Starting phenix.real_space_refine
on Thu Mar 13 00:45:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e33_30975/03_2025/7e33_30975_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e33_30975/03_2025/7e33_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_2025/7e33_30975.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e33_30975/03_2025/7e33_30975.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e33_30975/03_2025/7e33_30975_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e33_30975/03_2025/7e33_30975_neut.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.32, per 1000 atoms: 0.62
  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: 2.35
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.04
  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: 2.56

  Time building geometry restraints manager: 2.72 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:             0.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.060
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.200
-------------------------------------------------------------------------------
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   8713  Z= 0.248
  Angle     :  0.449  11.836  11801  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 : 6.58
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (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
 TRP   0.007   0.001   TRP R 331 
 HIS   0.002   0.000   HIS G  44 
 PHE   0.008   0.001   PHE R 152 
 TYR   0.008   0.001   TYR R 192 
 ARG   0.004   0.000   ARG A 205 

*********************** 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  : 0.886 
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: 1.1208
  time to fit residues: 211.2441
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  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0060
   chunk 42 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   overall best weight:    0.6796

-------------------------------------------------------------------------------
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 = 0.4182 r_free = 0.4182 target = 0.189740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.153698 restraints weight = 9516.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3803 rms_B_bonded: 2.24
r_work: 0.3577 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3427 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8713  Z= 0.203
  Angle     :  0.547   7.243  11801  Z= 0.292
  Chirality :  0.042   0.143   1354
  Planarity :  0.004   0.059   1470
  Dihedral  :  6.456 114.702   1185
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.26), residues: 1066
  helix:  2.31 (0.27), residues: 381
  sheet:  1.08 (0.32), residues: 263
  loop :  0.67 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.026   0.002   PHE E 212 
 TYR   0.012   0.001   TYR R 192 
 ARG   0.007   0.001   ARG E  18 

*********************** 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
  163 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 154
  time to evaluate  : 0.956 
Fit side-chains
REVERT: A  216 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7914 (mt-10)
REVERT: A  248 LYS cc_start: 0.7861 (mmtm) cc_final: 0.7448 (mmtm)
REVERT: A  297 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.5745 (tm-30)
REVERT: A  337 ASP cc_start: 0.7141 (m-30) cc_final: 0.6835 (m-30)
REVERT: B  189 SER cc_start: 0.8959 (p) cc_final: 0.8380 (t)
REVERT: E  179 GLN cc_start: 0.8639 (tt0) cc_final: 0.8433 (tt0)
REVERT: G   21 MET cc_start: 0.7748 (tmt) cc_final: 0.7460 (tmt)
REVERT: R   27 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6404 (mpp)
REVERT: R   85 MET cc_start: 0.6266 (ppp) cc_final: 0.5932 (ppp)
REVERT: R  144 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5819 (mt)
REVERT: R  350 ASP cc_start: 0.8554 (m-30) cc_final: 0.8335 (m-30)
  outliers start: 9
  outliers final: 2
  residues processed: 157
  average time/residue: 1.0516
  time to fit residues: 177.5543
Evaluate side-chains
  143 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 137
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 GLU
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 R residue   27 MET
Chi-restraints excluded: chain R residue  144 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   chunk 90 optimal weight:    0.5980
   chunk 34 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 80 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B 295 ASN
E  77 ASN
E  82 GLN
E 186 GLN
R  40 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.178188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.139710 restraints weight = 9612.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 2.29
r_work: 0.3383 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.2869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   8713  Z= 0.349
  Angle     :  0.597   8.379  11801  Z= 0.319
  Chirality :  0.044   0.141   1354
  Planarity :  0.004   0.045   1470
  Dihedral  :  6.974 117.568   1185
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.44 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.26), residues: 1066
  helix:  1.98 (0.26), residues: 374
  sheet:  0.63 (0.31), residues: 274
  loop :  0.51 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  99 
 HIS   0.007   0.001   HIS B  62 
 PHE   0.020   0.002   PHE E 212 
 TYR   0.014   0.002   TYR R 192 
 ARG   0.005   0.001   ARG A 208 

*********************** 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
  160 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A  208 ARG cc_start: 0.7805 (ttm-80) cc_final: 0.7435 (ttp80)
REVERT: A  216 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7979 (mt-10)
REVERT: A  248 LYS cc_start: 0.7815 (mmtm) cc_final: 0.7445 (mmtm)
REVERT: A  297 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.5806 (tm-30)
REVERT: B  175 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7105 (mp10)
REVERT: B  217 MET cc_start: 0.8319 (mtp) cc_final: 0.7025 (mmp)
REVERT: B  256 ARG cc_start: 0.7716 (mtm180) cc_final: 0.7389 (mtm180)
REVERT: E   43 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7593 (mmtm)
REVERT: E  140 MET cc_start: 0.8863 (mmp) cc_final: 0.7697 (mmt)
REVERT: E  179 GLN cc_start: 0.8728 (tt0) cc_final: 0.8502 (tt0)
  outliers start: 22
  outliers final: 9
  residues processed: 150
  average time/residue: 1.1775
  time to fit residues: 188.6834
Evaluate side-chains
  133 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
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  297 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   30 VAL
Chi-restraints excluded: chain R residue   50 THR
Chi-restraints excluded: chain R residue  144 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 102 optimal weight:    0.3980
   chunk 21 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   chunk 24 optimal weight:    9.9990
   chunk 88 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 72 optimal weight:    0.3980
   chunk 67 optimal weight:    8.9990
   chunk 20 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   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 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 = 0.4105 r_free = 0.4105 target = 0.181243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.144515 restraints weight = 9538.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.24
r_work: 0.3450 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8713  Z= 0.196
  Angle     :  0.532   7.482  11801  Z= 0.285
  Chirality :  0.041   0.133   1354
  Planarity :  0.004   0.037   1470
  Dihedral  :  6.694 115.823   1185
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 16.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.26), residues: 1066
  helix:  1.99 (0.26), residues: 379
  sheet:  0.53 (0.31), residues: 269
  loop :  0.46 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.003   0.001   HIS R 112 
 PHE   0.017   0.001   PHE E 212 
 TYR   0.014   0.001   TYR E 190 
 ARG   0.006   0.000   ARG A 208 

*********************** 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
  155 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7970 (m-30) cc_final: 0.7641 (m-30)
REVERT: A  195 HIS cc_start: 0.7367 (m-70) cc_final: 0.7136 (m-70)
REVERT: A  208 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7308 (ttp80)
REVERT: A  248 LYS cc_start: 0.7901 (mmtm) cc_final: 0.7507 (mmtm)
REVERT: A  297 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.5775 (tm-30)
REVERT: A  318 GLU cc_start: 0.7312 (tp30) cc_final: 0.6974 (tp30)
REVERT: A  337 ASP cc_start: 0.7203 (m-30) cc_final: 0.6943 (m-30)
REVERT: B  134 ARG cc_start: 0.8003 (ptp-110) cc_final: 0.7414 (ptt90)
REVERT: B  175 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7049 (mp10)
REVERT: B  217 MET cc_start: 0.8328 (mtp) cc_final: 0.6972 (mmp)
REVERT: B  256 ARG cc_start: 0.7736 (mtm180) cc_final: 0.7432 (mtm180)
REVERT: E   43 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7518 (mmtm)
REVERT: R   27 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6563 (mpp)
REVERT: R   85 MET cc_start: 0.6645 (ppp) cc_final: 0.6306 (ppp)
  outliers start: 19
  outliers final: 4
  residues processed: 148
  average time/residue: 1.1027
  time to fit residues: 174.7106
Evaluate side-chains
  134 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 126
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 74 optimal weight:    7.9990
   chunk 99 optimal weight:    7.9990
   chunk 73 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0770
   chunk 69 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 98 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.7740

-------------------------------------------------------------------------------
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  39 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 = 0.4101 r_free = 0.4101 target = 0.180658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.143294 restraints weight = 9541.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 2.20
r_work: 0.3451 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8713  Z= 0.209
  Angle     :  0.526   7.225  11801  Z= 0.282
  Chirality :  0.042   0.198   1354
  Planarity :  0.004   0.036   1470
  Dihedral  :  6.725 117.142   1185
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.33 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.26), residues: 1066
  helix:  1.96 (0.26), residues: 382
  sheet:  0.46 (0.32), residues: 269
  loop :  0.47 (0.32), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 112 
 PHE   0.011   0.001   PHE A 334 
 TYR   0.012   0.001   TYR E 190 
 ARG   0.008   0.000   ARG E  18 

*********************** 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
  156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.882 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7999 (m-30) cc_final: 0.7708 (m-30)
REVERT: A  195 HIS cc_start: 0.7495 (m-70) cc_final: 0.7273 (m170)
REVERT: A  208 ARG cc_start: 0.7821 (ttm-80) cc_final: 0.7454 (ttp80)
REVERT: A  252 SER cc_start: 0.8507 (m) cc_final: 0.8034 (p)
REVERT: A  297 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.5734 (tm-30)
REVERT: A  318 GLU cc_start: 0.7347 (tp30) cc_final: 0.6994 (tp30)
REVERT: A  337 ASP cc_start: 0.7331 (m-30) cc_final: 0.7071 (m-30)
REVERT: B  175 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7099 (mp10)
REVERT: B  217 MET cc_start: 0.8302 (mtp) cc_final: 0.6930 (mmp)
REVERT: B  256 ARG cc_start: 0.7760 (mtm180) cc_final: 0.7472 (mtm180)
REVERT: E   43 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7531 (mmtm)
REVERT: E  140 MET cc_start: 0.8924 (mmt) cc_final: 0.7682 (mmt)
REVERT: R   85 MET cc_start: 0.6132 (ppp) cc_final: 0.5913 (ppp)
REVERT: R  144 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6516 (mt)
  outliers start: 22
  outliers final: 7
  residues processed: 144
  average time/residue: 1.2378
  time to fit residues: 190.4376
Evaluate side-chains
  138 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  297 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  102 ASP
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  198 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 95 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9980
   chunk 88 optimal weight:    0.7980
   chunk 42 optimal weight:    4.9990
   chunk 18 optimal weight:    0.1980
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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  39 GLN
E  82 GLN
E 186 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.180873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.142857 restraints weight = 9616.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 2.27
r_work: 0.3438 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.3162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8713  Z= 0.211
  Angle     :  0.535   7.222  11801  Z= 0.285
  Chirality :  0.042   0.178   1354
  Planarity :  0.003   0.036   1470
  Dihedral  :  6.804 118.788   1185
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 19.04 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.27), residues: 1066
  helix:  1.89 (0.26), residues: 384
  sheet:  0.42 (0.32), residues: 269
  loop :  0.44 (0.33), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 211 
 HIS   0.003   0.001   HIS R 112 
 PHE   0.011   0.001   PHE A 334 
 TYR   0.012   0.001   TYR E 190 
 ARG   0.007   0.000   ARG B  19 

*********************** 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
  148 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 1.321 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7878 (m-30) cc_final: 0.7555 (m-30)
REVERT: A  195 HIS cc_start: 0.7282 (m-70) cc_final: 0.7011 (m-70)
REVERT: A  208 ARG cc_start: 0.7757 (ttm-80) cc_final: 0.7388 (ttp80)
REVERT: A  216 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7896 (mt-10)
REVERT: A  252 SER cc_start: 0.8405 (m) cc_final: 0.7973 (p)
REVERT: A  269 ASN cc_start: 0.8804 (m-40) cc_final: 0.8288 (m110)
REVERT: A  318 GLU cc_start: 0.7124 (tp30) cc_final: 0.6757 (tp30)
REVERT: A  337 ASP cc_start: 0.7140 (m-30) cc_final: 0.6874 (m-30)
REVERT: B  134 ARG cc_start: 0.7993 (ptp-110) cc_final: 0.7419 (ptt90)
REVERT: B  175 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.7063 (mp10)
REVERT: B  217 MET cc_start: 0.8113 (mtp) cc_final: 0.6865 (mmp)
REVERT: B  256 ARG cc_start: 0.7758 (mtm180) cc_final: 0.7434 (mtm180)
REVERT: E   43 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7581 (mmtm)
  outliers start: 16
  outliers final: 10
  residues processed: 137
  average time/residue: 1.2592
  time to fit residues: 184.5168
Evaluate side-chains
  143 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
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  331 ASN
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  228 ASP
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  198 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 40 optimal weight:    0.2980
   chunk 56 optimal weight:    0.6980
   chunk 91 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
E  39 GLN
E  82 GLN
E 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.181860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.144463 restraints weight = 9672.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.24
r_work: 0.3457 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.3234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8713  Z= 0.193
  Angle     :  0.542   7.236  11801  Z= 0.286
  Chirality :  0.042   0.177   1354
  Planarity :  0.004   0.039   1470
  Dihedral  :  6.788 118.266   1185
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.82 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.27), residues: 1066
  helix:  1.94 (0.26), residues: 385
  sheet:  0.44 (0.33), residues: 267
  loop :  0.46 (0.33), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS R 112 
 PHE   0.014   0.001   PHE A 250 
 TYR   0.012   0.001   TYR E 190 
 ARG   0.010   0.000   ARG E  18 

*********************** 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
  153 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 1.058 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7866 (m-30) cc_final: 0.7527 (m-30)
REVERT: A  195 HIS cc_start: 0.7186 (m-70) cc_final: 0.6974 (m-70)
REVERT: A  208 ARG cc_start: 0.7757 (ttm-80) cc_final: 0.7162 (ttp80)
REVERT: A  252 SER cc_start: 0.8188 (m) cc_final: 0.7799 (p)
REVERT: A  270 LYS cc_start: 0.8384 (mtmp) cc_final: 0.7734 (ptpp)
REVERT: A  297 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.5722 (tm-30)
REVERT: A  318 GLU cc_start: 0.7129 (tp30) cc_final: 0.6761 (tp30)
REVERT: A  330 LYS cc_start: 0.7445 (ttmm) cc_final: 0.7149 (mtmt)
REVERT: A  337 ASP cc_start: 0.7166 (m-30) cc_final: 0.6923 (m-30)
REVERT: B  175 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.7032 (mp10)
REVERT: B  217 MET cc_start: 0.8099 (mtp) cc_final: 0.6958 (mmp)
REVERT: B  256 ARG cc_start: 0.7736 (mtm180) cc_final: 0.7390 (mtm180)
REVERT: E   43 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7583 (mmtm)
REVERT: E  140 MET cc_start: 0.8868 (mmt) cc_final: 0.7824 (mmt)
REVERT: R   85 MET cc_start: 0.6686 (ppp) cc_final: 0.6312 (ppp)
  outliers start: 24
  outliers final: 9
  residues processed: 143
  average time/residue: 1.2755
  time to fit residues: 194.3240
Evaluate side-chains
  133 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  228 ASP
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  198 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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
E  39 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 = 0.3960 r_free = 0.3960 target = 0.167499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.124237 restraints weight = 9959.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.24
r_work: 0.3320 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.3642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   8713  Z= 0.393
  Angle     :  0.643   8.812  11801  Z= 0.340
  Chirality :  0.045   0.181   1354
  Planarity :  0.004   0.039   1470
  Dihedral  :  7.163 116.941   1185
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 19.14 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.26), residues: 1066
  helix:  1.58 (0.26), residues: 383
  sheet:  0.20 (0.32), residues: 269
  loop :  0.37 (0.33), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  99 
 HIS   0.007   0.001   HIS R 112 
 PHE   0.017   0.002   PHE A 334 
 TYR   0.013   0.002   TYR R 192 
 ARG   0.007   0.001   ARG B  19 

*********************** 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
  155 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 0.947 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7998 (m-30) cc_final: 0.7588 (m-30)
REVERT: A  208 ARG cc_start: 0.7788 (ttm-80) cc_final: 0.7411 (ttp80)
REVERT: A  252 SER cc_start: 0.8226 (m) cc_final: 0.7806 (p)
REVERT: A  318 GLU cc_start: 0.7288 (tp30) cc_final: 0.6905 (tp30)
REVERT: A  330 LYS cc_start: 0.7696 (ttmm) cc_final: 0.7143 (mttp)
REVERT: B  134 ARG cc_start: 0.8072 (ptp-110) cc_final: 0.7411 (ptt90)
REVERT: B  217 MET cc_start: 0.8370 (mtp) cc_final: 0.7028 (mmp)
REVERT: B  256 ARG cc_start: 0.7849 (mtm180) cc_final: 0.7604 (mtm180)
REVERT: E   43 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7633 (mmtm)
REVERT: R   85 MET cc_start: 0.6558 (ppp) cc_final: 0.6325 (ppp)
  outliers start: 21
  outliers final: 11
  residues processed: 142
  average time/residue: 1.0164
  time to fit residues: 155.5336
Evaluate side-chains
  138 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
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  264 ILE
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  196 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  102 ASP
Chi-restraints excluded: chain R residue  175 ILE
Chi-restraints excluded: chain R residue  198 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 21 optimal weight:   10.0000
   chunk 47 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 69 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 18 optimal weight:    0.4980
   chunk 54 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 85 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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
E  39 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 = 0.4015 r_free = 0.4015 target = 0.173061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.136523 restraints weight = 9841.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 2.17
r_work: 0.3423 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.3561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8713  Z= 0.202
  Angle     :  0.569   8.576  11801  Z= 0.298
  Chirality :  0.042   0.171   1354
  Planarity :  0.004   0.045   1470
  Dihedral  :  6.864 115.894   1185
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.27), residues: 1066
  helix:  1.67 (0.27), residues: 384
  sheet:  0.29 (0.33), residues: 266
  loop :  0.37 (0.33), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 211 
 HIS   0.003   0.001   HIS R 112 
 PHE   0.012   0.001   PHE A 250 
 TYR   0.012   0.001   TYR E 190 
 ARG   0.011   0.000   ARG E  18 

*********************** 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
  141 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.876 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7944 (m-30) cc_final: 0.7622 (m-30)
REVERT: A  208 ARG cc_start: 0.7775 (ttm-80) cc_final: 0.7538 (ttp80)
REVERT: A  252 SER cc_start: 0.8222 (m) cc_final: 0.7857 (p)
REVERT: A  269 ASN cc_start: 0.8986 (m-40) cc_final: 0.8445 (m110)
REVERT: A  270 LYS cc_start: 0.8428 (mtmp) cc_final: 0.7860 (ptpp)
REVERT: A  318 GLU cc_start: 0.7280 (tp30) cc_final: 0.7003 (tp30)
REVERT: A  330 LYS cc_start: 0.7616 (ttmm) cc_final: 0.7148 (mttp)
REVERT: A  331 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7455 (m110)
REVERT: B  130 GLU cc_start: 0.7684 (mp0) cc_final: 0.6963 (tt0)
REVERT: B  134 ARG cc_start: 0.8160 (ptp-110) cc_final: 0.7534 (ptt90)
REVERT: B  217 MET cc_start: 0.8328 (mtp) cc_final: 0.6959 (mmp)
REVERT: B  249 THR cc_start: 0.8658 (p) cc_final: 0.8297 (t)
REVERT: E   43 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7645 (mmtm)
  outliers start: 14
  outliers final: 8
  residues processed: 133
  average time/residue: 1.1411
  time to fit residues: 162.5466
Evaluate side-chains
  136 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  331 ASN
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   62 CYS
Chi-restraints excluded: chain R residue  198 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 102 optimal weight:    7.9990
   chunk 62 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 8 optimal weight:    0.6980
   chunk 71 optimal weight:    0.5980
   chunk 55 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 82 optimal weight:    5.9990
   chunk 74 optimal weight:    8.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    2.5984

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

Flipped N/Q/H residues before XYZ refinement:
E  39 GLN
E 186 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.172043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.135407 restraints weight = 9844.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 2.19
r_work: 0.3403 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.3580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.156   8713  Z= 0.394
  Angle     :  0.915  59.200  11801  Z= 0.536
  Chirality :  0.046   0.241   1354
  Planarity :  0.004   0.038   1470
  Dihedral  :  6.874 115.961   1185
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 20.53 %
    Favored  : 78.07 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.27), residues: 1066
  helix:  1.60 (0.26), residues: 384
  sheet:  0.29 (0.33), residues: 266
  loop :  0.37 (0.33), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 211 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.012   0.002   PHE A 250 
 TYR   0.011   0.001   TYR R 192 
 ARG   0.008   0.001   ARG B  19 

********************** 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
  143 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 1.026 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7963 (m-30) cc_final: 0.7581 (m-30)
REVERT: A  208 ARG cc_start: 0.7782 (ttm-80) cc_final: 0.7550 (ttp80)
REVERT: A  252 SER cc_start: 0.8236 (m) cc_final: 0.7872 (p)
REVERT: A  269 ASN cc_start: 0.8989 (m-40) cc_final: 0.8459 (m110)
REVERT: A  270 LYS cc_start: 0.8439 (mtmp) cc_final: 0.7869 (ptpp)
REVERT: A  318 GLU cc_start: 0.7320 (tp30) cc_final: 0.6959 (tp30)
REVERT: A  330 LYS cc_start: 0.7624 (ttmm) cc_final: 0.7266 (mppt)
REVERT: B   43 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8232 (mp)
REVERT: B  130 GLU cc_start: 0.7710 (mp0) cc_final: 0.7045 (tt0)
REVERT: B  134 ARG cc_start: 0.8178 (ptp-110) cc_final: 0.7550 (ptt90)
REVERT: B  217 MET cc_start: 0.8313 (mtp) cc_final: 0.7002 (mmp)
REVERT: B  249 THR cc_start: 0.8668 (p) cc_final: 0.8307 (t)
REVERT: E   43 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7653 (mmtm)
  outliers start: 13
  outliers final: 8
  residues processed: 134
  average time/residue: 1.1242
  time to fit residues: 162.0916
Evaluate side-chains
  138 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain B residue   43 ILE
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   62 CYS
Chi-restraints excluded: chain R residue  198 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 99 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
E  39 GLN
E 186 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.172086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.135372 restraints weight = 10017.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.22
r_work: 0.3398 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3261 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.3572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.156   8713  Z= 0.394
  Angle     :  0.915  59.200  11801  Z= 0.536
  Chirality :  0.046   0.241   1354
  Planarity :  0.004   0.038   1470
  Dihedral  :  6.874 115.961   1185
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 21.07 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.27), residues: 1066
  helix:  1.60 (0.26), residues: 384
  sheet:  0.29 (0.33), residues: 266
  loop :  0.37 (0.33), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 211 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.012   0.002   PHE A 250 
 TYR   0.011   0.001   TYR R 192 
 ARG   0.008   0.001   ARG B  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7194.85 seconds
wall clock time: 126 minutes 29.16 seconds (7589.16 seconds total)