Starting phenix.real_space_refine
on Tue Mar  3 20:01:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e33_30975/03_2026/7e33_30975_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e33_30975/03_2026/7e33_30975.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e33_30975/03_2026/7e33_30975.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e33_30975/03_2026/7e33_30975.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e33_30975/03_2026/7e33_30975_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e33_30975/03_2026/7e33_30975_neut.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
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      62      5.16       5
     C    5446      2.51       5
     N    1438      2.21       5
     O    1592      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8538
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1750
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2558
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
    Chain: "E"
      Number of atoms: 1762
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1762
          Classifications: {'peptide': 229}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 391
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
    Chain: "R"
      Number of atoms: 2060
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2060
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 7, 'TRANS': 249}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'HVU': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.75, per 1000 atoms: 0.20
  Number of scatterers: 8538
  At special positions: 0
  Unit cell: (107.635, 112.86, 114.95, 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      62     16.00
     O    1592      8.00
     N    1438      7.00
     C    5446      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  95 " - pdb=" SG  CYS R 173 " 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: 0.63
  Conformation dependent library (CDL) restraints added in 296.4 milliseconds
  

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2038

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 14 sheets defined
      40.1% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.595A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 202 through 204
      No H-bonds generated for 'chain 'A' and resid 202 through 204'
    Processing helix  chain 'A' and resid 211 through 218
      removed outlier: 4.574A  pdb=" N   GLY A 217 " --> pdb=" O   CYS A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.351A  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 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.685A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.572A  pdb=" N   PHE A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.791A  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 310
    Processing helix  chain 'A' and resid 327 through 351
    Processing helix  chain 'B' and resid 8 through 26
      removed outlier: 4.396A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 3.826A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.592A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 220 through 224
    Processing helix  chain 'G' and resid 14 through 24
    Processing helix  chain 'G' and resid 29 through 46
      removed outlier: 3.597A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   LYS G  46 " --> pdb=" O   GLU G  42 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 21 through 50
    Processing helix  chain 'R' and resid 51 through 54
    Processing helix  chain 'R' and resid 55 through 75
    Processing helix  chain 'R' and resid 75 through 85
    Processing helix  chain 'R' and resid 93 through 126
    Processing helix  chain 'R' and resid 128 through 134
      removed outlier: 4.111A  pdb=" N   ARG R 132 " --> pdb=" O   ILE R 128 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LYS R 133 " --> pdb=" O   GLU R 129 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 135 through 155
    Processing helix  chain 'R' and resid 179 through 191
    Processing helix  chain 'R' and resid 191 through 212
    Processing helix  chain 'R' and resid 283 through 316
      Proline residue:  R 306  - end of helix
    Processing helix  chain 'R' and resid 322 through 346
      removed outlier: 4.087A  pdb=" N   ASN R 336 " --> pdb=" O   LEU R 332 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   SER R 337 " --> pdb=" O   GLY R 333 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   LEU R 338 " --> pdb=" O   TYR R 334 " (cutoff:3.500A)
      Proline residue:  R 341  - end of helix
    Processing helix  chain 'R' and resid 348 through 358
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.567A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.487A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.326A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.468A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51
      removed outlier: 3.534A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.905A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.516A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 148
      removed outlier: 3.568A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.850A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.413A  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: 6.341A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.894A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   TYR B 289 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7
      removed outlier: 3.509A  pdb=" N   THR E  78 " --> pdb=" O   ASP E  73 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.772A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 116 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   THR E 118 " --> pdb=" O   GLY E  10 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.772A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 116 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   THR E 118 " --> pdb=" O   GLY E  10 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195
      removed outlier: 6.384A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   THR E 238 " --> pdb=" O   GLN E 231 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 194 through 195
      removed outlier: 6.384A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLY E 225 " --> pdb=" O   LEU E 245 " (cutoff:3.500A)

    456 hydrogen bonds defined for protein.
    1266 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: 1.35

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2724
        1.35 -     1.47: 2151
        1.47 -     1.58: 3748
        1.58 -     1.70: 0
        1.70 -     1.82: 90
  Bond restraints: 8713
  Sorted by residual:
  bond pdb=" NZ  HVU R 501 "
       pdb=" CA1 HVU R 501 "
    ideal  model  delta    sigma   weight residual
    1.454  1.318  0.136 2.00e-02 2.50e+03 4.63e+01
  bond pdb=" NZ  HVU R 501 "
       pdb=" CJ  HVU R 501 "
    ideal  model  delta    sigma   weight residual
    1.441  1.310  0.131 2.00e-02 2.50e+03 4.32e+01
  bond pdb=" NZ  HVU R 501 "
       pdb=" CF1 HVU R 501 "
    ideal  model  delta    sigma   weight residual
    1.449  1.342  0.107 2.00e-02 2.50e+03 2.89e+01
  bond pdb=" CD1 HVU R 501 "
       pdb=" NE1 HVU R 501 "
    ideal  model  delta    sigma   weight residual
    1.364  1.282  0.082 2.00e-02 2.50e+03 1.69e+01
  bond pdb=" CD2 HVU R 501 "
       pdb=" CE2 HVU R 501 "
    ideal  model  delta    sigma   weight residual
    1.412  1.489 -0.077 2.00e-02 2.50e+03 1.50e+01
  ... (remaining 8708 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 11739
        2.37 -     4.73: 52
        4.73 -     7.10: 9
        7.10 -     9.47: 0
        9.47 -    11.84: 1
  Bond angle restraints: 11801
  Sorted by residual:
  angle pdb=" CD1 HVU R 501 "
        pdb=" NE1 HVU R 501 "
        pdb=" CE2 HVU R 501 "
      ideal   model   delta    sigma   weight residual
     108.93  120.77  -11.84 3.00e+00 1.11e-01 1.56e+01
  angle pdb=" N   ARG E  67 "
        pdb=" CA  ARG E  67 "
        pdb=" C   ARG E  67 "
      ideal   model   delta    sigma   weight residual
     114.04  110.75    3.29 1.24e+00 6.50e-01 7.05e+00
  angle pdb=" CG  HVU R 501 "
        pdb=" CD1 HVU R 501 "
        pdb=" NE1 HVU R 501 "
      ideal   model   delta    sigma   weight residual
     110.60  104.25    6.35 3.00e+00 1.11e-01 4.48e+00
  angle pdb=" NE1 HVU R 501 "
        pdb=" CE2 HVU R 501 "
        pdb=" CZ2 HVU R 501 "
      ideal   model   delta    sigma   weight residual
     130.54  136.63   -6.09 3.00e+00 1.11e-01 4.12e+00
  angle pdb=" CD2 HVU R 501 "
        pdb=" CE2 HVU R 501 "
        pdb=" NE1 HVU R 501 "
      ideal   model   delta    sigma   weight residual
     107.63  101.78    5.85 3.00e+00 1.11e-01 3.81e+00
  ... (remaining 11796 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.44: 5004
       26.44 -    52.89: 164
       52.89 -    79.33: 10
       79.33 -   105.78: 4
      105.78 -   132.22: 1
  Dihedral angle restraints: 5183
    sinusoidal: 2026
      harmonic: 3157
  Sorted by residual:
  dihedral pdb=" CB1 HVU R 501 "
           pdb=" NZ  HVU R 501 "
           pdb=" CF1 HVU R 501 "
           pdb=" CA1 HVU R 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -69.87   62.35 -132.22     1      3.00e+01 1.11e-03 1.78e+01
  dihedral pdb=" CA  HVU R 501 "
           pdb=" NZ  HVU R 501 "
           pdb=" CA1 HVU R 501 "
           pdb=" CF1 HVU R 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      39.14  -59.98   99.12     1      3.00e+01 1.11e-03 1.24e+01
  dihedral pdb=" CB  HVU R 501 "
           pdb=" CB1 HVU R 501 "
           pdb=" CF1 HVU R 501 "
           pdb=" NZ  HVU R 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -29.70   60.47  -90.17     1      3.00e+01 1.11e-03 1.07e+01
  ... (remaining 5180 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1165
       0.051 -    0.101: 137
       0.101 -    0.152: 51
       0.152 -    0.202: 0
       0.202 -    0.253: 1
  Chirality restraints: 1354
  Sorted by residual:
  chirality pdb=" CB  HVU R 501 "
            pdb=" CA  HVU R 501 "
            pdb=" CB1 HVU R 501 "
            pdb=" CG  HVU R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.74    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CA  ILE B  81 "
            pdb=" N   ILE B  81 "
            pdb=" C   ILE B  81 "
            pdb=" CB  ILE B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.24e-01
  chirality pdb=" CA  VAL G  54 "
            pdb=" N   VAL G  54 "
            pdb=" C   VAL G  54 "
            pdb=" CB  VAL G  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.02e-01
  ... (remaining 1351 not shown)

  Planarity restraints: 1470
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.022 5.00e-02 4.00e+02   3.31e-02 1.75e+00
        pdb=" N   PRO B 236 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 340 "    0.015 5.00e-02 4.00e+02   2.33e-02 8.68e-01
        pdb=" N   PRO R 341 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO R 341 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO R 341 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET E 192 "    0.004 2.00e-02 2.50e+03   7.04e-03 4.96e-01
        pdb=" C   MET E 192 "   -0.012 2.00e-02 2.50e+03
        pdb=" O   MET E 192 "    0.005 2.00e-02 2.50e+03
        pdb=" N   SER E 193 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1467 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.51: 63
        2.51 -     3.11: 6529
        3.11 -     3.71: 13515
        3.71 -     4.30: 19320
        4.30 -     4.90: 32848
  Nonbonded interactions: 72275
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     1.918 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD2 ASP B 247 "
     model   vdw
     2.035 3.040
  nonbonded pdb=" O   ASP B 163 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.043 3.040
  nonbonded pdb=" O   ALA A 203 "
            pdb=" NH1 ARG A 205 "
     model   vdw
     2.130 3.120
  nonbonded pdb=" O   PRO R 341 "
            pdb=" OG1 THR R 345 "
     model   vdw
     2.153 3.040
  ... (remaining 72270 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:             0.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.980
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   19.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7028
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   0.136   8717  Z= 0.178
  Angle     :  0.449  11.836  11809  Z= 0.239
  Chirality :  0.038   0.253   1354
  Planarity :  0.002   0.033   1470
  Dihedral  : 12.839 132.220   3133
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.41 (0.27), residues: 1066
  helix:  2.93 (0.27), residues: 379
  sheet:  1.23 (0.31), residues: 269
  loop :  0.69 (0.33), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 205 
 TYR   0.008   0.001   TYR R 192 
 PHE   0.008   0.001   PHE R 152 
 TRP   0.007   0.001   TRP R 331 
 HIS   0.002   0.000   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 8713)
  covalent geometry    : angle       0.44903 (11801)
  SS BOND              : bond        0.00342 (    4)
  SS BOND              : angle       0.59981 (    8)
  hydrogen bonds       : bond        0.17985 (  440)
  hydrogen bonds       : angle       6.62775 ( 1266)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  243 MET cc_start: 0.8133 (tpp) cc_final: 0.7689 (tpt)
REVERT: B  188 MET cc_start: 0.7847 (mmm) cc_final: 0.7638 (mmm)
REVERT: B  221 THR cc_start: 0.7828 (m) cc_final: 0.7606 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.5140
  time to fit residues: 96.5297
Evaluate side-chains
  134 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.2980
   chunk 100 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 255 ASN
B 155 ASN
E  77 ASN
E 186 GLN
R 112 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.190259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.154241 restraints weight = 9580.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 2.26
r_work: 0.3585 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8717  Z= 0.135
  Angle     :  0.545   7.233  11809  Z= 0.291
  Chirality :  0.042   0.143   1354
  Planarity :  0.004   0.057   1470
  Dihedral  :  6.447 115.175   1185
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 12.41 %
    Favored  : 86.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.97 (0.26), residues: 1066
  helix:  2.34 (0.27), residues: 381
  sheet:  1.04 (0.32), residues: 265
  loop :  0.63 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  18 
 TYR   0.012   0.001   TYR R 192 
 PHE   0.026   0.002   PHE E 212 
 TRP   0.018   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8713)
  covalent geometry    : angle       0.54408 (11801)
  SS BOND              : bond        0.00779 (    4)
  SS BOND              : angle       1.20742 (    8)
  hydrogen bonds       : bond        0.03549 (  440)
  hydrogen bonds       : angle       4.80823 ( 1266)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 151
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7935 (m-30) cc_final: 0.7734 (m-30)
REVERT: A  248 LYS cc_start: 0.7841 (mmtm) cc_final: 0.7436 (mmtm)
REVERT: A  297 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.5764 (tm-30)
REVERT: A  337 ASP cc_start: 0.6940 (m-30) cc_final: 0.6642 (m-30)
REVERT: B  189 SER cc_start: 0.8883 (p) cc_final: 0.8295 (t)
REVERT: E  140 MET cc_start: 0.8798 (mmm) cc_final: 0.7744 (mmt)
REVERT: R   27 MET cc_start: 0.6689 (OUTLIER) cc_final: 0.6361 (mpp)
REVERT: R   85 MET cc_start: 0.6159 (ppp) cc_final: 0.5945 (ppp)
  outliers start: 9
  outliers final: 3
  residues processed: 154
  average time/residue: 0.4749
  time to fit residues: 78.4658
Evaluate side-chains
  136 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 131
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue   77 ASN
Chi-restraints excluded: chain R residue   27 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 43 optimal weight:    0.2980
   chunk 52 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0470
   chunk 10 optimal weight:    0.0570
   chunk 47 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 82 optimal weight:    5.9990
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
E  77 ASN
E 186 GLN
R  40 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.189914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.154274 restraints weight = 9568.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 2.26
r_work: 0.3584 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7255
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   8717  Z= 0.110
  Angle     :  0.499   7.179  11809  Z= 0.268
  Chirality :  0.040   0.135   1354
  Planarity :  0.003   0.046   1470
  Dihedral  :  6.373 115.570   1185
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.12 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.26), residues: 1066
  helix:  2.32 (0.27), residues: 377
  sheet:  0.98 (0.32), residues: 267
  loop :  0.53 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 208 
 TYR   0.011   0.001   TYR E 190 
 PHE   0.019   0.001   PHE E 212 
 TRP   0.016   0.001   TRP B 211 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 8713)
  covalent geometry    : angle       0.49827 (11801)
  SS BOND              : bond        0.00590 (    4)
  SS BOND              : angle       1.11448 (    8)
  hydrogen bonds       : bond        0.03180 (  440)
  hydrogen bonds       : angle       4.46756 ( 1266)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7926 (m-30) cc_final: 0.7713 (m-30)
REVERT: A  198 MET cc_start: 0.7826 (mtp) cc_final: 0.7624 (mtp)
REVERT: A  248 LYS cc_start: 0.7807 (mmtm) cc_final: 0.7434 (mmtm)
REVERT: A  337 ASP cc_start: 0.6957 (m-30) cc_final: 0.6646 (m-30)
REVERT: B  175 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6700 (mp10)
REVERT: B  217 MET cc_start: 0.8215 (mtp) cc_final: 0.6978 (mmp)
REVERT: E   43 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7516 (mmtm)
REVERT: E  179 GLN cc_start: 0.8614 (tt0) cc_final: 0.8307 (tt0)
REVERT: R   27 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.6362 (mpp)
  outliers start: 17
  outliers final: 3
  residues processed: 158
  average time/residue: 0.5027
  time to fit residues: 84.9895
Evaluate side-chains
  139 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 133
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   27 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 21 optimal weight:    8.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B 259 GLN
B 295 ASN
E  82 GLN
E 186 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.183239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.146673 restraints weight = 9653.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 2.25
r_work: 0.3477 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8717  Z= 0.142
  Angle     :  0.540   7.452  11809  Z= 0.288
  Chirality :  0.041   0.134   1354
  Planarity :  0.004   0.046   1470
  Dihedral  :  6.643 117.290   1185
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.29 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.26), residues: 1066
  helix:  2.08 (0.27), residues: 382
  sheet:  0.76 (0.31), residues: 268
  loop :  0.48 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 208 
 TYR   0.012   0.001   TYR R 192 
 PHE   0.016   0.002   PHE E 212 
 TRP   0.014   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 8713)
  covalent geometry    : angle       0.53892 (11801)
  SS BOND              : bond        0.00836 (    4)
  SS BOND              : angle       1.52621 (    8)
  hydrogen bonds       : bond        0.03200 (  440)
  hydrogen bonds       : angle       4.46638 ( 1266)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 145
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7991 (m-30) cc_final: 0.7666 (m-30)
REVERT: A  195 HIS cc_start: 0.7188 (m-70) cc_final: 0.6901 (m-70)
REVERT: A  208 ARG cc_start: 0.7696 (ttm-80) cc_final: 0.7324 (ttp80)
REVERT: A  216 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7927 (mt-10)
REVERT: A  248 LYS cc_start: 0.7899 (mmtm) cc_final: 0.7565 (mmtm)
REVERT: A  297 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.5716 (tm-30)
REVERT: A  308 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7959 (mp0)
REVERT: A  337 ASP cc_start: 0.7037 (m-30) cc_final: 0.6758 (m-30)
REVERT: B  175 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6787 (mp10)
REVERT: B  217 MET cc_start: 0.8161 (mtp) cc_final: 0.6952 (mmp)
REVERT: E   43 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7506 (mmtm)
REVERT: R   27 MET cc_start: 0.6786 (OUTLIER) cc_final: 0.6433 (mpp)
REVERT: R   85 MET cc_start: 0.6487 (ppp) cc_final: 0.6230 (ppp)
REVERT: R  144 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.6067 (mt)
  outliers start: 19
  outliers final: 6
  residues processed: 154
  average time/residue: 0.5073
  time to fit residues: 83.3724
Evaluate side-chains
  149 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   27 MET
Chi-restraints excluded: chain R residue  144 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 101 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 88 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0570
   chunk 81 optimal weight:    5.9990
   chunk 25 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.6500

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B 259 GLN
E  82 GLN
E 186 GLN
R  40 ASN
R 112 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.184120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.147084 restraints weight = 9632.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 2.23
r_work: 0.3499 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3354 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.2836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8717  Z= 0.124
  Angle     :  0.522   7.224  11809  Z= 0.279
  Chirality :  0.041   0.198   1354
  Planarity :  0.003   0.036   1470
  Dihedral  :  6.552 115.690   1185
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.83 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.26), residues: 1066
  helix:  1.96 (0.27), residues: 384
  sheet:  0.59 (0.32), residues: 268
  loop :  0.52 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 208 
 TYR   0.012   0.001   TYR E 190 
 PHE   0.014   0.001   PHE E 212 
 TRP   0.015   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8713)
  covalent geometry    : angle       0.52082 (11801)
  SS BOND              : bond        0.00683 (    4)
  SS BOND              : angle       1.33167 (    8)
  hydrogen bonds       : bond        0.03115 (  440)
  hydrogen bonds       : angle       4.38780 ( 1266)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8122 (m-30) cc_final: 0.7804 (m-30)
REVERT: A  195 HIS cc_start: 0.7280 (m-70) cc_final: 0.7063 (m-70)
REVERT: A  208 ARG cc_start: 0.7796 (ttm-80) cc_final: 0.7389 (ttp80)
REVERT: A  216 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8101 (mt-10)
REVERT: A  248 LYS cc_start: 0.7828 (mmtm) cc_final: 0.7381 (mmtm)
REVERT: A  252 SER cc_start: 0.8270 (m) cc_final: 0.7837 (p)
REVERT: A  297 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.5737 (tm-30)
REVERT: A  308 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7984 (mp0)
REVERT: A  318 GLU cc_start: 0.7405 (tp30) cc_final: 0.7026 (tp30)
REVERT: A  337 ASP cc_start: 0.7376 (m-30) cc_final: 0.7105 (m-30)
REVERT: B  134 ARG cc_start: 0.7975 (ptp-110) cc_final: 0.7424 (ptt90)
REVERT: B  175 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6862 (mp10)
REVERT: B  217 MET cc_start: 0.8325 (mtp) cc_final: 0.6980 (mmp)
REVERT: E   43 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7496 (mmtm)
REVERT: R   27 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6523 (mpp)
  outliers start: 22
  outliers final: 6
  residues processed: 144
  average time/residue: 0.5195
  time to fit residues: 79.6624
Evaluate side-chains
  139 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   27 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 81 optimal weight:    7.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 331 ASN
B 259 GLN
E  82 GLN
E 186 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.167041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.124187 restraints weight = 9854.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 2.22
r_work: 0.3307 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.3575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.075   8717  Z= 0.283
  Angle     :  0.664   9.220  11809  Z= 0.352
  Chirality :  0.046   0.188   1354
  Planarity :  0.004   0.039   1470
  Dihedral  :  7.322 118.599   1185
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.65 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.26), residues: 1066
  helix:  1.51 (0.26), residues: 383
  sheet:  0.30 (0.32), residues: 269
  loop :  0.38 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  18 
 TYR   0.016   0.002   TYR B  85 
 PHE   0.015   0.002   PHE E  68 
 TRP   0.021   0.002   TRP B  99 
 HIS   0.009   0.002   HIS R 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00665 ( 8713)
  covalent geometry    : angle       0.66200 (11801)
  SS BOND              : bond        0.01286 (    4)
  SS BOND              : angle       2.29930 (    8)
  hydrogen bonds       : bond        0.03875 (  440)
  hydrogen bonds       : angle       4.86540 ( 1266)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8051 (m-30) cc_final: 0.7672 (m-30)
REVERT: A  208 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.7390 (ttp80)
REVERT: A  216 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8214 (mt-10)
REVERT: A  248 LYS cc_start: 0.7834 (mmtm) cc_final: 0.7351 (mmtm)
REVERT: A  252 SER cc_start: 0.8245 (m) cc_final: 0.7832 (p)
REVERT: A  297 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.5788 (tm-30)
REVERT: A  308 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8146 (mp0)
REVERT: A  330 LYS cc_start: 0.7497 (ttmm) cc_final: 0.7135 (mtmt)
REVERT: B  175 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7164 (mp10)
REVERT: B  217 MET cc_start: 0.8358 (mtp) cc_final: 0.6961 (mmp)
REVERT: B  219 ARG cc_start: 0.7924 (mpt180) cc_final: 0.7634 (mpt180)
REVERT: B  256 ARG cc_start: 0.7835 (mtm180) cc_final: 0.7521 (mtm180)
REVERT: E   43 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7630 (mmtm)
REVERT: E  179 GLN cc_start: 0.8833 (tt0) cc_final: 0.8574 (tt0)
REVERT: R   27 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6654 (mpp)
REVERT: R   85 MET cc_start: 0.6608 (ppp) cc_final: 0.6281 (ppp)
  outliers start: 20
  outliers final: 8
  residues processed: 138
  average time/residue: 0.5531
  time to fit residues: 80.9360
Evaluate side-chains
  132 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   27 MET
Chi-restraints excluded: chain R residue  198 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 102 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0770
   chunk 25 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    0.8940

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 269 ASN
A 331 ASN
E  82 GLN
E 186 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.171479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.134192 restraints weight = 9920.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 2.18
r_work: 0.3389 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8717  Z= 0.149
  Angle     :  0.573   8.591  11809  Z= 0.301
  Chirality :  0.042   0.158   1354
  Planarity :  0.004   0.037   1470
  Dihedral  :  6.862 114.358   1185
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.72 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.27), residues: 1066
  helix:  1.61 (0.27), residues: 381
  sheet:  0.19 (0.32), residues: 271
  loop :  0.46 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  18 
 TYR   0.013   0.001   TYR E 190 
 PHE   0.013   0.001   PHE A 334 
 TRP   0.014   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 8713)
  covalent geometry    : angle       0.57167 (11801)
  SS BOND              : bond        0.00788 (    4)
  SS BOND              : angle       1.54006 (    8)
  hydrogen bonds       : bond        0.03380 (  440)
  hydrogen bonds       : angle       4.68503 ( 1266)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8020 (m-30) cc_final: 0.7696 (m-30)
REVERT: A  195 HIS cc_start: 0.7415 (m-70) cc_final: 0.7152 (m-70)
REVERT: A  208 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7405 (ttp80)
REVERT: A  252 SER cc_start: 0.8272 (m) cc_final: 0.7863 (p)
REVERT: A  297 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.5755 (tm-30)
REVERT: A  308 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8082 (mp0)
REVERT: A  318 GLU cc_start: 0.7288 (tp30) cc_final: 0.6931 (tp30)
REVERT: A  330 LYS cc_start: 0.7549 (ttmm) cc_final: 0.7226 (mtmt)
REVERT: B  134 ARG cc_start: 0.8149 (ptp-110) cc_final: 0.7547 (ptt90)
REVERT: B  217 MET cc_start: 0.8376 (mtp) cc_final: 0.7002 (mmp)
REVERT: B  219 ARG cc_start: 0.7896 (mpt180) cc_final: 0.7667 (mpt180)
REVERT: B  234 PHE cc_start: 0.9393 (OUTLIER) cc_final: 0.7853 (m-80)
REVERT: B  256 ARG cc_start: 0.7856 (mtm180) cc_final: 0.7535 (mtm180)
REVERT: E   43 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7653 (mmtm)
REVERT: R   27 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.6693 (mpp)
  outliers start: 26
  outliers final: 11
  residues processed: 144
  average time/residue: 0.5494
  time to fit residues: 84.0179
Evaluate side-chains
  141 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   27 MET
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue  198 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 88 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 21 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 269 ASN
B 259 GLN
E  82 GLN
E 186 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.167437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.124949 restraints weight = 9903.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.21
r_work: 0.3324 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.3771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068   8717  Z= 0.241
  Angle     :  0.650   8.416  11809  Z= 0.340
  Chirality :  0.045   0.155   1354
  Planarity :  0.004   0.039   1470
  Dihedral  :  7.270 119.323   1185
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.82 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.27), residues: 1066
  helix:  1.43 (0.27), residues: 381
  sheet:  0.09 (0.32), residues: 269
  loop :  0.36 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  19 
 TYR   0.012   0.001   TYR B  85 
 PHE   0.013   0.002   PHE A 334 
 TRP   0.017   0.002   TRP B  99 
 HIS   0.007   0.001   HIS R 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 ( 8713)
  covalent geometry    : angle       0.64807 (11801)
  SS BOND              : bond        0.01126 (    4)
  SS BOND              : angle       2.08139 (    8)
  hydrogen bonds       : bond        0.03656 (  440)
  hydrogen bonds       : angle       4.84674 ( 1266)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8006 (m-30) cc_final: 0.7629 (m-30)
REVERT: A   53 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6229 (mpt)
REVERT: A  195 HIS cc_start: 0.7296 (m-70) cc_final: 0.7080 (m-70)
REVERT: A  208 ARG cc_start: 0.7811 (ttm-80) cc_final: 0.7433 (ttp80)
REVERT: A  248 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7243 (mmtm)
REVERT: A  252 SER cc_start: 0.8225 (m) cc_final: 0.7831 (p)
REVERT: A  308 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8004 (mp0)
REVERT: A  309 ASP cc_start: 0.7810 (m-30) cc_final: 0.7270 (m-30)
REVERT: A  324 THR cc_start: 0.6977 (t) cc_final: 0.6706 (m)
REVERT: A  330 LYS cc_start: 0.7625 (ttmm) cc_final: 0.7154 (mttp)
REVERT: B  134 ARG cc_start: 0.8103 (ptp-110) cc_final: 0.7471 (ptt90)
REVERT: B  175 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7308 (mp10)
REVERT: B  217 MET cc_start: 0.8345 (mtp) cc_final: 0.6955 (mmp)
REVERT: B  234 PHE cc_start: 0.9445 (OUTLIER) cc_final: 0.7887 (m-80)
REVERT: B  256 ARG cc_start: 0.7859 (mtm180) cc_final: 0.7503 (mtm180)
REVERT: E   43 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7686 (mmtm)
REVERT: R   27 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.6660 (mpp)
  outliers start: 26
  outliers final: 10
  residues processed: 134
  average time/residue: 0.5170
  time to fit residues: 73.9459
Evaluate side-chains
  135 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   27 MET
Chi-restraints excluded: chain R residue   81 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 80 optimal weight:    0.0970
   chunk 17 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0070
   chunk 28 optimal weight:    0.5980
   chunk 66 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0870
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.3576

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
E  82 GLN
E 186 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.175063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.138777 restraints weight = 9802.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.17
r_work: 0.3453 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8717  Z= 0.116
  Angle     :  0.571   8.725  11809  Z= 0.296
  Chirality :  0.042   0.145   1354
  Planarity :  0.004   0.037   1470
  Dihedral  :  6.599 111.655   1185
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 20.21 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.27), residues: 1066
  helix:  1.64 (0.27), residues: 385
  sheet:  0.22 (0.33), residues: 260
  loop :  0.37 (0.33), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  19 
 TYR   0.012   0.001   TYR E 190 
 PHE   0.009   0.001   PHE A 334 
 TRP   0.014   0.001   TRP B 211 
 HIS   0.007   0.001   HIS A 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8713)
  covalent geometry    : angle       0.57064 (11801)
  SS BOND              : bond        0.00527 (    4)
  SS BOND              : angle       1.19115 (    8)
  hydrogen bonds       : bond        0.03130 (  440)
  hydrogen bonds       : angle       4.53092 ( 1266)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8059 (m-30) cc_final: 0.7746 (m-30)
REVERT: A  208 ARG cc_start: 0.7763 (ttm-80) cc_final: 0.7528 (ttp80)
REVERT: A  248 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7278 (mmtm)
REVERT: A  252 SER cc_start: 0.8232 (m) cc_final: 0.7885 (p)
REVERT: A  308 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8158 (mp0)
REVERT: A  309 ASP cc_start: 0.7695 (m-30) cc_final: 0.7154 (m-30)
REVERT: A  318 GLU cc_start: 0.7263 (tp30) cc_final: 0.7002 (tp30)
REVERT: A  324 THR cc_start: 0.6761 (t) cc_final: 0.6532 (m)
REVERT: A  330 LYS cc_start: 0.7603 (ttmm) cc_final: 0.7152 (mttp)
REVERT: B  130 GLU cc_start: 0.7817 (mp0) cc_final: 0.7146 (tt0)
REVERT: B  134 ARG cc_start: 0.8176 (ptp-110) cc_final: 0.7567 (ptt90)
REVERT: B  217 MET cc_start: 0.8216 (mtp) cc_final: 0.6994 (mmp)
REVERT: B  249 THR cc_start: 0.8631 (p) cc_final: 0.8315 (t)
REVERT: E   43 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7705 (mmtm)
REVERT: E   93 MET cc_start: 0.8274 (ttm) cc_final: 0.8017 (tpp)
REVERT: R   27 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.6639 (mpp)
  outliers start: 17
  outliers final: 7
  residues processed: 149
  average time/residue: 0.5240
  time to fit residues: 83.0004
Evaluate side-chains
  139 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   27 MET
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue  198 ILE
Chi-restraints excluded: chain R residue  338 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 43 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0020
   chunk 3 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9980
   chunk 82 optimal weight:    5.9990
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
E  82 GLN
E 186 GLN
R  40 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.174461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.138026 restraints weight = 9766.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 2.15
r_work: 0.3447 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3311 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8717  Z= 0.125
  Angle     :  0.575   8.711  11809  Z= 0.300
  Chirality :  0.042   0.157   1354
  Planarity :  0.004   0.048   1470
  Dihedral  :  6.679 112.932   1185
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 20.64 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.27), residues: 1066
  helix:  1.70 (0.27), residues: 383
  sheet:  0.25 (0.33), residues: 257
  loop :  0.41 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG E  18 
 TYR   0.011   0.001   TYR R 192 
 PHE   0.009   0.001   PHE A 334 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8713)
  covalent geometry    : angle       0.57379 (11801)
  SS BOND              : bond        0.00650 (    4)
  SS BOND              : angle       1.37031 (    8)
  hydrogen bonds       : bond        0.03094 (  440)
  hydrogen bonds       : angle       4.49868 ( 1266)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8023 (m-30) cc_final: 0.7698 (m-30)
REVERT: A  208 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7430 (ttp80)
REVERT: A  248 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7327 (mmtm)
REVERT: A  252 SER cc_start: 0.8251 (m) cc_final: 0.7914 (p)
REVERT: A  308 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8101 (mp0)
REVERT: A  318 GLU cc_start: 0.7213 (tp30) cc_final: 0.6879 (tp30)
REVERT: A  324 THR cc_start: 0.6839 (t) cc_final: 0.6583 (m)
REVERT: A  330 LYS cc_start: 0.7663 (ttmm) cc_final: 0.7215 (mttp)
REVERT: B  130 GLU cc_start: 0.7750 (mp0) cc_final: 0.7126 (tt0)
REVERT: B  134 ARG cc_start: 0.8158 (ptp-110) cc_final: 0.7548 (ptt90)
REVERT: B  189 SER cc_start: 0.8986 (p) cc_final: 0.8409 (t)
REVERT: B  217 MET cc_start: 0.8265 (mtp) cc_final: 0.6945 (mmp)
REVERT: B  249 THR cc_start: 0.8614 (p) cc_final: 0.8289 (t)
REVERT: E   43 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7692 (mmtm)
REVERT: E   59 TYR cc_start: 0.8362 (m-10) cc_final: 0.8124 (m-10)
REVERT: R   27 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6630 (mpp)
  outliers start: 14
  outliers final: 6
  residues processed: 137
  average time/residue: 0.4799
  time to fit residues: 70.4048
Evaluate side-chains
  140 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain R residue   27 MET
Chi-restraints excluded: chain R residue  198 ILE
Chi-restraints excluded: chain R residue  338 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0570
   chunk 58 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
E 186 GLN
R  40 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.173334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.136459 restraints weight = 9833.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 2.18
r_work: 0.3426 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.3593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8717  Z= 0.133
  Angle     :  0.582   9.669  11809  Z= 0.302
  Chirality :  0.042   0.168   1354
  Planarity :  0.004   0.038   1470
  Dihedral  :  6.699 113.034   1185
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 21.28 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.27), residues: 1066
  helix:  1.69 (0.27), residues: 384
  sheet:  0.26 (0.33), residues: 257
  loop :  0.41 (0.33), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  19 
 TYR   0.011   0.001   TYR R 192 
 PHE   0.010   0.001   PHE A 334 
 TRP   0.011   0.001   TRP B  99 
 HIS   0.004   0.001   HIS R 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8713)
  covalent geometry    : angle       0.58120 (11801)
  SS BOND              : bond        0.00684 (    4)
  SS BOND              : angle       1.44700 (    8)
  hydrogen bonds       : bond        0.03112 (  440)
  hydrogen bonds       : angle       4.49051 ( 1266)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3288.12 seconds
wall clock time: 56 minutes 51.51 seconds (3411.51 seconds total)