Starting phenix.real_space_refine
on Sat Aug 23 02:33:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sai_40270/08_2025/8sai_40270_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sai_40270/08_2025/8sai_40270.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sai_40270/08_2025/8sai_40270.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sai_40270/08_2025/8sai_40270.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sai_40270/08_2025/8sai_40270_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sai_40270/08_2025/8sai_40270_neut.cif"
  }
  resolution = 3.27
  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=   0.009 sd=   0.082
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      68      5.16       5
     C    5774      2.51       5
     N    1534      2.21       5
     O    1685      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9062
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2373
          Classifications: {'peptide': 291}
          Link IDs: {'PTRANS': 4, 'TRANS': 286}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "D"
      Number of atoms: 1824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1824
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 224}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 2611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2611
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Classifications: {'peptide': 1}
  Time building chain proxies: 2.04, per 1000 atoms: 0.23
  Number of scatterers: 9062
  At special positions: 0
  Unit cell: (92, 121.44, 132.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      68     16.00
     P       1     15.00
     O    1685      8.00
     N    1534      7.00
     C    5774      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 127 " - pdb=" SG  CYS A 204 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.04

  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 214.7 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2144

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 12 sheets defined
      36.3% alpha, 21.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 53 through 75
      removed outlier: 3.603A  pdb=" N   LEU A  57 " --> pdb=" O   LEU A  53 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL A  63 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ILE A  66 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 118
      removed outlier: 3.655A  pdb=" N   CYS A 106 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU A 107 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
      Proline residue:  A 108  - end of helix
      removed outlier: 3.550A  pdb=" N   ASN A 116 " --> pdb=" O   MET A 112 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   GLN A 117 " --> pdb=" O   TYR A 113 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ASN A 118 " --> pdb=" O   HIS A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 159
      removed outlier: 3.878A  pdb=" N   CYS A 127 " --> pdb=" O   GLY A 123 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ILE A 154 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LYS A 155 " --> pdb=" O   ASP A 151 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ILE A 156 " --> pdb=" O   ARG A 152 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ASN A 157 " --> pdb=" O   TYR A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 197
      removed outlier: 3.854A  pdb=" N   TYR A 173 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LYS A 195 " --> pdb=" O   ILE A 191 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   LYS A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   GLY A 197 " --> pdb=" O   THR A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 250
      removed outlier: 3.522A  pdb=" N   ASN A 220 " --> pdb=" O   GLU A 216 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU A 223 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL A 224 " --> pdb=" O   ASN A 220 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   VAL A 225 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   PHE A 227 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   TRP A 228 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU A 229 " --> pdb=" O   VAL A 225 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   LEU A 232 " --> pdb=" O   TRP A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 263
    Processing helix  chain 'A' and resid 267 through 279
      removed outlier: 3.645A  pdb=" N   VAL A 271 " --> pdb=" O   ASN A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 293
      removed outlier: 3.814A  pdb=" N   HIS A 283 " --> pdb=" O   PHE A 279 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   PHE A 287 " --> pdb=" O   HIS A 283 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   ILE A 288 " --> pdb=" O   ALA A 284 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   TYR A 289 " --> pdb=" O   PHE A 285 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER A 291 " --> pdb=" O   PHE A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 331
      Proline residue:  A 324  - end of helix
      removed outlier: 4.469A  pdb=" N   TYR A 327 " --> pdb=" O   ASP A 323 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   PHE A 328 " --> pdb=" O   PRO A 324 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LEU A 329 " --> pdb=" O   VAL A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 338
    Processing helix  chain 'C' and resid 7 through 22
      removed outlier: 3.922A  pdb=" N   GLN C  11 " --> pdb=" O   ALA C   7 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 45
      removed outlier: 3.525A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 48
      No H-bonds generated for 'chain 'C' and resid 46 through 48'
    Processing helix  chain 'D' and resid 6 through 28
      removed outlier: 3.579A  pdb=" N   LYS D  10 " --> pdb=" O   SER D   6 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ALA D  11 " --> pdb=" O   ALA D   7 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   ALA D  12 " --> pdb=" O   GLU D   8 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 53
      removed outlier: 3.574A  pdb=" N   MET D  53 " --> pdb=" O   ILE D  49 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 207 through 216
      removed outlier: 4.378A  pdb=" N   ILE D 212 " --> pdb=" O   LYS D 209 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   HIS D 213 " --> pdb=" O   LYS D 210 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 241 through 255
    Processing helix  chain 'D' and resid 270 through 279
      removed outlier: 4.637A  pdb=" N   LYS D 279 " --> pdb=" O   GLU D 275 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 282 through 286
    Processing helix  chain 'D' and resid 295 through 309
    Processing helix  chain 'D' and resid 327 through 352
      removed outlier: 3.908A  pdb=" N   ASN D 331 " --> pdb=" O   THR D 327 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY D 352 " --> pdb=" O   LEU D 348 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 25
      removed outlier: 3.523A  pdb=" N   CYS E  25 " --> pdb=" O   ALA E  21 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 29 through 35
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.841A  pdb=" N   PHE S  32 " --> pdb=" O   PHE S  29 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 185 through 190
      removed outlier: 3.713A  pdb=" N   ALA D 220 " --> pdb=" O   LYS D  35 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   CYS D 224 " --> pdb=" O   LEU D  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 47 through 52
      removed outlier: 4.078A  pdb=" N   ARG E  49 " --> pdb=" O   ILE E 338 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   PHE E 335 " --> pdb=" O   SER E 331 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   SER E 331 " --> pdb=" O   PHE E 335 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   CYS E 317 " --> pdb=" O   GLY E 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 58 through 63
      removed outlier: 7.005A  pdb=" N   ALA E  73 " --> pdb=" O   TYR E  59 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   MET E  61 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   VAL E  71 " --> pdb=" O   MET E  61 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   TRP E  63 " --> pdb=" O   LEU E  69 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   LEU E  69 " --> pdb=" O   TRP E  63 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   SER E  74 " --> pdb=" O   LYS E  78 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   LYS E  78 " --> pdb=" O   SER E  74 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   HIS E  91 " --> pdb=" O   ILE E  81 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ASP E  83 " --> pdb=" O   LYS E  89 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   LYS E  89 " --> pdb=" O   ASP E  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 102 through 105
      removed outlier: 6.240A  pdb=" N   CYS E 121 " --> pdb=" O   GLU E 138 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   GLU E 138 " --> pdb=" O   CYS E 121 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ILE E 123 " --> pdb=" O   SER E 136 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ARG E 134 " --> pdb=" O   ASN E 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 146 through 153
      removed outlier: 6.448A  pdb=" N   GLN E 156 " --> pdb=" O   LEU E 152 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ILE E 157 " --> pdb=" O   TRP E 169 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER E 161 " --> pdb=" O   THR E 165 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   THR E 165 " --> pdb=" O   SER E 161 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR E 178 " --> pdb=" O   LEU E 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 187 through 192
      removed outlier: 3.686A  pdb=" N   SER E 189 " --> pdb=" O   GLY E 202 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   SER E 207 " --> pdb=" O   ALA E 203 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLN E 220 " --> pdb=" O   LEU E 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 229 through 234
      removed outlier: 6.783A  pdb=" N   GLY E 244 " --> pdb=" O   ASN E 230 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   ILE E 232 " --> pdb=" O   ALA E 242 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ALA E 242 " --> pdb=" O   ILE E 232 " (cutoff:3.500A)
      removed outlier: 5.002A  pdb=" N   PHE E 234 " --> pdb=" O   ALA E 240 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   ALA E 240 " --> pdb=" O   PHE E 234 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   MET E 262 " --> pdb=" O   LEU E 252 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ASP E 254 " --> pdb=" O   GLU E 260 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   GLU E 260 " --> pdb=" O   ASP E 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 273 through 277
      removed outlier: 6.457A  pdb=" N   GLY E 288 " --> pdb=" O   THR E 274 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   VAL E 276 " --> pdb=" O   LEU E 286 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   LEU E 286 " --> pdb=" O   VAL E 276 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   CYS E 294 " --> pdb=" O   VAL E 307 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   VAL E 307 " --> pdb=" O   CYS E 294 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   VAL E 296 " --> pdb=" O   ALA E 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.614A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 116 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   THR S 118 " --> pdb=" O   GLY S  10 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL S  12 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 142
    Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.908A  pdb=" N   GLU S 246 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   THR S 243 " --> pdb=" O   TYR S 227 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)

    417 hydrogen bonds defined for protein.
    1179 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: 1.00

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1457
        1.30 -     1.43: 2440
        1.43 -     1.56: 5240
        1.56 -     1.69: 3
        1.69 -     1.82: 101
  Bond restraints: 9241
  Sorted by residual:
  bond pdb=" C   TYR A 261 "
       pdb=" O   TYR A 261 "
    ideal  model  delta    sigma   weight residual
    1.236  1.166  0.070 1.28e-02 6.10e+03 2.97e+01
  bond pdb=" CA  ARG A 208 "
       pdb=" C   ARG A 208 "
    ideal  model  delta    sigma   weight residual
    1.523  1.456  0.067 1.28e-02 6.10e+03 2.73e+01
  bond pdb=" C   ARG A 208 "
       pdb=" O   ARG A 208 "
    ideal  model  delta    sigma   weight residual
    1.234  1.176  0.058 1.22e-02 6.72e+03 2.29e+01
  bond pdb=" C5  S12 A 401 "
       pdb=" O52 S12 A 401 "
    ideal  model  delta    sigma   weight residual
    1.330  1.398 -0.068 2.00e-02 2.50e+03 1.15e+01
  bond pdb=" NE  ARG A 208 "
       pdb=" CZ  ARG A 208 "
    ideal  model  delta    sigma   weight residual
    1.326  1.302  0.024 1.10e-02 8.26e+03 4.73e+00
  ... (remaining 9236 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 12389
        2.48 -     4.96: 74
        4.96 -     7.44: 14
        7.44 -     9.93: 3
        9.93 -    12.41: 2
  Bond angle restraints: 12482
  Sorted by residual:
  angle pdb=" CA  PRO S  75 "
        pdb=" N   PRO S  75 "
        pdb=" CD  PRO S  75 "
      ideal   model   delta    sigma   weight residual
     112.00  104.21    7.79 1.40e+00 5.10e-01 3.09e+01
  angle pdb=" C   TYR A 261 "
        pdb=" N   ALA A 262 "
        pdb=" CA  ALA A 262 "
      ideal   model   delta    sigma   weight residual
     120.29  127.73   -7.44 1.42e+00 4.96e-01 2.74e+01
  angle pdb=" CA  LYS A 260 "
        pdb=" C   LYS A 260 "
        pdb=" N   TYR A 261 "
      ideal   model   delta    sigma   weight residual
     118.43  112.44    5.99 1.33e+00 5.65e-01 2.03e+01
  angle pdb=" O   LYS A 260 "
        pdb=" C   LYS A 260 "
        pdb=" N   TYR A 261 "
      ideal   model   delta    sigma   weight residual
     122.46  128.46   -6.00 1.38e+00 5.25e-01 1.89e+01
  angle pdb=" O3  S12 A 401 "
        pdb=" P   S12 A 401 "
        pdb=" O4  S12 A 401 "
      ideal   model   delta    sigma   weight residual
     121.84  109.43   12.41 3.00e+00 1.11e-01 1.71e+01
  ... (remaining 12477 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.84: 5285
       28.84 -    57.68: 204
       57.68 -    86.51: 12
       86.51 -   115.35: 0
      115.35 -   144.19: 1
  Dihedral angle restraints: 5502
    sinusoidal: 2174
      harmonic: 3328
  Sorted by residual:
  dihedral pdb=" CA  ASN A 116 "
           pdb=" C   ASN A 116 "
           pdb=" N   GLN A 117 "
           pdb=" CA  GLN A 117 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.11   23.89     0      5.00e+00 4.00e-02 2.28e+01
  dihedral pdb=" C4  S12 A 401 "
           pdb=" C5  S12 A 401 "
           pdb=" O52 S12 A 401 "
           pdb=" C6  S12 A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     176.02   31.83  144.19     1      3.00e+01 1.11e-03 1.93e+01
  dihedral pdb=" CA  ARG A 208 "
           pdb=" C   ARG A 208 "
           pdb=" N   ASP A 209 "
           pdb=" CA  ASP A 209 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.83  -19.17     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 5499 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1098
       0.045 -    0.091: 252
       0.091 -    0.136: 63
       0.136 -    0.182: 0
       0.182 -    0.227: 1
  Chirality restraints: 1414
  Sorted by residual:
  chirality pdb=" CA  ARG A 208 "
            pdb=" N   ARG A 208 "
            pdb=" C   ARG A 208 "
            pdb=" CB  ARG A 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CA  ILE E  93 "
            pdb=" N   ILE E  93 "
            pdb=" C   ILE E  93 "
            pdb=" CB  ILE E  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.57e-01
  chirality pdb=" CA  ILE S 216 "
            pdb=" N   ILE S 216 "
            pdb=" C   ILE S 216 "
            pdb=" CB  ILE S 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  ... (remaining 1411 not shown)

  Planarity restraints: 1566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "    0.084 5.00e-02 4.00e+02   1.22e-01 2.38e+01
        pdb=" N   PRO S  75 "   -0.211 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "    0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "    0.065 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 208 "    0.018 2.00e-02 2.50e+03   3.79e-02 1.44e+01
        pdb=" C   ARG A 208 "   -0.066 2.00e-02 2.50e+03
        pdb=" O   ARG A 208 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ASP A 209 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 323 "   -0.036 5.00e-02 4.00e+02   5.50e-02 4.84e+00
        pdb=" N   PRO A 324 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 324 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 324 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1563 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 549
        2.74 -     3.28: 8577
        3.28 -     3.82: 13942
        3.82 -     4.36: 16204
        4.36 -     4.90: 29563
  Nonbonded interactions: 68835
  Sorted by model distance:
  nonbonded pdb=" OG  SER E 245 "
            pdb=" OD1 ASP E 247 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OG  SER E  74 "
            pdb=" OD1 ASP E  76 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" NH1 ARG S 202 "
            pdb=" OE1 GLU S 220 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" OD1 ASN A 200 "
            pdb=" OG1 THR A 202 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OG1 THR E 274 "
            pdb=" O   VAL E 315 "
     model   vdw
     2.280 3.040
  ... (remaining 68830 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.710
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
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      :  0.003   0.089   9243  Z= 0.162
  Angle     :  0.567  12.408  12486  Z= 0.321
  Chirality :  0.039   0.227   1414
  Planarity :  0.004   0.122   1566
  Dihedral  : 13.992 144.191   3352
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.40 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.26), residues: 1133
  helix:  2.30 (0.28), residues: 379
  sheet:  1.13 (0.31), residues: 294
  loop : -1.14 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 208 
 TYR   0.020   0.001   TYR A 261 
 PHE   0.015   0.001   PHE A 279 
 TRP   0.014   0.001   TRP E 339 
 HIS   0.003   0.000   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9241)
  covalent geometry    : angle       0.56666 (12482)
  SS BOND              : bond        0.00304 (    2)
  SS BOND              : angle       0.90840 (    4)
  hydrogen bonds       : bond        0.15386 (  417)
  hydrogen bonds       : angle       4.91679 ( 1179)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 165
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A   74 ILE cc_start: 0.8371 (mm) cc_final: 0.8064 (mt)
REVERT: D  345 LYS cc_start: 0.8220 (ttpp) cc_final: 0.7941 (mttp)
REVERT: E  153 ASP cc_start: 0.7447 (p0) cc_final: 0.7197 (p0)
REVERT: S  154 SER cc_start: 0.7473 (m) cc_final: 0.7043 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 166
  average time/residue: 0.0903
  time to fit residues: 20.1483
Evaluate side-chains
  130 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.0670
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.0870
   chunk 106 optimal weight:    0.5980
   overall best weight:    0.4696

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

Flipped N/Q/H residues before XYZ refinement:
A 137 ASN
A 206 HIS
A 211 HIS
D 255 ASN
** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 110 ASN
E 175 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.124422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.098453 restraints weight = 16446.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.25
r_work: 0.3218 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9243  Z= 0.103
  Angle     :  0.486   6.334  12486  Z= 0.260
  Chirality :  0.040   0.166   1414
  Planarity :  0.004   0.072   1566
  Dihedral  :  6.169 100.271   1263
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  5.43 %
    Favored  : 93.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.26), residues: 1133
  helix:  2.41 (0.27), residues: 392
  sheet:  1.15 (0.31), residues: 290
  loop : -1.30 (0.27), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG S 202 
 TYR   0.023   0.001   TYR A  77 
 PHE   0.021   0.001   PHE A 205 
 TRP   0.010   0.001   TRP E 339 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 9241)
  covalent geometry    : angle       0.48540 (12482)
  SS BOND              : bond        0.00457 (    2)
  SS BOND              : angle       1.14988 (    4)
  hydrogen bonds       : bond        0.03777 (  417)
  hydrogen bonds       : angle       3.83733 ( 1179)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  279 PHE cc_start: 0.5905 (OUTLIER) cc_final: 0.4043 (t80)
REVERT: D  248 LYS cc_start: 0.8714 (tttt) cc_final: 0.8063 (mmtt)
REVERT: D  345 LYS cc_start: 0.8621 (ttpp) cc_final: 0.8334 (mttp)
REVERT: E  258 ASP cc_start: 0.6841 (t0) cc_final: 0.6528 (t0)
REVERT: S  154 SER cc_start: 0.7479 (m) cc_final: 0.7065 (p)
  outliers start: 10
  outliers final: 7
  residues processed: 137
  average time/residue: 0.0971
  time to fit residues: 17.9938
Evaluate side-chains
  127 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  279 PHE
Chi-restraints excluded: chain D residue  272 ASP
Chi-restraints excluded: chain D residue  306 GLN
Chi-restraints excluded: chain D residue  321 THR
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue  139 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 99 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 111 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 39 optimal weight:    0.0770
   chunk 103 optimal weight:    0.0040
   chunk 35 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.5750

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

Flipped N/Q/H residues before XYZ refinement:
A 206 HIS
A 319 ASN
** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.122606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.096724 restraints weight = 16438.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.21
r_work: 0.3196 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9243  Z= 0.100
  Angle     :  0.463   8.087  12486  Z= 0.248
  Chirality :  0.040   0.173   1414
  Planarity :  0.004   0.065   1566
  Dihedral  :  5.225  79.977   1263
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  8.55 %
    Favored  : 90.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.26), residues: 1133
  helix:  2.49 (0.27), residues: 392
  sheet:  1.18 (0.31), residues: 290
  loop : -1.32 (0.27), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 251 
 TYR   0.021   0.001   TYR A  77 
 PHE   0.020   0.001   PHE A 205 
 TRP   0.009   0.001   TRP E 339 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 9241)
  covalent geometry    : angle       0.46221 (12482)
  SS BOND              : bond        0.00472 (    2)
  SS BOND              : angle       1.08179 (    4)
  hydrogen bonds       : bond        0.03665 (  417)
  hydrogen bonds       : angle       3.67307 ( 1179)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  158 ARG cc_start: 0.4171 (tpm170) cc_final: 0.3152 (ttt180)
REVERT: D  248 LYS cc_start: 0.8743 (tttt) cc_final: 0.8132 (mmtt)
REVERT: D  275 GLU cc_start: 0.7948 (tp30) cc_final: 0.7705 (tm-30)
REVERT: D  345 LYS cc_start: 0.8628 (ttpp) cc_final: 0.8364 (mttp)
REVERT: E  258 ASP cc_start: 0.6919 (t0) cc_final: 0.6561 (t0)
REVERT: S  154 SER cc_start: 0.7421 (m) cc_final: 0.7010 (p)
  outliers start: 8
  outliers final: 5
  residues processed: 132
  average time/residue: 0.0985
  time to fit residues: 17.3919
Evaluate side-chains
  129 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 124
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain D residue  272 ASP
Chi-restraints excluded: chain D residue  306 GLN
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue  206 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 92 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 91 optimal weight:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 88 optimal weight:    0.7980
   chunk 59 optimal weight:    5.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.119261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.093377 restraints weight = 16543.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.17
r_work: 0.3140 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2998 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9243  Z= 0.120
  Angle     :  0.485   7.810  12486  Z= 0.260
  Chirality :  0.041   0.181   1414
  Planarity :  0.003   0.060   1566
  Dihedral  :  4.917  51.949   1261
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.86 %
    Favored  : 89.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.25), residues: 1133
  helix:  2.53 (0.27), residues: 392
  sheet:  1.07 (0.31), residues: 286
  loop : -1.42 (0.26), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 335 
 TYR   0.023   0.001   TYR A  77 
 PHE   0.017   0.001   PHE A 205 
 TRP   0.012   0.001   TRP E 339 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9241)
  covalent geometry    : angle       0.48449 (12482)
  SS BOND              : bond        0.00612 (    2)
  SS BOND              : angle       1.25435 (    4)
  hydrogen bonds       : bond        0.04101 (  417)
  hydrogen bonds       : angle       3.75214 ( 1179)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  105 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.8051 (m-10)
REVERT: D  248 LYS cc_start: 0.8843 (tttt) cc_final: 0.8306 (mmtt)
REVERT: E  258 ASP cc_start: 0.7095 (t0) cc_final: 0.6880 (t0)
REVERT: S  154 SER cc_start: 0.7498 (m) cc_final: 0.7070 (t)
  outliers start: 11
  outliers final: 8
  residues processed: 135
  average time/residue: 0.0974
  time to fit residues: 17.7772
Evaluate side-chains
  131 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 122
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain D residue  262 THR
Chi-restraints excluded: chain D residue  272 ASP
Chi-restraints excluded: chain D residue  306 GLN
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue  206 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   chunk 111 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0670
   chunk 28 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0270
   chunk 26 optimal weight:    0.7980
   chunk 59 optimal weight:    7.9990
   chunk 72 optimal weight:    6.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.120344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.094554 restraints weight = 16568.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 2.18
r_work: 0.3163 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9243  Z= 0.096
  Angle     :  0.461   9.094  12486  Z= 0.246
  Chirality :  0.040   0.197   1414
  Planarity :  0.003   0.043   1566
  Dihedral  :  4.655  50.135   1261
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 11.07 %
    Favored  : 87.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.25), residues: 1133
  helix:  2.61 (0.27), residues: 392
  sheet:  1.08 (0.31), residues: 285
  loop : -1.38 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 335 
 TYR   0.021   0.001   TYR A  77 
 PHE   0.018   0.001   PHE A 205 
 TRP   0.007   0.001   TRP S  47 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 9241)
  covalent geometry    : angle       0.46080 (12482)
  SS BOND              : bond        0.00445 (    2)
  SS BOND              : angle       1.12265 (    4)
  hydrogen bonds       : bond        0.03576 (  417)
  hydrogen bonds       : angle       3.64027 ( 1179)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  105 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.8025 (m-10)
REVERT: A  158 ARG cc_start: 0.3908 (tpm170) cc_final: 0.2805 (ttt180)
REVERT: A  251 ARG cc_start: 0.8821 (tmm-80) cc_final: 0.8556 (tmm-80)
REVERT: D  248 LYS cc_start: 0.8821 (tttt) cc_final: 0.8291 (mmtt)
REVERT: D  275 GLU cc_start: 0.7912 (tp30) cc_final: 0.7674 (tm-30)
REVERT: E  258 ASP cc_start: 0.7073 (t0) cc_final: 0.6861 (t0)
REVERT: S  154 SER cc_start: 0.7478 (m) cc_final: 0.7036 (t)
  outliers start: 12
  outliers final: 9
  residues processed: 128
  average time/residue: 0.0994
  time to fit residues: 17.1619
Evaluate side-chains
  130 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain D residue   28 GLU
Chi-restraints excluded: chain D residue  272 ASP
Chi-restraints excluded: chain D residue  306 GLN
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  327 VAL
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue  139 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 11 optimal weight:    0.3980
   chunk 83 optimal weight:    0.7980
   chunk 64 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 57 optimal weight:    4.9990
   chunk 112 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 119 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.119188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.093234 restraints weight = 16628.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.18
r_work: 0.3139 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9243  Z= 0.108
  Angle     :  0.470   7.762  12486  Z= 0.252
  Chirality :  0.040   0.202   1414
  Planarity :  0.003   0.043   1566
  Dihedral  :  4.664  52.004   1261
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.17 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.25), residues: 1133
  helix:  2.62 (0.27), residues: 392
  sheet:  1.02 (0.30), residues: 286
  loop : -1.41 (0.26), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 335 
 TYR   0.021   0.001   TYR A  77 
 PHE   0.017   0.001   PHE A 205 
 TRP   0.009   0.001   TRP E 339 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 9241)
  covalent geometry    : angle       0.46924 (12482)
  SS BOND              : bond        0.00478 (    2)
  SS BOND              : angle       1.06680 (    4)
  hydrogen bonds       : bond        0.03772 (  417)
  hydrogen bonds       : angle       3.66291 ( 1179)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A  105 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.8041 (m-10)
REVERT: A  158 ARG cc_start: 0.4039 (tpm170) cc_final: 0.3061 (ttt180)
REVERT: A  251 ARG cc_start: 0.8809 (tmm-80) cc_final: 0.8605 (ttp-170)
REVERT: D  248 LYS cc_start: 0.8830 (tttt) cc_final: 0.8326 (mmtt)
REVERT: S   93 MET cc_start: 0.8191 (ttm) cc_final: 0.7974 (ttm)
REVERT: S  154 SER cc_start: 0.7495 (m) cc_final: 0.7053 (t)
  outliers start: 15
  outliers final: 12
  residues processed: 132
  average time/residue: 0.0939
  time to fit residues: 16.8406
Evaluate side-chains
  131 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  114 HIS
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain D residue  272 ASP
Chi-restraints excluded: chain D residue  306 GLN
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  327 VAL
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  206 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0030
   chunk 88 optimal weight:    3.9990
   chunk 21 optimal weight:    0.4980
   chunk 82 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9980
   chunk 58 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.119419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.093526 restraints weight = 16547.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.17
r_work: 0.3144 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9243  Z= 0.103
  Angle     :  0.475   9.090  12486  Z= 0.254
  Chirality :  0.040   0.203   1414
  Planarity :  0.003   0.043   1566
  Dihedral  :  4.699  54.094   1261
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.57 %
    Favored  : 87.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.25), residues: 1133
  helix:  2.67 (0.27), residues: 392
  sheet:  1.02 (0.30), residues: 286
  loop : -1.42 (0.26), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 208 
 TYR   0.019   0.001   TYR A  77 
 PHE   0.018   0.001   PHE A 205 
 TRP   0.008   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 9241)
  covalent geometry    : angle       0.47504 (12482)
  SS BOND              : bond        0.00450 (    2)
  SS BOND              : angle       1.12426 (    4)
  hydrogen bonds       : bond        0.03630 (  417)
  hydrogen bonds       : angle       3.61373 ( 1179)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A  105 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.8004 (m-10)
REVERT: A  158 ARG cc_start: 0.3991 (tpm170) cc_final: 0.3085 (ttt180)
REVERT: D  248 LYS cc_start: 0.8832 (tttt) cc_final: 0.8324 (mmtt)
REVERT: D  275 GLU cc_start: 0.7983 (tp30) cc_final: 0.7755 (tm-30)
REVERT: E   38 ASP cc_start: 0.7886 (t0) cc_final: 0.7642 (t0)
REVERT: S   93 MET cc_start: 0.8185 (ttm) cc_final: 0.7950 (ttm)
REVERT: S  154 SER cc_start: 0.7493 (m) cc_final: 0.7052 (t)
  outliers start: 14
  outliers final: 12
  residues processed: 130
  average time/residue: 0.0923
  time to fit residues: 16.2796
Evaluate side-chains
  131 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  114 HIS
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain D residue  272 ASP
Chi-restraints excluded: chain D residue  306 GLN
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  327 VAL
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   11 LEU
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  206 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 88 optimal weight:    0.0670
   chunk 58 optimal weight:    8.9990
   chunk 90 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 95 optimal weight:    0.0980
   chunk 42 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 111 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.120484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.094732 restraints weight = 16481.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 2.16
r_work: 0.3163 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.2661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9243  Z= 0.093
  Angle     :  0.459   9.149  12486  Z= 0.244
  Chirality :  0.040   0.211   1414
  Planarity :  0.003   0.043   1566
  Dihedral  :  4.684  57.068   1261
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 11.57 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.25), residues: 1133
  helix:  2.69 (0.27), residues: 394
  sheet:  1.07 (0.31), residues: 285
  loop : -1.43 (0.26), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 208 
 TYR   0.020   0.001   TYR A  77 
 PHE   0.017   0.001   PHE A 205 
 TRP   0.008   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 9241)
  covalent geometry    : angle       0.45864 (12482)
  SS BOND              : bond        0.00398 (    2)
  SS BOND              : angle       1.01750 (    4)
  hydrogen bonds       : bond        0.03335 (  417)
  hydrogen bonds       : angle       3.52866 ( 1179)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  105 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.8004 (m-10)
REVERT: A  189 MET cc_start: 0.6780 (tpp) cc_final: 0.6359 (tpt)
REVERT: D  248 LYS cc_start: 0.8823 (tttt) cc_final: 0.8318 (mmtt)
REVERT: E   38 ASP cc_start: 0.7885 (t0) cc_final: 0.7642 (t0)
REVERT: S   93 MET cc_start: 0.8220 (ttm) cc_final: 0.7981 (ttm)
REVERT: S  154 SER cc_start: 0.7463 (m) cc_final: 0.7029 (t)
  outliers start: 16
  outliers final: 14
  residues processed: 125
  average time/residue: 0.0872
  time to fit residues: 15.1547
Evaluate side-chains
  127 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 PHE
Chi-restraints excluded: chain A residue  114 HIS
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain D residue  272 ASP
Chi-restraints excluded: chain D residue  306 GLN
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  218 CYS
Chi-restraints excluded: chain E residue  259 GLN
Chi-restraints excluded: chain E residue  327 VAL
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  206 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.117460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.091551 restraints weight = 16574.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.17
r_work: 0.3107 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9243  Z= 0.132
  Angle     :  0.503   7.188  12486  Z= 0.270
  Chirality :  0.041   0.202   1414
  Planarity :  0.003   0.044   1566
  Dihedral  :  4.913  59.441   1261
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 11.87 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.25), residues: 1133
  helix:  2.58 (0.27), residues: 394
  sheet:  1.01 (0.30), residues: 288
  loop : -1.54 (0.26), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 335 
 TYR   0.020   0.001   TYR A  77 
 PHE   0.020   0.001   PHE A 205 
 TRP   0.009   0.001   TRP E 339 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9241)
  covalent geometry    : angle       0.50250 (12482)
  SS BOND              : bond        0.00572 (    2)
  SS BOND              : angle       1.20824 (    4)
  hydrogen bonds       : bond        0.04163 (  417)
  hydrogen bonds       : angle       3.72635 ( 1179)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.206 
Fit side-chains
REVERT: A  189 MET cc_start: 0.6748 (tpp) cc_final: 0.6343 (tpt)
REVERT: D  248 LYS cc_start: 0.8775 (tttt) cc_final: 0.8245 (mmtt)
REVERT: E   49 ARG cc_start: 0.7582 (mtt-85) cc_final: 0.7253 (mtp85)
REVERT: S   93 MET cc_start: 0.8291 (ttm) cc_final: 0.8033 (ttm)
REVERT: S  154 SER cc_start: 0.7438 (m) cc_final: 0.7003 (t)
  outliers start: 16
  outliers final: 14
  residues processed: 134
  average time/residue: 0.0963
  time to fit residues: 17.3296
Evaluate side-chains
  133 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 HIS
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain D residue  306 GLN
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  218 CYS
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  263 THR
Chi-restraints excluded: chain E residue  327 VAL
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  206 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 103 optimal weight:    0.1980
   chunk 26 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.117666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.091753 restraints weight = 16494.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.16
r_work: 0.3110 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9243  Z= 0.128
  Angle     :  0.523   9.507  12486  Z= 0.278
  Chirality :  0.042   0.258   1414
  Planarity :  0.003   0.052   1566
  Dihedral  :  4.974  56.906   1261
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.47 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.25), residues: 1133
  helix:  2.60 (0.27), residues: 394
  sheet:  1.04 (0.31), residues: 281
  loop : -1.53 (0.26), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 158 
 TYR   0.019   0.001   TYR A  77 
 PHE   0.021   0.001   PHE A 205 
 TRP   0.009   0.001   TRP S  47 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9241)
  covalent geometry    : angle       0.52258 (12482)
  SS BOND              : bond        0.00538 (    2)
  SS BOND              : angle       1.19523 (    4)
  hydrogen bonds       : bond        0.04080 (  417)
  hydrogen bonds       : angle       3.73792 ( 1179)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 MET cc_start: 0.6799 (tpp) cc_final: 0.6433 (tpt)
REVERT: D  248 LYS cc_start: 0.8747 (tttt) cc_final: 0.8213 (mmtt)
REVERT: E   49 ARG cc_start: 0.7555 (mtt-85) cc_final: 0.7225 (mtp85)
REVERT: S   93 MET cc_start: 0.8299 (ttm) cc_final: 0.8043 (ttm)
REVERT: S  154 SER cc_start: 0.7448 (m) cc_final: 0.7009 (t)
  outliers start: 16
  outliers final: 14
  residues processed: 128
  average time/residue: 0.0980
  time to fit residues: 17.0038
Evaluate side-chains
  128 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 HIS
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain D residue  306 GLN
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  218 CYS
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  263 THR
Chi-restraints excluded: chain E residue  327 VAL
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  206 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0170
   chunk 15 optimal weight:    0.0870
   chunk 81 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 96 optimal weight:    0.0970
   chunk 97 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0170
   chunk 98 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.2232

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

Flipped N/Q/H residues before XYZ refinement:
** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.120912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.095305 restraints weight = 16350.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.17
r_work: 0.3173 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9243  Z= 0.095
  Angle     :  0.482   8.367  12486  Z= 0.259
  Chirality :  0.041   0.273   1414
  Planarity :  0.003   0.043   1566
  Dihedral  :  4.817  57.380   1261
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 13.18 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.25), residues: 1133
  helix:  2.73 (0.27), residues: 393
  sheet:  1.12 (0.31), residues: 276
  loop : -1.45 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 158 
 TYR   0.020   0.001   TYR A  77 
 PHE   0.021   0.001   PHE A 205 
 TRP   0.009   0.001   TRP S  47 
 HIS   0.002   0.000   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 ( 9241)
  covalent geometry    : angle       0.48157 (12482)
  SS BOND              : bond        0.00324 (    2)
  SS BOND              : angle       1.01035 (    4)
  hydrogen bonds       : bond        0.03190 (  417)
  hydrogen bonds       : angle       3.56398 ( 1179)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2134.26 seconds
wall clock time: 37 minutes 9.55 seconds (2229.55 seconds total)