.8435 (t80)
REVERT: R  305 GLU cc_start: 0.8487 (pm20) cc_final: 0.8144 (pm20)
REVERT: G   17 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8475 (pt0)
REVERT: G   21 MET cc_start: 0.8201 (tpt) cc_final: 0.7791 (tpt)
REVERT: G   24 ASN cc_start: 0.9238 (t0) cc_final: 0.8615 (m110)
REVERT: G   28 ILE cc_start: 0.8815 (mp) cc_final: 0.8570 (mp)
REVERT: G   29 LYS cc_start: 0.9310 (mmmt) cc_final: 0.9016 (mmmt)
REVERT: L    1 TYR cc_start: 0.7271 (t80) cc_final: 0.6929 (t80)
  outliers start: 29
  outliers final: 9
  residues processed: 177
  average time/residue: 1.2956
  time to fit residues: 242.5717
Evaluate side-chains
  159 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 149
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain R residue   73 MET
Chi-restraints excluded: chain R residue   96 ILE
Chi-restraints excluded: chain R residue  102 HIS
Chi-restraints excluded: chain R residue  117 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 99 optimal weight:   20.0000
   chunk 97 optimal weight:    0.8980
   chunk 98 optimal weight:    6.9990
   chunk 71 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
B  75 GLN
R 291 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.126558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.089966 restraints weight = 16020.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 3.90
r_work: 0.3114 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.3455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8389  Z= 0.225
  Angle     :  0.628  13.614  11360  Z= 0.315
  Chirality :  0.042   0.189   1291
  Planarity :  0.004   0.042   1444
  Dihedral  :  4.651  48.659   1135
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 17.09 %
    Favored  : 79.25 %
  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:  0.28 (0.27), residues: 1025
  helix:  1.63 (0.27), residues: 399
  sheet: -0.23 (0.33), residues: 240
  loop : -1.03 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.003   0.001   HIS R 261 
 PHE   0.012   0.001   PHE R 259 
 TYR   0.010   0.001   TYR L   1 
 ARG   0.009   0.001   ARG L   7 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 158
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ASP cc_start: 0.8490 (t0) cc_final: 0.7869 (t0)
REVERT: A  253 TYR cc_start: 0.8800 (m-80) cc_final: 0.8278 (m-80)
REVERT: A  279 ASN cc_start: 0.9146 (t0) cc_final: 0.8906 (t0)
REVERT: A  349 SER cc_start: 0.9336 (OUTLIER) cc_final: 0.8902 (p)
REVERT: B   32 GLN cc_start: 0.8874 (mt0) cc_final: 0.8632 (mt0)
REVERT: B  172 GLU cc_start: 0.9264 (mm-30) cc_final: 0.9036 (tp30)
REVERT: B  227 SER cc_start: 0.8918 (t) cc_final: 0.8692 (p)
REVERT: B  280 LYS cc_start: 0.8980 (tptp) cc_final: 0.8153 (tptp)
REVERT: B  291 ASP cc_start: 0.8905 (m-30) cc_final: 0.8508 (m-30)
REVERT: B  292 PHE cc_start: 0.9192 (m-10) cc_final: 0.8936 (m-10)
REVERT: R   41 LYS cc_start: 0.8588 (ttpt) cc_final: 0.8153 (tmmt)
REVERT: R   65 ARG cc_start: 0.8484 (tpp-160) cc_final: 0.8058 (ttm170)
REVERT: R  111 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8384 (tp-100)
REVERT: R  115 HIS cc_start: 0.8031 (m90) cc_final: 0.7137 (m90)
REVERT: R  116 MET cc_start: 0.8852 (tmm) cc_final: 0.8075 (tpt)
REVERT: R  191 CYS cc_start: 0.8454 (t) cc_final: 0.8091 (t)
REVERT: R  277 TYR cc_start: 0.8901 (t80) cc_final: 0.8479 (t80)
REVERT: R  281 PHE cc_start: 0.8319 (t80) cc_final: 0.8038 (t80)
REVERT: R  305 GLU cc_start: 0.8409 (pm20) cc_final: 0.8028 (pm20)
REVERT: R  307 ARG cc_start: 0.8672 (mmm-85) cc_final: 0.8470 (mmm-85)
REVERT: R  308 ASN cc_start: 0.8729 (m-40) cc_final: 0.8195 (p0)
REVERT: G   17 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8559 (pt0)
REVERT: G   21 MET cc_start: 0.8295 (tpt) cc_final: 0.7837 (tpt)
REVERT: G   24 ASN cc_start: 0.9206 (t0) cc_final: 0.8638 (m110)
REVERT: G   28 ILE cc_start: 0.8886 (mp) cc_final: 0.8659 (mp)
REVERT: L    1 TYR cc_start: 0.7376 (t80) cc_final: 0.6995 (t80)
  outliers start: 33
  outliers final: 12
  residues processed: 172
  average time/residue: 1.2983
  time to fit residues: 237.1129
Evaluate side-chains
  162 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 149
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue   93 LEU
Chi-restraints excluded: chain R residue   96 ILE
Chi-restraints excluded: chain R residue  102 HIS
Chi-restraints excluded: chain R residue  117 ASP
Chi-restraints excluded: chain G residue   19 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 30 optimal weight:    0.0470
   chunk 57 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 37 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 230 ASN
** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.126292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.089276 restraints weight = 15729.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 3.83
r_work: 0.3137 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.3762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8389  Z= 0.183
  Angle     :  0.619  13.633  11360  Z= 0.310
  Chirality :  0.041   0.160   1291
  Planarity :  0.003   0.042   1444
  Dihedral  :  4.527  48.099   1135
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 19.31 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.27), residues: 1025
  helix:  1.79 (0.27), residues: 399
  sheet: -0.12 (0.33), residues: 245
  loop : -0.92 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.003   0.000   HIS R 261 
 PHE   0.011   0.001   PHE R 310 
 TYR   0.014   0.001   TYR N  60 
 ARG   0.007   0.001   ARG R 151 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 164
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.9412 (tmmt) cc_final: 0.9054 (pptt)
REVERT: A  229 ASP cc_start: 0.8467 (t0) cc_final: 0.7813 (t0)
REVERT: A  253 TYR cc_start: 0.8744 (m-80) cc_final: 0.8218 (m-80)
REVERT: A  279 ASN cc_start: 0.9178 (t0) cc_final: 0.8932 (t0)
REVERT: B   32 GLN cc_start: 0.8906 (mt0) cc_final: 0.8691 (mt0)
REVERT: B  172 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8819 (tp30)
REVERT: B  175 GLN cc_start: 0.8721 (mp10) cc_final: 0.8501 (mp10)
REVERT: B  217 MET cc_start: 0.8727 (pmt) cc_final: 0.8212 (pmm)
REVERT: B  280 LYS cc_start: 0.8989 (tptp) cc_final: 0.8269 (tptp)
REVERT: B  291 ASP cc_start: 0.8911 (m-30) cc_final: 0.8508 (m-30)
REVERT: B  292 PHE cc_start: 0.9200 (m-10) cc_final: 0.8922 (m-10)
REVERT: R   41 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8125 (tmmt)
REVERT: R   65 ARG cc_start: 0.8517 (tpp-160) cc_final: 0.8051 (ttm170)
REVERT: R   85 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8667 (ppp)
REVERT: R  111 GLN cc_start: 0.8962 (tp-100) cc_final: 0.8371 (tp-100)
REVERT: R  115 HIS cc_start: 0.7830 (m90) cc_final: 0.7061 (m90)
REVERT: R  191 CYS cc_start: 0.8491 (t) cc_final: 0.8152 (t)
REVERT: R  253 PHE cc_start: 0.8820 (m-10) cc_final: 0.8059 (t80)
REVERT: R  277 TYR cc_start: 0.8862 (t80) cc_final: 0.8455 (t80)
REVERT: R  281 PHE cc_start: 0.8252 (t80) cc_final: 0.8012 (t80)
REVERT: R  305 GLU cc_start: 0.8438 (pm20) cc_final: 0.8178 (pm20)
REVERT: R  307 ARG cc_start: 0.8715 (mmm-85) cc_final: 0.8375 (mmm-85)
REVERT: R  308 ASN cc_start: 0.8740 (m-40) cc_final: 0.8241 (p0)
REVERT: G   17 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8564 (pt0)
REVERT: G   21 MET cc_start: 0.8411 (tpt) cc_final: 0.7877 (tpt)
REVERT: G   24 ASN cc_start: 0.9200 (t0) cc_final: 0.8725 (m110)
REVERT: G   28 ILE cc_start: 0.8906 (mp) cc_final: 0.8656 (mp)
REVERT: L    1 TYR cc_start: 0.7375 (t80) cc_final: 0.7022 (t80)
REVERT: N   47 TRP cc_start: 0.8323 (t60) cc_final: 0.8054 (t60)
REVERT: N   83 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7532 (mmt)
  outliers start: 27
  outliers final: 12
  residues processed: 177
  average time/residue: 1.3573
  time to fit residues: 254.6441
Evaluate side-chains
  156 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 142
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue   85 MET
Chi-restraints excluded: chain R residue   96 ILE
Chi-restraints excluded: chain R residue  102 HIS
Chi-restraints excluded: chain R residue  201 LEU
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue   83 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 80 optimal weight:    0.6980
   chunk 93 optimal weight:    8.9990
   chunk 84 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 52 optimal weight:    0.8980
   chunk 68 optimal weight:    0.3980
   chunk 71 optimal weight:    0.0470
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   5 HIS
N  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.126463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.089823 restraints weight = 15696.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 3.80
r_work: 0.3153 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.3997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8389  Z= 0.176
  Angle     :  0.623  12.707  11360  Z= 0.309
  Chirality :  0.042   0.148   1291
  Planarity :  0.003   0.042   1444
  Dihedral  :  4.442  47.802   1135
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 20.31 %
    Favored  : 76.14 %
  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:  0.61 (0.27), residues: 1025
  helix:  1.88 (0.27), residues: 399
  sheet: -0.05 (0.32), residues: 245
  loop : -0.84 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.003   0.000   HIS R 261 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.008   0.001   TYR L   1 
 ARG   0.008   0.000   ARG R 151 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 153
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ASP cc_start: 0.8537 (t0) cc_final: 0.7900 (t0)
REVERT: A  253 TYR cc_start: 0.8752 (m-80) cc_final: 0.8403 (m-80)
REVERT: A  279 ASN cc_start: 0.9210 (t0) cc_final: 0.8965 (t0)
REVERT: B   59 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.8361 (m-80)
REVERT: B  172 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8845 (tp30)
REVERT: B  175 GLN cc_start: 0.8709 (mp10) cc_final: 0.8472 (mp10)
REVERT: B  217 MET cc_start: 0.8728 (pmt) cc_final: 0.8206 (pmm)
REVERT: B  226 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7719 (mm-30)
REVERT: B  234 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.8033 (m-80)
REVERT: B  280 LYS cc_start: 0.8939 (tptp) cc_final: 0.8041 (tptp)
REVERT: B  291 ASP cc_start: 0.8912 (m-30) cc_final: 0.8550 (m-30)
REVERT: B  292 PHE cc_start: 0.9204 (m-10) cc_final: 0.8936 (m-10)
REVERT: R   41 LYS cc_start: 0.8452 (ttpt) cc_final: 0.7996 (tmmt)
REVERT: R   82 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8401 (p)
REVERT: R   85 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8537 (ppp)
REVERT: R  191 CYS cc_start: 0.8498 (t) cc_final: 0.8165 (t)
REVERT: R  253 PHE cc_start: 0.8774 (m-10) cc_final: 0.7991 (t80)
REVERT: R  277 TYR cc_start: 0.8836 (t80) cc_final: 0.8398 (t80)
REVERT: R  281 PHE cc_start: 0.8217 (t80) cc_final: 0.7972 (t80)
REVERT: R  305 GLU cc_start: 0.8347 (pm20) cc_final: 0.7987 (pm20)
REVERT: R  307 ARG cc_start: 0.8793 (mmm-85) cc_final: 0.8470 (mmm-85)
REVERT: R  308 ASN cc_start: 0.8691 (m-40) cc_final: 0.8245 (p0)
REVERT: G   17 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8565 (pt0)
REVERT: G   21 MET cc_start: 0.8498 (tpt) cc_final: 0.7970 (tpt)
REVERT: G   24 ASN cc_start: 0.9161 (t0) cc_final: 0.8737 (m110)
REVERT: G   28 ILE cc_start: 0.8956 (mp) cc_final: 0.8723 (mp)
REVERT: G   38 MET cc_start: 0.9145 (ttp) cc_final: 0.8779 (tmm)
REVERT: G   47 GLU cc_start: 0.8218 (pm20) cc_final: 0.7888 (pm20)
REVERT: L    1 TYR cc_start: 0.7393 (t80) cc_final: 0.7062 (t80)
REVERT: N   47 TRP cc_start: 0.8409 (t60) cc_final: 0.8148 (t60)
REVERT: N   83 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7468 (mmt)
  outliers start: 32
  outliers final: 9
  residues processed: 169
  average time/residue: 1.1015
  time to fit residues: 198.5118
Evaluate side-chains
  162 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain R residue   82 VAL
Chi-restraints excluded: chain R residue   85 MET
Chi-restraints excluded: chain R residue  102 HIS
Chi-restraints excluded: chain R residue  117 ASP
Chi-restraints excluded: chain N residue   83 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   chunk 83 optimal weight:    0.6980
   chunk 94 optimal weight:    6.9990
   chunk 80 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 97 optimal weight:    0.4980
   chunk 50 optimal weight:    4.9990
   chunk 93 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
N  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.130040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.093219 restraints weight = 15927.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 3.88
r_work: 0.3131 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.4106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8389  Z= 0.203
  Angle     :  0.647  14.127  11360  Z= 0.322
  Chirality :  0.041   0.180   1291
  Planarity :  0.004   0.043   1444
  Dihedral  :  4.426  47.840   1135
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.09 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.27), residues: 1025
  helix:  1.87 (0.27), residues: 399
  sheet:  0.03 (0.33), residues: 238
  loop : -0.83 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 234 
 HIS   0.003   0.001   HIS R 261 
 PHE   0.012   0.001   PHE R 310 
 TYR   0.014   0.001   TYR N  60 
 ARG   0.009   0.001   ARG L   7 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 146
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.9381 (tmmt) cc_final: 0.8894 (pptt)
REVERT: A   59 GLN cc_start: 0.8661 (tt0) cc_final: 0.8281 (tt0)
REVERT: A  229 ASP cc_start: 0.8554 (t0) cc_final: 0.7904 (t0)
REVERT: A  253 TYR cc_start: 0.8794 (m-80) cc_final: 0.8443 (m-80)
REVERT: A  279 ASN cc_start: 0.9227 (t0) cc_final: 0.8964 (t0)
REVERT: B  172 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8978 (tp30)
REVERT: B  175 GLN cc_start: 0.8727 (mp10) cc_final: 0.8494 (mp10)
REVERT: B  226 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7761 (mm-30)
REVERT: B  234 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.8049 (m-80)
REVERT: B  280 LYS cc_start: 0.8909 (tptp) cc_final: 0.8101 (tptp)
REVERT: B  291 ASP cc_start: 0.8926 (m-30) cc_final: 0.8541 (m-30)
REVERT: B  292 PHE cc_start: 0.9230 (m-10) cc_final: 0.8966 (m-10)
REVERT: R   41 LYS cc_start: 0.8554 (ttpt) cc_final: 0.8205 (tmmt)
REVERT: R   82 VAL cc_start: 0.8645 (p) cc_final: 0.8431 (p)
REVERT: R   85 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8568 (ppp)
REVERT: R  116 MET cc_start: 0.8295 (ppp) cc_final: 0.7812 (mtt)
REVERT: R  156 MET cc_start: 0.8563 (tpp) cc_final: 0.8283 (tpp)
REVERT: R  191 CYS cc_start: 0.8505 (t) cc_final: 0.8184 (t)
REVERT: R  253 PHE cc_start: 0.8782 (m-10) cc_final: 0.8003 (t80)
REVERT: R  277 TYR cc_start: 0.8867 (t80) cc_final: 0.8473 (t80)
REVERT: R  281 PHE cc_start: 0.8259 (t80) cc_final: 0.8030 (t80)
REVERT: R  291 ASN cc_start: 0.8025 (t0) cc_final: 0.7638 (t0)
REVERT: R  307 ARG cc_start: 0.8753 (mmm-85) cc_final: 0.8454 (mmm-85)
REVERT: R  308 ASN cc_start: 0.8713 (m-40) cc_final: 0.8268 (p0)
REVERT: G   17 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8557 (pt0)
REVERT: G   21 MET cc_start: 0.8582 (tpt) cc_final: 0.8307 (tpt)
REVERT: G   28 ILE cc_start: 0.8909 (mp) cc_final: 0.8658 (mp)
REVERT: G   38 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8773 (tmm)
REVERT: G   47 GLU cc_start: 0.8297 (pm20) cc_final: 0.7904 (pm20)
REVERT: L    1 TYR cc_start: 0.7477 (t80) cc_final: 0.7159 (t80)
REVERT: N   83 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7479 (mmt)
  outliers start: 28
  outliers final: 14
  residues processed: 162
  average time/residue: 1.2952
  time to fit residues: 222.6055
Evaluate side-chains
  157 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue   85 MET
Chi-restraints excluded: chain R residue  102 HIS
Chi-restraints excluded: chain R residue  117 ASP
Chi-restraints excluded: chain R residue  201 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   83 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
R  70 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.125792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.088747 restraints weight = 16017.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 3.84
r_work: 0.3134 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.4214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8389  Z= 0.204
  Angle     :  0.646  13.444  11360  Z= 0.323
  Chirality :  0.041   0.156   1291
  Planarity :  0.004   0.043   1444
  Dihedral  :  4.440  47.821   1135
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 20.75 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.27), residues: 1025
  helix:  1.90 (0.27), residues: 394
  sheet:  0.01 (0.33), residues: 250
  loop : -0.78 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP N  47 
 HIS   0.003   0.001   HIS R 261 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.008   0.001   ARG R 151 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 146
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.9397 (tmmt) cc_final: 0.9029 (pptt)
REVERT: A  229 ASP cc_start: 0.8511 (t0) cc_final: 0.7857 (t0)
REVERT: A  253 TYR cc_start: 0.8805 (m-80) cc_final: 0.8467 (m-80)
REVERT: A  279 ASN cc_start: 0.9225 (t0) cc_final: 0.8962 (t0)
REVERT: B  172 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8908 (tp30)
REVERT: B  175 GLN cc_start: 0.8758 (mp10) cc_final: 0.8518 (mp10)
REVERT: B  217 MET cc_start: 0.8800 (pmt) cc_final: 0.8303 (pmm)
REVERT: B  226 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7772 (mm-30)
REVERT: B  234 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.8034 (m-80)
REVERT: B  280 LYS cc_start: 0.8934 (tptp) cc_final: 0.8141 (tptp)
REVERT: B  291 ASP cc_start: 0.8909 (m-30) cc_final: 0.8527 (m-30)
REVERT: B  292 PHE cc_start: 0.9289 (m-10) cc_final: 0.9035 (m-10)
REVERT: R   41 LYS cc_start: 0.8588 (ttpt) cc_final: 0.8282 (tmmt)
REVERT: R   82 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8424 (p)
REVERT: R   85 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8558 (ppp)
REVERT: R  116 MET cc_start: 0.8313 (ppp) cc_final: 0.7811 (mmt)
REVERT: R  156 MET cc_start: 0.8562 (tpp) cc_final: 0.8255 (tpp)
REVERT: R  191 CYS cc_start: 0.8529 (t) cc_final: 0.8201 (t)
REVERT: R  253 PHE cc_start: 0.8820 (m-10) cc_final: 0.8002 (t80)
REVERT: R  277 TYR cc_start: 0.8863 (t80) cc_final: 0.8383 (t80)
REVERT: R  281 PHE cc_start: 0.8266 (t80) cc_final: 0.8045 (t80)
REVERT: R  291 ASN cc_start: 0.8096 (t0) cc_final: 0.7743 (t0)
REVERT: R  305 GLU cc_start: 0.8447 (pm20) cc_final: 0.8147 (pm20)
REVERT: R  307 ARG cc_start: 0.8787 (mmm-85) cc_final: 0.8476 (mmm-85)
REVERT: G   17 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8601 (pt0)
REVERT: G   21 MET cc_start: 0.8586 (tpt) cc_final: 0.8339 (tpt)
REVERT: G   38 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8712 (tmm)
REVERT: G   47 GLU cc_start: 0.8375 (pm20) cc_final: 0.8009 (pm20)
REVERT: L    1 TYR cc_start: 0.7558 (t80) cc_final: 0.7285 (t80)
REVERT: N   83 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7621 (mmt)
REVERT: N  117 TYR cc_start: 0.8090 (m-80) cc_final: 0.7792 (m-10)
  outliers start: 25
  outliers final: 15
  residues processed: 160
  average time/residue: 1.2239
  time to fit residues: 207.9445
Evaluate side-chains
  163 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 ASN
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue   82 VAL
Chi-restraints excluded: chain R residue   85 MET
Chi-restraints excluded: chain R residue   96 ILE
Chi-restraints excluded: chain R residue  102 HIS
Chi-restraints excluded: chain R residue  117 ASP
Chi-restraints excluded: chain R residue  201 LEU
Chi-restraints excluded: chain R residue  217 HIS
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   83 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 93 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.130463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.093085 restraints weight = 16328.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 3.95
r_work: 0.3127 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.4349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8389  Z= 0.217
  Angle     :  0.684  13.234  11360  Z= 0.339
  Chirality :  0.042   0.159   1291
  Planarity :  0.004   0.041   1444
  Dihedral  :  4.480  48.003   1135
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 21.75 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.27), residues: 1025
  helix:  1.86 (0.27), residues: 394
  sheet: -0.05 (0.33), residues: 250
  loop : -0.75 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP N  47 
 HIS   0.003   0.001   HIS R 261 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.019   0.001   TYR R  74 
 ARG   0.008   0.001   ARG R 151 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 154
  time to evaluate  : 1.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ASP cc_start: 0.8536 (t0) cc_final: 0.7865 (t0)
REVERT: A  253 TYR cc_start: 0.8803 (m-80) cc_final: 0.8410 (m-80)
REVERT: A  279 ASN cc_start: 0.9219 (t0) cc_final: 0.8958 (t0)
REVERT: B  172 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8911 (tp30)
REVERT: B  175 GLN cc_start: 0.8782 (mp10) cc_final: 0.8539 (mp10)
REVERT: B  217 MET cc_start: 0.8758 (pmt) cc_final: 0.8242 (pmm)
REVERT: B  234 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.8025 (m-80)
REVERT: B  280 LYS cc_start: 0.8965 (tptp) cc_final: 0.8225 (tptp)
REVERT: B  291 ASP cc_start: 0.8921 (m-30) cc_final: 0.8534 (m-30)
REVERT: B  292 PHE cc_start: 0.9280 (m-10) cc_final: 0.9025 (m-10)
REVERT: R   37 GLN cc_start: 0.8829 (tp40) cc_final: 0.8625 (tm-30)
REVERT: R   41 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8363 (tmmt)
REVERT: R   73 MET cc_start: 0.8970 (ptm) cc_final: 0.8227 (ppp)
REVERT: R   82 VAL cc_start: 0.8623 (OUTLIER) cc_final: 0.8402 (p)
REVERT: R   85 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8569 (ppp)
REVERT: R  116 MET cc_start: 0.8197 (ppp) cc_final: 0.7835 (mtt)
REVERT: R  156 MET cc_start: 0.8591 (tpp) cc_final: 0.8294 (tpp)
REVERT: R  171 CYS cc_start: 0.8928 (m) cc_final: 0.8625 (m)
REVERT: R  191 CYS cc_start: 0.8542 (t) cc_final: 0.8055 (t)
REVERT: R  253 PHE cc_start: 0.8807 (m-10) cc_final: 0.8018 (t80)
REVERT: R  277 TYR cc_start: 0.8889 (t80) cc_final: 0.8473 (t80)
REVERT: R  281 PHE cc_start: 0.8303 (t80) cc_final: 0.8041 (t80)
REVERT: R  307 ARG cc_start: 0.8743 (mmm-85) cc_final: 0.8480 (mmm-85)
REVERT: G   21 MET cc_start: 0.8613 (tpt) cc_final: 0.8337 (tpt)
REVERT: G   38 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8675 (tmm)
REVERT: G   47 GLU cc_start: 0.8474 (pm20) cc_final: 0.8136 (pm20)
REVERT: L    1 TYR cc_start: 0.7650 (t80) cc_final: 0.7241 (t80)
REVERT: N   83 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7622 (mmt)
REVERT: N  117 TYR cc_start: 0.8145 (m-80) cc_final: 0.7538 (m-10)
  outliers start: 23
  outliers final: 17
  residues processed: 166
  average time/residue: 1.2384
  time to fit residues: 218.0110
Evaluate side-chains
  165 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 ASN
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue   82 VAL
Chi-restraints excluded: chain R residue   85 MET
Chi-restraints excluded: chain R residue   96 ILE
Chi-restraints excluded: chain R residue  102 HIS
Chi-restraints excluded: chain R residue  201 LEU
Chi-restraints excluded: chain R residue  217 HIS
Chi-restraints excluded: chain R residue  245 THR
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   83 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 100 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 90 optimal weight:    0.9990
   chunk 88 optimal weight:    0.2980
   chunk 97 optimal weight:    0.0270
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** B  17 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 = 0.3912 r_free = 0.3912 target = 0.127263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.090209 restraints weight = 16004.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 3.85
r_work: 0.3159 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.4483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8389  Z= 0.195
  Angle     :  0.691  13.085  11360  Z= 0.343
  Chirality :  0.042   0.162   1291
  Planarity :  0.004   0.072   1444
  Dihedral  :  4.439  47.556   1135
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 22.86 %
    Favored  : 75.25 %
  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:  0.69 (0.27), residues: 1025
  helix:  1.87 (0.27), residues: 393
  sheet:  0.08 (0.33), residues: 244
  loop : -0.72 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP N  47 
 HIS   0.003   0.001   HIS R 261 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.011   0.001   TYR R  74 
 ARG   0.018   0.001   ARG L   7 

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.9397 (tmmt) cc_final: 0.9015 (pptt)
REVERT: A   59 GLN cc_start: 0.8664 (tt0) cc_final: 0.8264 (tt0)
REVERT: A  229 ASP cc_start: 0.8493 (t0) cc_final: 0.7797 (t0)
REVERT: A  253 TYR cc_start: 0.8740 (m-80) cc_final: 0.8379 (m-80)
REVERT: A  279 ASN cc_start: 0.9223 (t0) cc_final: 0.9008 (t0)
REVERT: A  390 GLN cc_start: 0.9359 (tt0) cc_final: 0.8931 (tm-30)
REVERT: B  172 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8930 (tp30)
REVERT: B  175 GLN cc_start: 0.8757 (mp10) cc_final: 0.8493 (mp10)
REVERT: B  217 MET cc_start: 0.8813 (pmt) cc_final: 0.8289 (pmm)
REVERT: B  226 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7745 (tp30)
REVERT: B  234 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7972 (m-80)
REVERT: B  254 ASP cc_start: 0.8084 (t0) cc_final: 0.7574 (t0)
REVERT: B  280 LYS cc_start: 0.8985 (tptp) cc_final: 0.8267 (tptp)
REVERT: B  291 ASP cc_start: 0.8930 (m-30) cc_final: 0.8525 (m-30)
REVERT: B  292 PHE cc_start: 0.9333 (m-10) cc_final: 0.9065 (m-10)
REVERT: R   37 GLN cc_start: 0.8807 (tp40) cc_final: 0.8601 (tm-30)
REVERT: R   41 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8371 (tmmt)
REVERT: R   73 MET cc_start: 0.9026 (ptm) cc_final: 0.8218 (ppp)
REVERT: R   85 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8473 (ppp)
REVERT: R   97 MET cc_start: 0.8748 (tpt) cc_final: 0.8545 (ttt)
REVERT: R  116 MET cc_start: 0.8230 (ppp) cc_final: 0.7808 (mtt)
REVERT: R  156 MET cc_start: 0.8596 (tpp) cc_final: 0.8319 (tpp)
REVERT: R  171 CYS cc_start: 0.8915 (m) cc_final: 0.8605 (m)
REVERT: R  253 PHE cc_start: 0.8808 (m-10) cc_final: 0.8017 (t80)
REVERT: R  277 TYR cc_start: 0.8873 (t80) cc_final: 0.8399 (t80)
REVERT: R  281 PHE cc_start: 0.8296 (t80) cc_final: 0.8057 (t80)
REVERT: R  291 ASN cc_start: 0.7985 (t0) cc_final: 0.7636 (t0)
REVERT: R  305 GLU cc_start: 0.8513 (pm20) cc_final: 0.8173 (pp20)
REVERT: R  307 ARG cc_start: 0.8753 (mmm-85) cc_final: 0.8508 (mmm-85)
REVERT: G   38 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8196 (tmm)
REVERT: G   42 GLU cc_start: 0.8862 (pp20) cc_final: 0.8660 (pm20)
REVERT: G   47 GLU cc_start: 0.8508 (pm20) cc_final: 0.8213 (pm20)
REVERT: L    1 TYR cc_start: 0.7359 (t80) cc_final: 0.7093 (t80)
REVERT: N   83 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7618 (mmt)
  outliers start: 17
  outliers final: 13
  residues processed: 159
  average time/residue: 1.2078
  time to fit residues: 204.0830
Evaluate side-chains
  158 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 ASN
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   85 MET
Chi-restraints excluded: chain R residue  102 HIS
Chi-restraints excluded: chain R residue  201 LEU
Chi-restraints excluded: chain R residue  217 HIS
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   83 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0170
   chunk 28 optimal weight:    4.9990
   chunk 95 optimal weight:    8.9990
   chunk 21 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 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 = 0.3912 r_free = 0.3912 target = 0.127322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.089969 restraints weight = 16242.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 3.87
r_work: 0.3158 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.4645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8389  Z= 0.210
  Angle     :  0.723  12.995  11360  Z= 0.356
  Chirality :  0.043   0.189   1291
  Planarity :  0.004   0.060   1444
  Dihedral  :  4.414  47.615   1135
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 23.42 %
    Favored  : 74.58 %
  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:  0.70 (0.27), residues: 1025
  helix:  1.87 (0.27), residues: 386
  sheet:  0.06 (0.33), residues: 235
  loop : -0.62 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP N  47 
 HIS   0.003   0.001   HIS R 261 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.015   0.001   TYR N  60 
 ARG   0.016   0.001   ARG L   7 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7799.41 seconds
wall clock time: 136 minutes 4.96 seconds (8164.96 seconds total)