Starting phenix.real_space_refine
on Sat Aug 23 01:36:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xqp_38584/08_2025/8xqp_38584.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xqp_38584/08_2025/8xqp_38584.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xqp_38584/08_2025/8xqp_38584.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xqp_38584/08_2025/8xqp_38584.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xqp_38584/08_2025/8xqp_38584.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xqp_38584/08_2025/8xqp_38584.cif"
  }
  resolution = 3.29
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    5753      2.51       5
     N    1520      2.21       5
     O    1656      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8987
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1805
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "R"
      Number of atoms: 2317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2317
          Classifications: {'peptide': 286}
          Link IDs: {'PTRANS': 3, 'TRANS': 282}
          Chain breaks: 2
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 53
          Unusual residues: {'CLR': 1, 'GOQ': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.46, per 1000 atoms: 0.27
  Number of scatterers: 8987
  At special positions: 0
  Unit cell: (88.4, 120.64, 126.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      58     16.00
     O    1656      8.00
     N    1520      7.00
     C    5753      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 359.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2126

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 14 sheets defined
      40.6% alpha, 22.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 45
    Processing helix  chain 'A' and resid 60 through 70
    Processing helix  chain 'A' and resid 211 through 218
      removed outlier: 3.561A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   GLY A 217 " --> pdb=" O   CYS A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.019A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 4.226A  pdb=" N   THR A 279 " --> pdb=" O   GLN A 275 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 352
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.756A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 23
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'R' and resid 3 through 37
      removed outlier: 3.588A  pdb=" N   LYS R  37 " --> pdb=" O   ILE R  33 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 43 through 71
    Processing helix  chain 'R' and resid 72 through 77
      removed outlier: 3.788A  pdb=" N   PHE R  76 " --> pdb=" O   PHE R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 79 through 112
    Processing helix  chain 'R' and resid 116 through 125
    Processing helix  chain 'R' and resid 125 through 162
      removed outlier: 4.244A  pdb=" N   SER R 138 " --> pdb=" O   LEU R 134 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   VAL R 139 " --> pdb=" O   LEU R 135 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   PHE R 140 " --> pdb=" O   VAL R 136 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 173 through 215
      Proline residue:  R 190  - end of helix
      removed outlier: 3.671A  pdb=" N   LEU R 193 " --> pdb=" O   ILE R 189 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 222 through 228
    Processing helix  chain 'R' and resid 232 through 253
      removed outlier: 3.514A  pdb=" N   LEU R 239 " --> pdb=" O   THR R 235 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 260 through 270
    Processing helix  chain 'R' and resid 270 through 275
    Processing helix  chain 'R' and resid 275 through 284
      removed outlier: 3.598A  pdb=" N   VAL R 279 " --> pdb=" O   CYS R 275 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 284 through 299
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.881A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.633A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.194A  pdb=" N   VAL A  49 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   LEU A  51 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   CYS A 220 " --> pdb=" O   LYS A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 6.450A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.760A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.037A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.212A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.108A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.657A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.319A  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: 7.167A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.962A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.643A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.525A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 6 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12
    Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60
      removed outlier: 5.905A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60
      removed outlier: 5.905A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.548A  pdb=" N   GLY S 213 " --> pdb=" O   LEU S 233 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)

    498 hydrogen bonds defined for protein.
    1419 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.31

  Time building geometry restraints manager: 1.23 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 1436
        1.28 -     1.41: 2354
        1.41 -     1.55: 5289
        1.55 -     1.68: 12
        1.68 -     1.81: 86
  Bond restraints: 9177
  Sorted by residual:
  bond pdb=" C   CYS R 275 "
       pdb=" O   CYS R 275 "
    ideal  model  delta    sigma   weight residual
    1.236  1.141  0.095 1.15e-02 7.56e+03 6.79e+01
  bond pdb=" C   TYR R 272 "
       pdb=" O   TYR R 272 "
    ideal  model  delta    sigma   weight residual
    1.244  1.176  0.067 9.80e-03 1.04e+04 4.73e+01
  bond pdb=" N   MET R 270 "
       pdb=" CA  MET R 270 "
    ideal  model  delta    sigma   weight residual
    1.456  1.383  0.074 1.31e-02 5.83e+03 3.17e+01
  bond pdb=" C   TYR R 272 "
       pdb=" N   PRO R 273 "
    ideal  model  delta    sigma   weight residual
    1.335  1.272  0.063 1.30e-02 5.92e+03 2.35e+01
  bond pdb=" C   MET R 270 "
       pdb=" O   MET R 270 "
    ideal  model  delta    sigma   weight residual
    1.236  1.175  0.061 1.31e-02 5.83e+03 2.14e+01
  ... (remaining 9172 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.74: 12279
        2.74 -     5.47: 125
        5.47 -     8.21: 10
        8.21 -    10.94: 2
       10.94 -    13.68: 5
  Bond angle restraints: 12421
  Sorted by residual:
  angle pdb=" N   CYS R 278 "
        pdb=" CA  CYS R 278 "
        pdb=" C   CYS R 278 "
      ideal   model   delta    sigma   weight residual
     112.23  100.90   11.33 1.26e+00 6.30e-01 8.09e+01
  angle pdb=" N   HIS R 276 "
        pdb=" CA  HIS R 276 "
        pdb=" C   HIS R 276 "
      ideal   model   delta    sigma   weight residual
     110.80  124.48  -13.68 2.13e+00 2.20e-01 4.12e+01
  angle pdb=" CA  CYS R 278 "
        pdb=" C   CYS R 278 "
        pdb=" O   CYS R 278 "
      ideal   model   delta    sigma   weight residual
     119.79  125.20   -5.41 1.18e+00 7.18e-01 2.10e+01
  angle pdb=" CA  CYS R 278 "
        pdb=" C   CYS R 278 "
        pdb=" N   VAL R 279 "
      ideal   model   delta    sigma   weight residual
     117.82  111.58    6.24 1.42e+00 4.96e-01 1.93e+01
  angle pdb=" N   SER R 277 "
        pdb=" CA  SER R 277 "
        pdb=" C   SER R 277 "
      ideal   model   delta    sigma   weight residual
     113.17  108.34    4.83 1.26e+00 6.30e-01 1.47e+01
  ... (remaining 12416 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.20: 4678
       17.20 -    34.39: 579
       34.39 -    51.59: 160
       51.59 -    68.79: 36
       68.79 -    85.99: 10
  Dihedral angle restraints: 5463
    sinusoidal: 2177
      harmonic: 3286
  Sorted by residual:
  dihedral pdb=" N   HIS R 276 "
           pdb=" C   HIS R 276 "
           pdb=" CA  HIS R 276 "
           pdb=" CB  HIS R 276 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  142.33  -19.53     0      2.50e+00 1.60e-01 6.10e+01
  dihedral pdb=" C   HIS R 276 "
           pdb=" N   HIS R 276 "
           pdb=" CA  HIS R 276 "
           pdb=" CB  HIS R 276 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -141.88   19.28     0      2.50e+00 1.60e-01 5.95e+01
  dihedral pdb=" CD  ARG S  98 "
           pdb=" NE  ARG S  98 "
           pdb=" CZ  ARG S  98 "
           pdb=" NH1 ARG S  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   57.40  -57.40     1      1.00e+01 1.00e-02 4.43e+01
  ... (remaining 5460 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.200: 1411
       0.200 -    0.401: 3
       0.401 -    0.601: 1
       0.601 -    0.802: 0
       0.802 -    1.002: 1
  Chirality restraints: 1416
  Sorted by residual:
  chirality pdb=" CA  HIS R 276 "
            pdb=" N   HIS R 276 "
            pdb=" C   HIS R 276 "
            pdb=" CB  HIS R 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.51    1.00 2.00e-01 2.50e+01 2.51e+01
  chirality pdb=" CA  TYR R 272 "
            pdb=" N   TYR R 272 "
            pdb=" C   TYR R 272 "
            pdb=" CB  TYR R 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.02e+00
  chirality pdb=" CB  VAL A  49 "
            pdb=" CA  VAL A  49 "
            pdb=" CG1 VAL A  49 "
            pdb=" CG2 VAL A  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.82e+00
  ... (remaining 1413 not shown)

  Planarity restraints: 1547
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG S  98 "    0.937 9.50e-02 1.11e+02   4.20e-01 1.07e+02
        pdb=" NE  ARG S  98 "   -0.055 2.00e-02 2.50e+03
        pdb=" CZ  ARG S  98 "   -0.014 2.00e-02 2.50e+03
        pdb=" NH1 ARG S  98 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG S  98 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR R 272 "   -0.069 5.00e-02 4.00e+02   1.04e-01 1.73e+01
        pdb=" N   PRO R 273 "    0.180 5.00e-02 4.00e+02
        pdb=" CA  PRO R 273 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO R 273 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE R  72 "   -0.053 5.00e-02 4.00e+02   8.02e-02 1.03e+01
        pdb=" N   PRO R  73 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO R  73 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO R  73 "   -0.044 5.00e-02 4.00e+02
  ... (remaining 1544 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 437
        2.72 -     3.26: 9224
        3.26 -     3.81: 15660
        3.81 -     4.35: 18769
        4.35 -     4.90: 31481
  Nonbonded interactions: 75571
  Sorted by model distance:
  nonbonded pdb=" OG  SER S 149 "
            pdb=" O   LYS S 151 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   ILE S 126 "
            pdb=" OG1 THR S 226 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   TYR S 102 "
            pdb=" OG  SER S 105 "
     model   vdw
     2.234 3.040
  ... (remaining 75566 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:             1.700
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.010
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.095   9179  Z= 0.289
  Angle     :  0.709  13.677  12425  Z= 0.389
  Chirality :  0.054   1.002   1416
  Planarity :  0.012   0.420   1547
  Dihedral  : 16.653  85.987   3331
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 30.28 %
    Favored  : 69.41 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.26), residues: 1118
  helix:  2.16 (0.26), residues: 422
  sheet: -0.79 (0.31), residues: 287
  loop : -0.76 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  36 
 TYR   0.022   0.002   TYR S 102 
 PHE   0.031   0.002   PHE A 189 
 TRP   0.042   0.002   TRP R  66 
 HIS   0.012   0.001   HIS R 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 9177)
  covalent geometry    : angle       0.70862 (12421)
  SS BOND              : bond        0.00289 (    2)
  SS BOND              : angle       1.09255 (    4)
  hydrogen bonds       : bond        0.17183 (  484)
  hydrogen bonds       : angle       7.04584 ( 1419)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 276
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 VAL cc_start: 0.8424 (t) cc_final: 0.8194 (t)
REVERT: A  192 LYS cc_start: 0.8170 (mttp) cc_final: 0.7957 (mmtp)
REVERT: A  232 MET cc_start: 0.6453 (mmm) cc_final: 0.6137 (mmm)
REVERT: A  317 LYS cc_start: 0.7821 (ptmm) cc_final: 0.7590 (ptmm)
REVERT: B  196 THR cc_start: 0.7927 (p) cc_final: 0.7650 (p)
REVERT: B  209 LYS cc_start: 0.8346 (mttm) cc_final: 0.8018 (mttm)
REVERT: B  214 ARG cc_start: 0.7127 (mtp85) cc_final: 0.6927 (mtp85)
REVERT: R   62 ILE cc_start: 0.8286 (tp) cc_final: 0.7307 (pt)
REVERT: R   98 TRP cc_start: 0.8446 (m100) cc_final: 0.7846 (m100)
REVERT: R  125 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7494 (mtt180)
REVERT: R  273 PRO cc_start: 0.8493 (OUTLIER) cc_final: 0.8180 (Cg_endo)
REVERT: S   73 ASP cc_start: 0.7167 (t0) cc_final: 0.6839 (t70)
REVERT: S  219 GLN cc_start: 0.8058 (pp30) cc_final: 0.7824 (pp30)
  outliers start: 3
  outliers final: 2
  residues processed: 278
  average time/residue: 0.1258
  time to fit residues: 45.4772
Evaluate side-chains
  278 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 275
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  270 MET
Chi-restraints excluded: chain R residue  272 TYR
Chi-restraints excluded: chain R residue  273 PRO
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 106 optimal weight:    0.0980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 301 ASN
B  32 GLN
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.158000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.133747 restraints weight = 14352.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 2.65
r_work: 0.3566 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.0979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9179  Z= 0.156
  Angle     :  0.601  10.930  12425  Z= 0.316
  Chirality :  0.043   0.219   1416
  Planarity :  0.005   0.080   1547
  Dihedral  :  5.905  85.980   1298
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 24.80 %
    Favored  : 71.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.26), residues: 1118
  helix:  2.29 (0.26), residues: 429
  sheet: -0.77 (0.31), residues: 286
  loop : -0.79 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 150 
 TYR   0.031   0.002   TYR S 223 
 PHE   0.016   0.001   PHE R 236 
 TRP   0.019   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9177)
  covalent geometry    : angle       0.60077 (12421)
  SS BOND              : bond        0.00369 (    2)
  SS BOND              : angle       1.05214 (    4)
  hydrogen bonds       : bond        0.04332 (  484)
  hydrogen bonds       : angle       4.89090 ( 1419)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 270
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 VAL cc_start: 0.8231 (t) cc_final: 0.7999 (t)
REVERT: A   61 LYS cc_start: 0.6693 (mtmt) cc_final: 0.6251 (ttpp)
REVERT: A  192 LYS cc_start: 0.8253 (mttp) cc_final: 0.7997 (mmtp)
REVERT: A  201 VAL cc_start: 0.7589 (OUTLIER) cc_final: 0.7374 (t)
REVERT: A  232 MET cc_start: 0.6519 (mmm) cc_final: 0.6213 (mmm)
REVERT: A  317 LYS cc_start: 0.7723 (ptmm) cc_final: 0.7357 (ttpp)
REVERT: B   15 LYS cc_start: 0.8952 (mtpt) cc_final: 0.8662 (mtpt)
REVERT: B   68 ARG cc_start: 0.5904 (ttp-170) cc_final: 0.5368 (ttp-170)
REVERT: B  129 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.6565 (mmp80)
REVERT: B  196 THR cc_start: 0.7912 (p) cc_final: 0.7640 (p)
REVERT: B  197 ARG cc_start: 0.7376 (ttm-80) cc_final: 0.7148 (mtp85)
REVERT: B  209 LYS cc_start: 0.8351 (mttm) cc_final: 0.8017 (mttm)
REVERT: B  214 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7233 (mtp85)
REVERT: B  217 MET cc_start: 0.6505 (ppp) cc_final: 0.6262 (ppp)
REVERT: C   22 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6641 (mp0)
REVERT: R   65 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8782 (m)
REVERT: R  125 ARG cc_start: 0.7901 (mtt180) cc_final: 0.7449 (mtt180)
REVERT: R  147 LEU cc_start: 0.6635 (pp) cc_final: 0.6099 (tt)
REVERT: R  205 MET cc_start: 0.8287 (tpp) cc_final: 0.7761 (tpp)
REVERT: S  157 ASN cc_start: 0.8242 (p0) cc_final: 0.8005 (p0)
  outliers start: 37
  outliers final: 18
  residues processed: 290
  average time/residue: 0.1196
  time to fit residues: 45.5275
Evaluate side-chains
  285 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 263
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  129 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain C residue   18 GLN
Chi-restraints excluded: chain C residue   22 GLU
Chi-restraints excluded: chain R residue   59 VAL
Chi-restraints excluded: chain R residue   65 SER
Chi-restraints excluded: chain R residue  272 TYR
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9990
   chunk 15 optimal weight:    7.9990
   chunk 55 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 331 ASN
B 220 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.157376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.132810 restraints weight = 14305.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 2.62
r_work: 0.3568 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.1308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9179  Z= 0.185
  Angle     :  0.587   8.839  12425  Z= 0.309
  Chirality :  0.042   0.237   1416
  Planarity :  0.005   0.064   1547
  Dihedral  :  5.807  87.398   1292
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 24.90 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.26), residues: 1118
  helix:  2.28 (0.25), residues: 430
  sheet: -0.97 (0.30), residues: 288
  loop : -0.70 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  36 
 TYR   0.035   0.002   TYR S 223 
 PHE   0.019   0.002   PHE A 196 
 TRP   0.019   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 9177)
  covalent geometry    : angle       0.58727 (12421)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       0.91400 (    4)
  hydrogen bonds       : bond        0.04113 (  484)
  hydrogen bonds       : angle       4.57871 ( 1419)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 265
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 VAL cc_start: 0.8269 (t) cc_final: 0.8043 (t)
REVERT: A  192 LYS cc_start: 0.8265 (mttp) cc_final: 0.7970 (mmtp)
REVERT: A  219 THR cc_start: 0.8352 (p) cc_final: 0.7975 (t)
REVERT: A  232 MET cc_start: 0.6621 (mmm) cc_final: 0.6321 (mmm)
REVERT: A  242 ARG cc_start: 0.7709 (mtt180) cc_final: 0.7289 (mtt180)
REVERT: A  245 GLU cc_start: 0.8001 (tp30) cc_final: 0.7702 (tp30)
REVERT: A  317 LYS cc_start: 0.7759 (ptmm) cc_final: 0.7300 (ttpp)
REVERT: A  346 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7387 (tm-30)
REVERT: B   15 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8693 (mtpt)
REVERT: B   68 ARG cc_start: 0.5839 (ttp-170) cc_final: 0.5252 (ttp-170)
REVERT: B  196 THR cc_start: 0.7920 (p) cc_final: 0.7644 (p)
REVERT: B  197 ARG cc_start: 0.7420 (ttm-80) cc_final: 0.7162 (mtp85)
REVERT: B  209 LYS cc_start: 0.8496 (mttm) cc_final: 0.8293 (mttp)
REVERT: B  214 ARG cc_start: 0.7800 (mtp85) cc_final: 0.7315 (mtp85)
REVERT: B  217 MET cc_start: 0.6635 (ppp) cc_final: 0.5979 (ppp)
REVERT: B  219 ARG cc_start: 0.7298 (mmm-85) cc_final: 0.7071 (mmt90)
REVERT: B  314 ARG cc_start: 0.7679 (mtp180) cc_final: 0.7242 (ttm170)
REVERT: C   22 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6661 (mp0)
REVERT: C   27 ARG cc_start: 0.7159 (mtm-85) cc_final: 0.6450 (mmt90)
REVERT: R  125 ARG cc_start: 0.7852 (mtt180) cc_final: 0.7410 (mtt180)
REVERT: R  147 LEU cc_start: 0.6655 (pp) cc_final: 0.6163 (tt)
REVERT: R  205 MET cc_start: 0.8298 (tpp) cc_final: 0.7857 (tpp)
REVERT: S  146 SER cc_start: 0.7796 (p) cc_final: 0.7584 (t)
  outliers start: 43
  outliers final: 25
  residues processed: 289
  average time/residue: 0.1249
  time to fit residues: 46.8702
Evaluate side-chains
  288 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 262
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain C residue   22 GLU
Chi-restraints excluded: chain R residue   59 VAL
Chi-restraints excluded: chain R residue   65 SER
Chi-restraints excluded: chain R residue  215 THR
Chi-restraints excluded: chain R residue  272 TYR
Chi-restraints excluded: chain R residue  287 LEU
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   58 ILE
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  203 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.157266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.132705 restraints weight = 14463.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 2.64
r_work: 0.3538 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9179  Z= 0.217
  Angle     :  0.600   7.690  12425  Z= 0.317
  Chirality :  0.043   0.242   1416
  Planarity :  0.005   0.065   1547
  Dihedral  :  5.864  89.326   1292
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 24.90 %
    Favored  : 70.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.26), residues: 1118
  helix:  2.24 (0.25), residues: 431
  sheet: -1.07 (0.29), residues: 288
  loop : -0.75 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  36 
 TYR   0.035   0.002   TYR S 223 
 PHE   0.019   0.002   PHE A 196 
 TRP   0.019   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 9177)
  covalent geometry    : angle       0.59969 (12421)
  SS BOND              : bond        0.00202 (    2)
  SS BOND              : angle       0.57370 (    4)
  hydrogen bonds       : bond        0.04106 (  484)
  hydrogen bonds       : angle       4.52620 ( 1419)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 263
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 VAL cc_start: 0.8232 (t) cc_final: 0.8031 (t)
REVERT: A  189 PHE cc_start: 0.8193 (p90) cc_final: 0.7907 (p90)
REVERT: A  192 LYS cc_start: 0.8141 (mttp) cc_final: 0.7860 (mmtp)
REVERT: A  219 THR cc_start: 0.8339 (p) cc_final: 0.8002 (t)
REVERT: A  232 MET cc_start: 0.6679 (mmm) cc_final: 0.6322 (mmm)
REVERT: A  242 ARG cc_start: 0.7814 (mtt180) cc_final: 0.7381 (mtt180)
REVERT: A  245 GLU cc_start: 0.8029 (tp30) cc_final: 0.7712 (tp30)
REVERT: A  274 PHE cc_start: 0.7021 (t80) cc_final: 0.6622 (t80)
REVERT: A  317 LYS cc_start: 0.7731 (ptmm) cc_final: 0.7276 (ttpp)
REVERT: A  346 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7390 (tm-30)
REVERT: B   15 LYS cc_start: 0.8985 (mtpt) cc_final: 0.8662 (mtpt)
REVERT: B   68 ARG cc_start: 0.5819 (ttp-170) cc_final: 0.5231 (ttp-170)
REVERT: B   76 ASP cc_start: 0.6798 (p0) cc_final: 0.6536 (p0)
REVERT: B  196 THR cc_start: 0.7962 (p) cc_final: 0.7676 (p)
REVERT: B  197 ARG cc_start: 0.7550 (ttm-80) cc_final: 0.7234 (mtp-110)
REVERT: B  214 ARG cc_start: 0.7840 (mtp85) cc_final: 0.7428 (mtp85)
REVERT: C   27 ARG cc_start: 0.7105 (mtm-85) cc_final: 0.6402 (mmt90)
REVERT: R   66 TRP cc_start: 0.7634 (t60) cc_final: 0.7317 (t60)
REVERT: R   99 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8273 (tp)
REVERT: R  125 ARG cc_start: 0.7856 (mtt180) cc_final: 0.7383 (mtt180)
REVERT: R  147 LEU cc_start: 0.6847 (pp) cc_final: 0.6361 (tt)
REVERT: R  205 MET cc_start: 0.8259 (tpp) cc_final: 0.7682 (tpp)
REVERT: R  268 MET cc_start: 0.7756 (tmm) cc_final: 0.7455 (tmm)
REVERT: S  146 SER cc_start: 0.7802 (p) cc_final: 0.7587 (t)
REVERT: S  222 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6943 (mm-30)
  outliers start: 50
  outliers final: 33
  residues processed: 291
  average time/residue: 0.1273
  time to fit residues: 47.9799
Evaluate side-chains
  297 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 263
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain R residue   59 VAL
Chi-restraints excluded: chain R residue   65 SER
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  272 TYR
Chi-restraints excluded: chain R residue  287 LEU
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   58 ILE
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 89 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 97 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.158548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.134399 restraints weight = 14245.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.62
r_work: 0.3558 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9179  Z= 0.163
  Angle     :  0.570   7.194  12425  Z= 0.299
  Chirality :  0.042   0.227   1416
  Planarity :  0.004   0.062   1547
  Dihedral  :  5.728  88.848   1292
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 25.61 %
    Favored  : 69.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.26), residues: 1118
  helix:  2.40 (0.25), residues: 425
  sheet: -1.03 (0.29), residues: 289
  loop : -0.60 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  36 
 TYR   0.034   0.002   TYR S 223 
 PHE   0.018   0.001   PHE A 196 
 TRP   0.017   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9177)
  covalent geometry    : angle       0.56997 (12421)
  SS BOND              : bond        0.00111 (    2)
  SS BOND              : angle       0.73457 (    4)
  hydrogen bonds       : bond        0.03849 (  484)
  hydrogen bonds       : angle       4.41332 ( 1419)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 273
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 VAL cc_start: 0.8295 (t) cc_final: 0.8059 (t)
REVERT: A   29 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7084 (mm-30)
REVERT: A  189 PHE cc_start: 0.8148 (p90) cc_final: 0.7770 (p90)
REVERT: A  192 LYS cc_start: 0.8144 (mttp) cc_final: 0.7879 (mmtp)
REVERT: A  232 MET cc_start: 0.6732 (mmm) cc_final: 0.6400 (mmm)
REVERT: A  242 ARG cc_start: 0.7819 (mtt180) cc_final: 0.7214 (mtt-85)
REVERT: A  245 GLU cc_start: 0.8003 (tp30) cc_final: 0.7656 (tp30)
REVERT: A  274 PHE cc_start: 0.7040 (t80) cc_final: 0.6643 (t80)
REVERT: A  317 LYS cc_start: 0.7719 (ptmm) cc_final: 0.7286 (ttpp)
REVERT: A  346 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7366 (tm-30)
REVERT: B   68 ARG cc_start: 0.5847 (ttp-170) cc_final: 0.5463 (ttt-90)
REVERT: B   76 ASP cc_start: 0.6724 (p0) cc_final: 0.6434 (p0)
REVERT: B  127 LYS cc_start: 0.8405 (mmmm) cc_final: 0.7906 (mttm)
REVERT: B  196 THR cc_start: 0.7953 (p) cc_final: 0.7666 (p)
REVERT: B  197 ARG cc_start: 0.7523 (ttm-80) cc_final: 0.7068 (mtp-110)
REVERT: B  214 ARG cc_start: 0.7735 (mtp85) cc_final: 0.7032 (mtp85)
REVERT: B  266 HIS cc_start: 0.7745 (t70) cc_final: 0.7500 (t70)
REVERT: B  284 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8040 (tp)
REVERT: B  314 ARG cc_start: 0.7736 (mtp180) cc_final: 0.7095 (ttm-80)
REVERT: C   21 MET cc_start: 0.7313 (mmm) cc_final: 0.6996 (mmm)
REVERT: R   37 LYS cc_start: 0.7645 (pttp) cc_final: 0.7337 (pptt)
REVERT: R   66 TRP cc_start: 0.7598 (t60) cc_final: 0.7245 (t60)
REVERT: R   99 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8208 (tp)
REVERT: R  125 ARG cc_start: 0.7821 (mtt180) cc_final: 0.7415 (mtt180)
REVERT: R  147 LEU cc_start: 0.6825 (pp) cc_final: 0.6320 (tt)
REVERT: R  205 MET cc_start: 0.8239 (tpp) cc_final: 0.7649 (tpp)
REVERT: S  133 SER cc_start: 0.5372 (t) cc_final: 0.5136 (p)
REVERT: S  222 GLU cc_start: 0.7381 (mm-30) cc_final: 0.6892 (mm-30)
REVERT: S  232 LYS cc_start: 0.7922 (tptm) cc_final: 0.7498 (tptm)
  outliers start: 53
  outliers final: 39
  residues processed: 303
  average time/residue: 0.1216
  time to fit residues: 48.3516
Evaluate side-chains
  309 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 268
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain R residue   59 VAL
Chi-restraints excluded: chain R residue   65 SER
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  272 TYR
Chi-restraints excluded: chain R residue  287 LEU
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   58 ILE
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 64 optimal weight:    0.8980
   chunk 105 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 17 optimal weight:    0.2980
   chunk 26 optimal weight:    0.9990
   chunk 107 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.156987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.132750 restraints weight = 14354.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 2.63
r_work: 0.3561 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7063
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9179  Z= 0.166
  Angle     :  0.583   8.808  12425  Z= 0.303
  Chirality :  0.042   0.214   1416
  Planarity :  0.004   0.064   1547
  Dihedral  :  5.753  88.505   1292
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 26.73 %
    Favored  : 67.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.26), residues: 1118
  helix:  2.39 (0.25), residues: 425
  sheet: -1.03 (0.28), residues: 290
  loop : -0.60 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  36 
 TYR   0.034   0.002   TYR S 223 
 PHE   0.016   0.001   PHE R 186 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 9177)
  covalent geometry    : angle       0.58261 (12421)
  SS BOND              : bond        0.00152 (    2)
  SS BOND              : angle       0.62813 (    4)
  hydrogen bonds       : bond        0.03842 (  484)
  hydrogen bonds       : angle       4.38241 ( 1419)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 271
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 VAL cc_start: 0.8290 (t) cc_final: 0.8081 (t)
REVERT: A   29 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7078 (mm-30)
REVERT: A  189 PHE cc_start: 0.8139 (p90) cc_final: 0.7889 (p90)
REVERT: A  192 LYS cc_start: 0.8121 (mttp) cc_final: 0.7855 (mmtp)
REVERT: A  219 THR cc_start: 0.8346 (p) cc_final: 0.7994 (t)
REVERT: A  232 MET cc_start: 0.6686 (mmm) cc_final: 0.6325 (mmm)
REVERT: A  242 ARG cc_start: 0.7814 (mtt180) cc_final: 0.7471 (mtt180)
REVERT: A  245 GLU cc_start: 0.8012 (tp30) cc_final: 0.7668 (tp30)
REVERT: A  274 PHE cc_start: 0.7052 (t80) cc_final: 0.6668 (t80)
REVERT: A  317 LYS cc_start: 0.7744 (ptmm) cc_final: 0.7315 (ttpp)
REVERT: A  346 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7385 (tm-30)
REVERT: B   68 ARG cc_start: 0.5849 (ttp-170) cc_final: 0.5489 (ttt-90)
REVERT: B  127 LYS cc_start: 0.8332 (mmmm) cc_final: 0.7925 (mttm)
REVERT: B  196 THR cc_start: 0.7956 (p) cc_final: 0.7669 (p)
REVERT: B  197 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.7234 (mtp-110)
REVERT: B  214 ARG cc_start: 0.7731 (mtp85) cc_final: 0.7352 (mtp85)
REVERT: B  284 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8030 (tp)
REVERT: B  314 ARG cc_start: 0.7749 (mtp180) cc_final: 0.7110 (ttm-80)
REVERT: C   22 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6550 (mp0)
REVERT: R   99 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8214 (tp)
REVERT: R  108 PHE cc_start: 0.8454 (t80) cc_final: 0.7960 (t80)
REVERT: R  125 ARG cc_start: 0.7789 (mtt180) cc_final: 0.7286 (mtt180)
REVERT: R  140 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7298 (t80)
REVERT: R  143 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6590 (tt)
REVERT: R  147 LEU cc_start: 0.6842 (pp) cc_final: 0.6352 (tt)
REVERT: R  191 PHE cc_start: 0.6720 (t80) cc_final: 0.6479 (t80)
REVERT: R  205 MET cc_start: 0.8233 (tpp) cc_final: 0.7642 (tpp)
REVERT: R  268 MET cc_start: 0.7804 (tmm) cc_final: 0.7530 (tmm)
REVERT: S  222 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6849 (mm-30)
  outliers start: 53
  outliers final: 39
  residues processed: 301
  average time/residue: 0.1196
  time to fit residues: 47.1535
Evaluate side-chains
  311 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 267
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain C residue   22 GLU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain R residue   59 VAL
Chi-restraints excluded: chain R residue   65 SER
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  143 LEU
Chi-restraints excluded: chain R residue  272 TYR
Chi-restraints excluded: chain R residue  287 LEU
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   58 ILE
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
** S 130 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 = 0.4036 r_free = 0.4036 target = 0.157687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.133578 restraints weight = 14446.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.65
r_work: 0.3549 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7074
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9179  Z= 0.193
  Angle     :  0.596   7.663  12425  Z= 0.311
  Chirality :  0.043   0.217   1416
  Planarity :  0.004   0.064   1547
  Dihedral  :  5.803  89.132   1292
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 26.52 %
    Favored  : 67.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.26), residues: 1118
  helix:  2.37 (0.25), residues: 425
  sheet: -1.04 (0.28), residues: 290
  loop : -0.60 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  36 
 TYR   0.036   0.002   TYR S 223 
 PHE   0.018   0.002   PHE A 196 
 TRP   0.016   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 9177)
  covalent geometry    : angle       0.59605 (12421)
  SS BOND              : bond        0.00128 (    2)
  SS BOND              : angle       0.53902 (    4)
  hydrogen bonds       : bond        0.03922 (  484)
  hydrogen bonds       : angle       4.41862 ( 1419)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 269
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 PHE cc_start: 0.8141 (p90) cc_final: 0.7867 (p90)
REVERT: A  192 LYS cc_start: 0.8132 (mttp) cc_final: 0.7858 (mmtp)
REVERT: A  219 THR cc_start: 0.8364 (p) cc_final: 0.8038 (t)
REVERT: A  232 MET cc_start: 0.6747 (mmm) cc_final: 0.6310 (mmm)
REVERT: A  242 ARG cc_start: 0.7870 (mtt180) cc_final: 0.7530 (mtt180)
REVERT: A  245 GLU cc_start: 0.8011 (tp30) cc_final: 0.7654 (tp30)
REVERT: A  317 LYS cc_start: 0.7730 (ptmm) cc_final: 0.7252 (ptmm)
REVERT: A  346 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7364 (tm-30)
REVERT: B   15 LYS cc_start: 0.8994 (mtpt) cc_final: 0.8620 (mtpt)
REVERT: B   31 SER cc_start: 0.7548 (OUTLIER) cc_final: 0.7058 (p)
REVERT: B   68 ARG cc_start: 0.5860 (ttp-170) cc_final: 0.5462 (ttp-110)
REVERT: B   76 ASP cc_start: 0.6738 (p0) cc_final: 0.6522 (p0)
REVERT: B  196 THR cc_start: 0.7971 (p) cc_final: 0.7693 (p)
REVERT: B  197 ARG cc_start: 0.7553 (ttm-80) cc_final: 0.7258 (mtp85)
REVERT: B  214 ARG cc_start: 0.7752 (mtp85) cc_final: 0.7357 (mtp85)
REVERT: B  284 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8014 (tp)
REVERT: C   21 MET cc_start: 0.7385 (mmm) cc_final: 0.7027 (mmm)
REVERT: C   22 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6693 (mp0)
REVERT: R   37 LYS cc_start: 0.7589 (pttp) cc_final: 0.7325 (pptt)
REVERT: R   66 TRP cc_start: 0.7658 (t60) cc_final: 0.7277 (t60)
REVERT: R   99 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8229 (tp)
REVERT: R  108 PHE cc_start: 0.8466 (t80) cc_final: 0.7963 (t80)
REVERT: R  125 ARG cc_start: 0.7818 (mtt180) cc_final: 0.7333 (mtt180)
REVERT: R  140 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7279 (t80)
REVERT: R  147 LEU cc_start: 0.6847 (pp) cc_final: 0.6335 (tt)
REVERT: R  191 PHE cc_start: 0.6836 (t80) cc_final: 0.6570 (t80)
REVERT: R  205 MET cc_start: 0.8247 (tpp) cc_final: 0.7626 (tpp)
REVERT: R  268 MET cc_start: 0.7808 (tmm) cc_final: 0.7501 (tmm)
REVERT: S  222 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6891 (mm-30)
REVERT: S  232 LYS cc_start: 0.7947 (tptm) cc_final: 0.7488 (tptm)
  outliers start: 57
  outliers final: 42
  residues processed: 302
  average time/residue: 0.1217
  time to fit residues: 47.9905
Evaluate side-chains
  317 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 270
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   22 GLU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain R residue   59 VAL
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  132 VAL
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  243 PHE
Chi-restraints excluded: chain R residue  272 TYR
Chi-restraints excluded: chain R residue  287 LEU
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   58 ILE
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 50 optimal weight:    0.0010
   chunk 57 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 35 optimal weight:    0.4980
   chunk 72 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
** S 130 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 = 0.4048 r_free = 0.4048 target = 0.158996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.135151 restraints weight = 14297.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 2.65
r_work: 0.3565 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9179  Z= 0.152
  Angle     :  0.593   9.206  12425  Z= 0.305
  Chirality :  0.042   0.204   1416
  Planarity :  0.004   0.065   1547
  Dihedral  :  5.704  88.535   1292
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 26.32 %
    Favored  : 68.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.26), residues: 1118
  helix:  2.45 (0.26), residues: 425
  sheet: -1.00 (0.28), residues: 290
  loop : -0.60 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  36 
 TYR   0.034   0.002   TYR S 223 
 PHE   0.016   0.001   PHE R 106 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 9177)
  covalent geometry    : angle       0.59286 (12421)
  SS BOND              : bond        0.00155 (    2)
  SS BOND              : angle       0.67567 (    4)
  hydrogen bonds       : bond        0.03744 (  484)
  hydrogen bonds       : angle       4.35802 ( 1419)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 270
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  192 LYS cc_start: 0.8129 (mttp) cc_final: 0.7864 (mmtp)
REVERT: A  232 MET cc_start: 0.6717 (mmm) cc_final: 0.6309 (mmm)
REVERT: A  242 ARG cc_start: 0.7861 (mtt180) cc_final: 0.7526 (mtt180)
REVERT: A  245 GLU cc_start: 0.7979 (tp30) cc_final: 0.7641 (tp30)
REVERT: A  274 PHE cc_start: 0.7041 (t80) cc_final: 0.6705 (t80)
REVERT: A  317 LYS cc_start: 0.7716 (ptmm) cc_final: 0.7227 (ptmm)
REVERT: A  346 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7360 (tm-30)
REVERT: B   15 LYS cc_start: 0.8958 (mtpt) cc_final: 0.8628 (mtpt)
REVERT: B   31 SER cc_start: 0.7647 (OUTLIER) cc_final: 0.7116 (p)
REVERT: B   68 ARG cc_start: 0.5817 (ttp-170) cc_final: 0.5462 (ttt-90)
REVERT: B  127 LYS cc_start: 0.8332 (mmmm) cc_final: 0.7837 (mttm)
REVERT: B  159 THR cc_start: 0.7623 (OUTLIER) cc_final: 0.7374 (p)
REVERT: B  196 THR cc_start: 0.7958 (p) cc_final: 0.7652 (p)
REVERT: B  197 ARG cc_start: 0.7501 (ttm-80) cc_final: 0.7180 (mtp85)
REVERT: B  284 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8030 (tp)
REVERT: B  314 ARG cc_start: 0.7749 (mtp180) cc_final: 0.7169 (ttm170)
REVERT: C   21 MET cc_start: 0.7374 (mmm) cc_final: 0.6993 (mmm)
REVERT: C   22 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6679 (mp0)
REVERT: R   37 LYS cc_start: 0.7613 (pttp) cc_final: 0.7353 (pptt)
REVERT: R   66 TRP cc_start: 0.7629 (t60) cc_final: 0.7250 (t60)
REVERT: R   99 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8195 (tp)
REVERT: R  108 PHE cc_start: 0.8450 (t80) cc_final: 0.7905 (t80)
REVERT: R  125 ARG cc_start: 0.7787 (mtt180) cc_final: 0.7339 (mtt180)
REVERT: R  140 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7259 (t80)
REVERT: R  143 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6709 (tt)
REVERT: R  147 LEU cc_start: 0.6810 (pp) cc_final: 0.6302 (tt)
REVERT: R  191 PHE cc_start: 0.6773 (t80) cc_final: 0.6505 (t80)
REVERT: R  205 MET cc_start: 0.8221 (tpp) cc_final: 0.7617 (tpp)
REVERT: R  268 MET cc_start: 0.7661 (tmm) cc_final: 0.7359 (tmm)
REVERT: S   20 LEU cc_start: 0.7955 (mt) cc_final: 0.7740 (mm)
REVERT: S  222 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6828 (mm-30)
REVERT: S  232 LYS cc_start: 0.7914 (tptm) cc_final: 0.7450 (tptm)
  outliers start: 54
  outliers final: 38
  residues processed: 298
  average time/residue: 0.1132
  time to fit residues: 44.3002
Evaluate side-chains
  312 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 267
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  129 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain C residue   22 GLU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain R residue   59 VAL
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  132 VAL
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  143 LEU
Chi-restraints excluded: chain R residue  255 GLU
Chi-restraints excluded: chain R residue  287 LEU
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   58 ILE
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 95 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 67 optimal weight:    0.6980
   chunk 98 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 16 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0670
   chunk 86 optimal weight:    0.5980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
R  24 ASN
** S 130 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 = 0.4049 r_free = 0.4049 target = 0.158979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.135460 restraints weight = 14315.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 2.61
r_work: 0.3574 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7047
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9179  Z= 0.143
  Angle     :  0.610   9.356  12425  Z= 0.312
  Chirality :  0.043   0.205   1416
  Planarity :  0.004   0.065   1547
  Dihedral  :  5.443  87.937   1290
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 26.63 %
    Favored  : 68.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.26), residues: 1118
  helix:  2.48 (0.26), residues: 425
  sheet: -0.96 (0.28), residues: 290
  loop : -0.58 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  36 
 TYR   0.033   0.002   TYR S 223 
 PHE   0.023   0.001   PHE A 189 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9177)
  covalent geometry    : angle       0.61021 (12421)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       0.62597 (    4)
  hydrogen bonds       : bond        0.03697 (  484)
  hydrogen bonds       : angle       4.34006 ( 1419)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 271
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LYS cc_start: 0.6771 (mtmt) cc_final: 0.6356 (ttpp)
REVERT: A  192 LYS cc_start: 0.8136 (mttp) cc_final: 0.7862 (mmtp)
REVERT: A  219 THR cc_start: 0.8319 (p) cc_final: 0.7931 (t)
REVERT: A  232 MET cc_start: 0.6752 (mmm) cc_final: 0.6371 (mmm)
REVERT: A  242 ARG cc_start: 0.7843 (mtt180) cc_final: 0.7483 (mtt180)
REVERT: A  245 GLU cc_start: 0.7989 (tp30) cc_final: 0.7653 (tp30)
REVERT: A  274 PHE cc_start: 0.7035 (t80) cc_final: 0.6717 (t80)
REVERT: A  305 ASN cc_start: 0.7776 (m110) cc_final: 0.7451 (m110)
REVERT: A  317 LYS cc_start: 0.7702 (ptmm) cc_final: 0.7209 (ptmm)
REVERT: A  346 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7363 (tm-30)
REVERT: B   15 LYS cc_start: 0.8944 (mtpt) cc_final: 0.8616 (mtpt)
REVERT: B   68 ARG cc_start: 0.5813 (ttp-170) cc_final: 0.5473 (ttt-90)
REVERT: B  127 LYS cc_start: 0.8312 (mmmm) cc_final: 0.7815 (mttm)
REVERT: B  196 THR cc_start: 0.7946 (p) cc_final: 0.7645 (p)
REVERT: B  197 ARG cc_start: 0.7482 (ttm-80) cc_final: 0.7202 (mtp85)
REVERT: B  214 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7232 (mtp85)
REVERT: B  284 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8033 (tp)
REVERT: C   22 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6615 (mp0)
REVERT: C   27 ARG cc_start: 0.7045 (mtm-85) cc_final: 0.6638 (mmt90)
REVERT: R   37 LYS cc_start: 0.7568 (pttp) cc_final: 0.7315 (pptt)
REVERT: R   99 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8192 (tp)
REVERT: R  125 ARG cc_start: 0.7774 (mtt180) cc_final: 0.7347 (mtt180)
REVERT: R  140 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7262 (t80)
REVERT: R  143 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6676 (tt)
REVERT: R  147 LEU cc_start: 0.6801 (pp) cc_final: 0.6294 (tp)
REVERT: R  191 PHE cc_start: 0.6720 (t80) cc_final: 0.6457 (t80)
REVERT: R  205 MET cc_start: 0.8240 (tpp) cc_final: 0.7606 (tpp)
REVERT: R  231 LYS cc_start: 0.7617 (tttt) cc_final: 0.7415 (tttt)
REVERT: R  268 MET cc_start: 0.7642 (tmm) cc_final: 0.7310 (tmm)
REVERT: S  222 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6842 (mm-30)
  outliers start: 49
  outliers final: 37
  residues processed: 296
  average time/residue: 0.1105
  time to fit residues: 42.5845
Evaluate side-chains
  311 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 269
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  129 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   22 GLU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain R residue   59 VAL
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  132 VAL
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  143 LEU
Chi-restraints excluded: chain R residue  255 GLU
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   58 ILE
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 107 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 59 optimal weight:    0.0030
   chunk 83 optimal weight:    0.1980
   chunk 57 optimal weight:    5.9990
   chunk 77 optimal weight:    0.0670
   overall best weight:    0.2728

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

Flipped N/Q/H residues before XYZ refinement:
** S 130 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 = 0.4073 r_free = 0.4073 target = 0.160423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.136585 restraints weight = 14389.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 2.64
r_work: 0.3580 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7013
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9179  Z= 0.113
  Angle     :  0.595   9.199  12425  Z= 0.302
  Chirality :  0.042   0.185   1416
  Planarity :  0.004   0.066   1547
  Dihedral  :  5.279  86.145   1290
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 27.54 %
    Favored  : 68.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.26), residues: 1118
  helix:  2.52 (0.25), residues: 424
  sheet: -0.87 (0.29), residues: 288
  loop : -0.58 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  36 
 TYR   0.031   0.002   TYR S 223 
 PHE   0.018   0.001   PHE A 196 
 TRP   0.020   0.001   TRP B 332 
 HIS   0.004   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 9177)
  covalent geometry    : angle       0.59485 (12421)
  SS BOND              : bond        0.00193 (    2)
  SS BOND              : angle       0.76210 (    4)
  hydrogen bonds       : bond        0.03467 (  484)
  hydrogen bonds       : angle       4.21905 ( 1419)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 280
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LYS cc_start: 0.7932 (ttmm) cc_final: 0.7630 (mtpp)
REVERT: A   61 LYS cc_start: 0.6710 (mtmt) cc_final: 0.6374 (ttpp)
REVERT: A  192 LYS cc_start: 0.8244 (mttp) cc_final: 0.7939 (mmtp)
REVERT: A  232 MET cc_start: 0.6763 (mmm) cc_final: 0.6406 (mmm)
REVERT: A  242 ARG cc_start: 0.7727 (mtt180) cc_final: 0.7425 (mtt180)
REVERT: A  245 GLU cc_start: 0.7974 (tp30) cc_final: 0.7644 (tp30)
REVERT: A  274 PHE cc_start: 0.7021 (t80) cc_final: 0.6664 (t80)
REVERT: A  305 ASN cc_start: 0.7704 (m110) cc_final: 0.7497 (m110)
REVERT: A  317 LYS cc_start: 0.7712 (ptmm) cc_final: 0.7332 (ttpp)
REVERT: B   15 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8615 (mtpt)
REVERT: B   68 ARG cc_start: 0.5791 (ttp-170) cc_final: 0.5399 (ttp-110)
REVERT: B  127 LYS cc_start: 0.8264 (mmmm) cc_final: 0.7797 (mttm)
REVERT: B  129 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6670 (mmm-85)
REVERT: B  196 THR cc_start: 0.7899 (p) cc_final: 0.7598 (p)
REVERT: B  197 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.7176 (mtp-110)
REVERT: B  214 ARG cc_start: 0.7621 (mtp85) cc_final: 0.7218 (mtp85)
REVERT: B  258 ASP cc_start: 0.6490 (t0) cc_final: 0.6228 (t0)
REVERT: B  284 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8030 (tp)
REVERT: C   22 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6666 (mp0)
REVERT: C   27 ARG cc_start: 0.7071 (mtm-85) cc_final: 0.6670 (mmt90)
REVERT: R   37 LYS cc_start: 0.7537 (pttp) cc_final: 0.7269 (pptt)
REVERT: R   99 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8128 (tp)
REVERT: R  108 PHE cc_start: 0.8458 (t80) cc_final: 0.8073 (t80)
REVERT: R  125 ARG cc_start: 0.7832 (mtt180) cc_final: 0.7283 (mtt180)
REVERT: R  140 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7257 (t80)
REVERT: R  143 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6700 (tt)
REVERT: R  147 LEU cc_start: 0.6733 (pp) cc_final: 0.6202 (tt)
REVERT: R  205 MET cc_start: 0.8224 (tpp) cc_final: 0.7570 (tpp)
REVERT: R  268 MET cc_start: 0.7588 (tmm) cc_final: 0.7265 (tmm)
REVERT: S  222 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6755 (mm-30)
  outliers start: 39
  outliers final: 27
  residues processed: 300
  average time/residue: 0.1156
  time to fit residues: 45.4539
Evaluate side-chains
  307 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 274
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  129 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   22 GLU
Chi-restraints excluded: chain R residue   59 VAL
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  132 VAL
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  143 LEU
Chi-restraints excluded: chain R residue  255 GLU
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   58 ILE
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 55 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 76 optimal weight:    0.4980
   chunk 77 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
C  44 HIS
** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.158888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.135035 restraints weight = 14204.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 2.63
r_work: 0.3577 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9179  Z= 0.164
  Angle     :  0.628   9.193  12425  Z= 0.319
  Chirality :  0.043   0.207   1416
  Planarity :  0.004   0.066   1547
  Dihedral  :  5.428  87.362   1290
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 28.86 %
    Favored  : 67.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.26), residues: 1118
  helix:  2.53 (0.25), residues: 424
  sheet: -0.91 (0.29), residues: 290
  loop : -0.59 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  36 
 TYR   0.033   0.002   TYR S 223 
 PHE   0.025   0.002   PHE A 189 
 TRP   0.045   0.002   TRP R  89 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 9177)
  covalent geometry    : angle       0.62820 (12421)
  SS BOND              : bond        0.00168 (    2)
  SS BOND              : angle       0.59155 (    4)
  hydrogen bonds       : bond        0.03639 (  484)
  hydrogen bonds       : angle       4.28864 ( 1419)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2245.01 seconds
wall clock time: 39 minutes 25.04 seconds (2365.04 seconds total)