Starting phenix.real_space_refine
on Thu Sep 26 11:45:59 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbx_33108/09_2024/7xbx_33108.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbx_33108/09_2024/7xbx_33108.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbx_33108/09_2024/7xbx_33108.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbx_33108/09_2024/7xbx_33108.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbx_33108/09_2024/7xbx_33108.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbx_33108/09_2024/7xbx_33108.cif"
  }
  resolution = 3.4
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 263 atoms to isotropic.
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
     S      45      5.16       5
     C    4260      2.51       5
     N    1080      2.21       5
     O    1231      1.98       5
     H    6028      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 12644
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 3128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 3128
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 2, 'TRANS': 213}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 123
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 109
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 68
    Chain: "D"
      Number of atoms: 4293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 4293
          Classifications: {'peptide': 311}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 305}
          Unresolved non-hydrogen bonds: 143
          Unresolved non-hydrogen angles: 170
          Unresolved non-hydrogen dihedrals: 119
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 13}
          Unresolved non-hydrogen planarities: 112
    Chain: "E"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 414
          Classifications: {'peptide': 33}
          Link IDs: {'PTRANS': 4, 'TRANS': 28}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "R"
      Number of atoms: 4753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 4753
          Classifications: {'peptide': 349}
          Link IDs: {'PTRANS': 10, 'TRANS': 338}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 379
          Unresolved non-hydrogen angles: 471
          Unresolved non-hydrogen dihedrals: 338
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 5, 'PCA:plan-2': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 6, 'TYR:plan': 4, 'PHE:plan': 10, 'GLU:plan': 7, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 241
    Chain: "R"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.69, per 1000 atoms: 0.53
  Number of scatterers: 12644
  At special positions: 0
  Unit cell: (112.86, 131.67, 74.195, 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      45     16.00
     O    1231      8.00
     N    1080      7.00
     C    4260      6.00
     H    6028      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R   8 " - pdb=" SG  CYS R  34 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  12 " - pdb=" SG  CYS R  50 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  35 " - pdb=" SG  CYS R 278 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 204 " - pdb=" SG  CYS R 277 " 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: 3.33
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1722

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 9 sheets defined
      43.9% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'C' and resid 6 through 32
    Processing helix  chain 'C' and resid 45 through 51
    Processing helix  chain 'C' and resid 207 through 213
      removed outlier: 3.830A  pdb=" N   TRP C 211 " --> pdb=" O   GLU C 207 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   HIS C 213 " --> pdb=" O   LYS C 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 214 through 216
      No H-bonds generated for 'chain 'C' and resid 214 through 216'
    Processing helix  chain 'C' and resid 228 through 230
      No H-bonds generated for 'chain 'C' and resid 228 through 230'
    Processing helix  chain 'C' and resid 242 through 255
    Processing helix  chain 'C' and resid 270 through 279
      removed outlier: 3.876A  pdb=" N   GLU C 275 " --> pdb=" O   LYS C 271 " (cutoff:3.500A)
      removed outlier: 4.861A  pdb=" N   GLU C 276 " --> pdb=" O   ASP C 272 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 311
      removed outlier: 3.672A  pdb=" N   ASN C 311 " --> pdb=" O   PHE C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 327 through 348
      removed outlier: 3.959A  pdb=" N   ASN C 331 " --> pdb=" O   THR C 327 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 32 through 36
      removed outlier: 4.307A  pdb=" N   ASN D  36 " --> pdb=" O   ILE D  33 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 30 through 44
    Processing helix  chain 'R' and resid 29 through 34
      removed outlier: 3.846A  pdb=" N   SER R  33 " --> pdb=" O   GLN R  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 56 through 66
      removed outlier: 3.823A  pdb=" N   ASP R  60 " --> pdb=" O   GLN R  56 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   ALA R  61 " --> pdb=" O   TRP R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 127 through 160
      removed outlier: 3.504A  pdb=" N   PHE R 131 " --> pdb=" O   ASP R 127 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE R 138 " --> pdb=" O   VAL R 134 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 196
      Proline residue:  R 187  - end of helix
      removed outlier: 3.516A  pdb=" N   ASN R 195 " --> pdb=" O   HIS R 191 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 202 through 235
    Processing helix  chain 'R' and resid 235 through 243
      removed outlier: 4.148A  pdb=" N   MET R 240 " --> pdb=" O   ALA R 236 " (cutoff:3.500A)
      removed outlier: 5.643A  pdb=" N   ASN R 241 " --> pdb=" O   ALA R 237 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 244 through 269
      Proline residue:  R 265  - end of helix
      removed outlier: 4.490A  pdb=" N   PHE R 269 " --> pdb=" O   PRO R 265 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 282 through 286
      removed outlier: 3.516A  pdb=" N   GLN R 286 " --> pdb=" O   GLU R 283 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 287 through 300
      removed outlier: 3.515A  pdb=" N   VAL R 291 " --> pdb=" O   GLU R 287 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 302 through 323
    Processing helix  chain 'R' and resid 329 through 360
      removed outlier: 3.558A  pdb=" N   ILE R 335 " --> pdb=" O   ALA R 331 " (cutoff:3.500A)
      Proline residue:  R 348  - end of helix
      removed outlier: 3.614A  pdb=" N   LEU R 360 " --> pdb=" O   GLU R 356 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 366 through 399
      removed outlier: 3.671A  pdb=" N   CYS R 389 " --> pdb=" O   PHE R 385 " (cutoff:3.500A)
      Proline residue:  R 392  - end of helix
    Processing helix  chain 'R' and resid 400 through 410
    Processing sheet with id=AA1, first strand: chain 'C' and resid 185 through 191
      removed outlier: 3.574A  pdb=" N   VAL C 185 " --> pdb=" O   ASP C 200 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   MET C 198 " --> pdb=" O   THR C 187 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU C  38 " --> pdb=" O   PHE C 199 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   LEU C  37 " --> pdb=" O   ILE C 222 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   CYS C 224 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   LEU C  39 " --> pdb=" O   CYS C 224 " (cutoff:3.500A)
      removed outlier: 8.291A  pdb=" N   ALA C 226 " --> pdb=" O   LEU C  39 " (cutoff:3.500A)
      removed outlier: 5.746A  pdb=" N   ILE C 221 " --> pdb=" O   ILE C 265 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   PHE C 267 " --> pdb=" O   ILE C 221 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   PHE C 223 " --> pdb=" O   PHE C 267 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   ASN C 269 " --> pdb=" O   PHE C 223 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   VAL C 225 " --> pdb=" O   ASN C 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 47 through 51
      removed outlier: 3.527A  pdb=" N   ARG D  49 " --> pdb=" O   ILE D 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 61 through 63
      removed outlier: 3.583A  pdb=" N   HIS D  62 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   SER D  72 " --> pdb=" O   ILE D  80 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ILE D  80 " --> pdb=" O   SER D  72 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   HIS D  91 " --> pdb=" O   ILE D  81 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ASP D  83 " --> pdb=" O   LYS D  89 " (cutoff:3.500A)
      removed outlier: 5.651A  pdb=" N   LYS D  89 " --> pdb=" O   ASP D  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 103 through 105
      removed outlier: 5.702A  pdb=" N   CYS D 121 " --> pdb=" O   GLU D 138 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   GLU D 138 " --> pdb=" O   CYS D 121 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ILE D 123 " --> pdb=" O   SER D 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 150
      removed outlier: 3.663A  pdb=" N   THR D 178 " --> pdb=" O   LEU D 168 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   ASP D 170 " --> pdb=" O   GLN D 176 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLN D 176 " --> pdb=" O   ASP D 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 187 through 192
      removed outlier: 7.049A  pdb=" N   GLY D 202 " --> pdb=" O   MET D 188 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   LEU D 190 " --> pdb=" O   VAL D 200 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   VAL D 200 " --> pdb=" O   LEU D 190 " (cutoff:3.500A)
      removed outlier: 4.976A  pdb=" N   LEU D 192 " --> pdb=" O   LEU D 198 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   LEU D 198 " --> pdb=" O   LEU D 192 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   PHE D 199 " --> pdb=" O   TRP D 211 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   TRP D 211 " --> pdb=" O   PHE D 199 " (cutoff:3.500A)
      removed outlier: 5.023A  pdb=" N   SER D 201 " --> pdb=" O   LYS D 209 " (cutoff:3.500A)
      removed outlier: 4.701A  pdb=" N   LYS D 209 " --> pdb=" O   SER D 201 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   ALA D 203 " --> pdb=" O   SER D 207 " (cutoff:3.500A)
      removed outlier: 5.683A  pdb=" N   SER D 207 " --> pdb=" O   ALA D 203 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLN D 220 " --> pdb=" O   LEU D 210 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   ASP D 212 " --> pdb=" O   CYS D 218 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   CYS D 218 " --> pdb=" O   ASP D 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 234
      removed outlier: 3.671A  pdb=" N   ALA D 231 " --> pdb=" O   GLY D 244 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   THR D 249 " --> pdb=" O   SER D 245 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   MET D 262 " --> pdb=" O   LEU D 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 273 through 278
      removed outlier: 3.908A  pdb=" N   SER D 275 " --> pdb=" O   GLY D 288 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   ASP D 298 " --> pdb=" O   ARG D 304 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   ARG D 304 " --> pdb=" O   ASP D 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 271 through 272

    347 hydrogen bonds defined for protein.
    1008 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: 4.62

  Time building geometry restraints manager: 3.98 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 6000
        1.04 -     1.23: 180
        1.23 -     1.43: 2662
        1.43 -     1.63: 3884
        1.63 -     1.83: 56
  Bond restraints: 12782
  Sorted by residual:
  bond pdb=" C5  CLR R 501 "
       pdb=" C6  CLR R 501 "
    ideal  model  delta    sigma   weight residual
    1.332  1.463 -0.131 2.00e-02 2.50e+03 4.27e+01
  bond pdb=" C5  CLR R 502 "
       pdb=" C6  CLR R 502 "
    ideal  model  delta    sigma   weight residual
    1.332  1.463 -0.131 2.00e-02 2.50e+03 4.27e+01
  bond pdb=" N   PCA R   1 "
       pdb=" CD  PCA R   1 "
    ideal  model  delta    sigma   weight residual
    1.345  1.465 -0.120 2.00e-02 2.50e+03 3.58e+01
  bond pdb=" C3  CLR R 502 "
       pdb=" O1  CLR R 502 "
    ideal  model  delta    sigma   weight residual
    1.413  1.300  0.113 2.00e-02 2.50e+03 3.18e+01
  bond pdb=" C3  CLR R 501 "
       pdb=" O1  CLR R 501 "
    ideal  model  delta    sigma   weight residual
    1.413  1.300  0.113 2.00e-02 2.50e+03 3.17e+01
  ... (remaining 12777 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     9.14: 22925
        9.14 -    18.28: 1
       18.28 -    27.43: 0
       27.43 -    36.57: 0
       36.57 -    45.71: 1
  Bond angle restraints: 22927
  Sorted by residual:
  angle pdb=" CD  PCA R   1 "
        pdb=" N   PCA R   1 "
        pdb=" H   PCA R   1 "
      ideal   model   delta    sigma   weight residual
     120.30   74.59   45.71 3.00e+00 1.11e-01 2.32e+02
  angle pdb=" CA  PCA R   1 "
        pdb=" N   PCA R   1 "
        pdb=" CD  PCA R   1 "
      ideal   model   delta    sigma   weight residual
     114.17  103.35   10.82 3.00e+00 1.11e-01 1.30e+01
  angle pdb=" N   PCA R   1 "
        pdb=" CD  PCA R   1 "
        pdb=" CG  PCA R   1 "
      ideal   model   delta    sigma   weight residual
     107.23  114.76   -7.53 3.00e+00 1.11e-01 6.30e+00
  angle pdb=" CA  CYS R 277 "
        pdb=" CB  CYS R 277 "
        pdb=" SG  CYS R 277 "
      ideal   model   delta    sigma   weight residual
     114.40  120.10   -5.70 2.30e+00 1.89e-01 6.15e+00
  angle pdb=" CB  ARG R 293 "
        pdb=" CG  ARG R 293 "
        pdb=" CD  ARG R 293 "
      ideal   model   delta    sigma   weight residual
     111.30  116.00   -4.70 2.30e+00 1.89e-01 4.18e+00
  ... (remaining 22922 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.67: 5682
       15.67 -    31.34: 410
       31.34 -    47.01: 122
       47.01 -    62.67: 51
       62.67 -    78.34: 3
  Dihedral angle restraints: 6268
    sinusoidal: 3147
      harmonic: 3121
  Sorted by residual:
  dihedral pdb=" CB  CYS R 204 "
           pdb=" SG  CYS R 204 "
           pdb=" SG  CYS R 277 "
           pdb=" CB  CYS R 277 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -128.07   42.07     1      1.00e+01 1.00e-02 2.47e+01
  dihedral pdb=" CA  CYS R   8 "
           pdb=" CB  CYS R   8 "
           pdb=" SG  CYS R   8 "
           pdb=" SG  CYS R  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00    2.56  -75.56     1      2.00e+01 2.50e-03 1.80e+01
  dihedral pdb=" SG  CYS R 204 "
           pdb=" CB  CYS R 277 "
           pdb=" SG  CYS R 277 "
           pdb=" CA  CYS R 277 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00  -13.85  -59.15     1      2.00e+01 2.50e-03 1.17e+01
  ... (remaining 6265 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 951
       0.047 -    0.094: 137
       0.094 -    0.141: 48
       0.141 -    0.188: 3
       0.188 -    0.235: 2
  Chirality restraints: 1141
  Sorted by residual:
  chirality pdb=" C14 CLR R 501 "
            pdb=" C13 CLR R 501 "
            pdb=" C15 CLR R 501 "
            pdb=" C8  CLR R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.55    0.24 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" C14 CLR R 502 "
            pdb=" C13 CLR R 502 "
            pdb=" C15 CLR R 502 "
            pdb=" C8  CLR R 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.53    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" C3  CLR R 502 "
            pdb=" C2  CLR R 502 "
            pdb=" C4  CLR R 502 "
            pdb=" O1  CLR R 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.46   -2.29   -0.17 2.00e-01 2.50e+01 7.03e-01
  ... (remaining 1138 not shown)

  Planarity restraints: 2035
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   PCA R   1 "    0.289 2.00e-02 2.50e+03   2.69e-01 1.08e+03
        pdb=" CA  PCA R   1 "    0.142 2.00e-02 2.50e+03
        pdb=" CG  PCA R   1 "   -0.174 2.00e-02 2.50e+03
        pdb=" CD  PCA R   1 "    0.105 2.00e-02 2.50e+03
        pdb=" OE  PCA R   1 "    0.152 2.00e-02 2.50e+03
        pdb=" H   PCA R   1 "   -0.514 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 287 "    0.027 5.00e-02 4.00e+02   4.15e-02 2.76e+00
        pdb=" N   PRO C 288 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO C 288 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C 288 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 189 "   -0.004 2.00e-02 2.50e+03   6.77e-03 1.83e+00
        pdb=" CG  TRP R 189 "    0.022 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 189 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 189 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 189 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 189 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 189 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 189 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 189 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 189 "    0.000 2.00e-02 2.50e+03
        pdb=" HD1 TRP R 189 "   -0.004 2.00e-02 2.50e+03
        pdb=" HE1 TRP R 189 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE3 TRP R 189 "    0.000 2.00e-02 2.50e+03
        pdb=" HZ2 TRP R 189 "   -0.000 2.00e-02 2.50e+03
        pdb=" HZ3 TRP R 189 "   -0.000 2.00e-02 2.50e+03
        pdb=" HH2 TRP R 189 "    0.000 2.00e-02 2.50e+03
  ... (remaining 2032 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 648
        2.19 -     2.79: 25019
        2.79 -     3.40: 34276
        3.40 -     4.00: 43591
        4.00 -     4.60: 67214
  Nonbonded interactions: 170748
  Sorted by model distance:
  nonbonded pdb=" O   ASN D 230 "
            pdb="HD21 ASN D 230 "
     model   vdw
     1.588 2.450
  nonbonded pdb=" O   ARG D 314 "
            pdb=" H   TRP D 332 "
     model   vdw
     1.662 2.450
  nonbonded pdb=" O   GLY D  77 "
            pdb=" H   LEU D  95 "
     model   vdw
     1.691 2.450
  nonbonded pdb=" O   PHE R 343 "
            pdb=" HG1 THR R 347 "
     model   vdw
     1.692 2.450
  nonbonded pdb=" O   GLY D 144 "
            pdb=" HG  SER D 161 "
     model   vdw
     1.710 2.450
  ... (remaining 170743 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:             1.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.220
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     29.930
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6092
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   0.131   6754  Z= 0.280
  Angle     :  0.513  10.822   9252  Z= 0.250
  Chirality :  0.040   0.235   1141
  Planarity :  0.002   0.042   1155
  Dihedral  : 12.584  78.343   2283
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.00 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.30), residues: 892
  helix:  2.88 (0.28), residues: 363
  sheet: -0.18 (0.44), residues: 152
  loop : -0.65 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP R 189 
 HIS   0.011   0.001   HIS R   2 
 PHE   0.015   0.001   PHE R 211 
 TYR   0.009   0.001   TYR R 140 
 ARG   0.021   0.001   ARG R 293 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue LYS   54 is missing expected H atoms. Skipping.
Residue LYS  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue TYR  287 is missing expected H atoms. Skipping.
Residue LYS  330 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue MET  217 is missing expected H atoms. Skipping.
Residue MET  262 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue MET  325 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   32 is missing expected H atoms. Skipping.
Residue MET   38 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS    7 is missing expected H atoms. Skipping.
Residue MET   15 is missing expected H atoms. Skipping.
Residue LYS   18 is missing expected H atoms. Skipping.
Residue ILE   19 is missing expected H atoms. Skipping.
Residue LEU   23 is missing expected H atoms. Skipping.
Residue SER   33 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   59 is missing expected H atoms. Skipping.
Residue MET   62 is missing expected H atoms. Skipping.
Residue TYR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  152 is missing expected H atoms. Skipping.
Residue LYS  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue LYS  165 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue TYR  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  203 is missing expected H atoms. Skipping.
Residue LYS  205 is missing expected H atoms. Skipping.
Residue MET  268 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue TYR  281 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue LYS  324 is missing expected H atoms. Skipping.
Residue LYS  327 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue LYS  359 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue TYR  361 is missing expected H atoms. Skipping.
Residue MET  369 is missing expected H atoms. Skipping.
Residue LYS  371 is missing expected H atoms. Skipping.
Residue SER  386 is missing expected H atoms. Skipping.
Residue LEU  390 is missing expected H atoms. Skipping.
Residue LEU  393 is missing expected H atoms. Skipping.
Evaluate side-chains
  170 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 169
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  183 VAL cc_start: 0.7704 (t) cc_final: 0.7324 (p)
REVERT: R  337 LEU cc_start: 0.7992 (mp) cc_final: 0.7780 (mp)
  outliers start: 1
  outliers final: 0
  residues processed: 170
  average time/residue: 0.3051
  time to fit residues: 72.1322
Evaluate side-chains
  131 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 51 optimal weight:    0.4980
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
C 331 ASN
D 230 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6288
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6754  Z= 0.192
  Angle     :  0.495   4.887   9252  Z= 0.268
  Chirality :  0.039   0.168   1141
  Planarity :  0.003   0.037   1155
  Dihedral  :  3.366  20.201   1074
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 10.61 %
    Favored  : 88.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.29), residues: 892
  helix:  2.55 (0.27), residues: 369
  sheet: -0.14 (0.45), residues: 142
  loop : -0.86 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 297 
 HIS   0.009   0.001   HIS C 322 
 PHE   0.017   0.002   PHE C 307 
 TYR   0.011   0.001   TYR D 105 
 ARG   0.003   0.001   ARG R 293 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue LYS   54 is missing expected H atoms. Skipping.
Residue LYS  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue TYR  287 is missing expected H atoms. Skipping.
Residue LYS  330 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue MET  217 is missing expected H atoms. Skipping.
Residue MET  262 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue MET  325 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   32 is missing expected H atoms. Skipping.
Residue MET   38 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS    7 is missing expected H atoms. Skipping.
Residue MET   15 is missing expected H atoms. Skipping.
Residue LYS   18 is missing expected H atoms. Skipping.
Residue ILE   19 is missing expected H atoms. Skipping.
Residue LEU   23 is missing expected H atoms. Skipping.
Residue SER   33 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   59 is missing expected H atoms. Skipping.
Residue MET   62 is missing expected H atoms. Skipping.
Residue TYR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  152 is missing expected H atoms. Skipping.
Residue LYS  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue LYS  165 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue TYR  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  203 is missing expected H atoms. Skipping.
Residue LYS  205 is missing expected H atoms. Skipping.
Residue MET  268 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue TYR  281 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue LYS  324 is missing expected H atoms. Skipping.
Residue LYS  327 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue LYS  359 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue TYR  361 is missing expected H atoms. Skipping.
Residue MET  369 is missing expected H atoms. Skipping.
Residue LYS  371 is missing expected H atoms. Skipping.
Residue SER  386 is missing expected H atoms. Skipping.
Residue LEU  390 is missing expected H atoms. Skipping.
Residue LEU  393 is missing expected H atoms. Skipping.
Evaluate side-chains
  152 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 145
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  105 TYR cc_start: 0.6818 (t80) cc_final: 0.5934 (t80)
REVERT: R  183 VAL cc_start: 0.7651 (t) cc_final: 0.7323 (p)
  outliers start: 7
  outliers final: 4
  residues processed: 150
  average time/residue: 0.3217
  time to fit residues: 68.5828
Evaluate side-chains
  136 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 132
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  283 LEU
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain R residue   13 SER
Chi-restraints excluded: chain R residue  285 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 87 optimal weight:    8.9990
   chunk 72 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 64 optimal weight:    7.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
D 230 ASN
R 350 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6362
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6754  Z= 0.175
  Angle     :  0.462   5.293   9252  Z= 0.251
  Chirality :  0.037   0.158   1141
  Planarity :  0.003   0.038   1155
  Dihedral  :  3.293  22.500   1074
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 13.42 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.29), residues: 892
  helix:  2.64 (0.27), residues: 368
  sheet: -0.70 (0.45), residues: 132
  loop : -0.91 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 297 
 HIS   0.007   0.001   HIS C 322 
 PHE   0.014   0.001   PHE C 196 
 TYR   0.010   0.001   TYR R 313 
 ARG   0.003   0.000   ARG R 293 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue LYS   54 is missing expected H atoms. Skipping.
Residue LYS  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue TYR  287 is missing expected H atoms. Skipping.
Residue LYS  330 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue MET  217 is missing expected H atoms. Skipping.
Residue MET  262 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue MET  325 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   32 is missing expected H atoms. Skipping.
Residue MET   38 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS    7 is missing expected H atoms. Skipping.
Residue MET   15 is missing expected H atoms. Skipping.
Residue LYS   18 is missing expected H atoms. Skipping.
Residue ILE   19 is missing expected H atoms. Skipping.
Residue LEU   23 is missing expected H atoms. Skipping.
Residue SER   33 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   59 is missing expected H atoms. Skipping.
Residue MET   62 is missing expected H atoms. Skipping.
Residue TYR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  152 is missing expected H atoms. Skipping.
Residue LYS  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue LYS  165 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue TYR  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  203 is missing expected H atoms. Skipping.
Residue LYS  205 is missing expected H atoms. Skipping.
Residue MET  268 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue TYR  281 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue LYS  324 is missing expected H atoms. Skipping.
Residue LYS  327 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue LYS  359 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue TYR  361 is missing expected H atoms. Skipping.
Residue MET  369 is missing expected H atoms. Skipping.
Residue LYS  371 is missing expected H atoms. Skipping.
Residue SER  386 is missing expected H atoms. Skipping.
Residue LEU  390 is missing expected H atoms. Skipping.
Residue LEU  393 is missing expected H atoms. Skipping.
Evaluate side-chains
  148 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 138
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  105 TYR cc_start: 0.6955 (t80) cc_final: 0.5877 (t80)
REVERT: D  196 THR cc_start: 0.6357 (p) cc_final: 0.6129 (p)
REVERT: D  211 TRP cc_start: 0.5965 (m-10) cc_final: 0.5761 (m-10)
  outliers start: 10
  outliers final: 6
  residues processed: 145
  average time/residue: 0.3013
  time to fit residues: 62.3946
Evaluate side-chains
  132 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 126
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain D residue   88 ASN
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue  238 ASN
Chi-restraints excluded: chain R residue  295 VAL
Chi-restraints excluded: chain R residue  316 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 81 optimal weight:    7.9990
   chunk 86 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
C 204 GLN
C 244 HIS
D 230 ASN
** R   2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 325 ASN
R 350 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6538
moved from start:          0.3519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6754  Z= 0.288
  Angle     :  0.526   4.365   9252  Z= 0.292
  Chirality :  0.039   0.151   1141
  Planarity :  0.004   0.041   1155
  Dihedral  :  4.037  27.473   1074
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.60 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.29), residues: 892
  helix:  2.17 (0.27), residues: 376
  sheet: -1.14 (0.44), residues: 144
  loop : -1.26 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D  99 
 HIS   0.006   0.001   HIS D  54 
 PHE   0.015   0.002   PHE C 196 
 TYR   0.016   0.002   TYR D 105 
 ARG   0.003   0.000   ARG D 304 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue LYS   54 is missing expected H atoms. Skipping.
Residue LYS  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue TYR  287 is missing expected H atoms. Skipping.
Residue LYS  330 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue MET  217 is missing expected H atoms. Skipping.
Residue MET  262 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue MET  325 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   32 is missing expected H atoms. Skipping.
Residue MET   38 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS    7 is missing expected H atoms. Skipping.
Residue MET   15 is missing expected H atoms. Skipping.
Residue LYS   18 is missing expected H atoms. Skipping.
Residue ILE   19 is missing expected H atoms. Skipping.
Residue LEU   23 is missing expected H atoms. Skipping.
Residue SER   33 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   59 is missing expected H atoms. Skipping.
Residue MET   62 is missing expected H atoms. Skipping.
Residue TYR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  152 is missing expected H atoms. Skipping.
Residue LYS  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue LYS  165 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue TYR  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  203 is missing expected H atoms. Skipping.
Residue LYS  205 is missing expected H atoms. Skipping.
Residue MET  268 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue TYR  281 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue LYS  324 is missing expected H atoms. Skipping.
Residue LYS  327 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue LYS  359 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue TYR  361 is missing expected H atoms. Skipping.
Residue MET  369 is missing expected H atoms. Skipping.
Residue LYS  371 is missing expected H atoms. Skipping.
Residue SER  386 is missing expected H atoms. Skipping.
Residue LEU  390 is missing expected H atoms. Skipping.
Residue LEU  393 is missing expected H atoms. Skipping.
Evaluate side-chains
  165 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 146
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  297 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7972 (mp0)
REVERT: D  196 THR cc_start: 0.6528 (p) cc_final: 0.6273 (p)
  outliers start: 19
  outliers final: 13
  residues processed: 158
  average time/residue: 0.3108
  time to fit residues: 69.8421
Evaluate side-chains
  149 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain D residue   88 ASN
Chi-restraints excluded: chain D residue  230 ASN
Chi-restraints excluded: chain R residue   13 SER
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue  173 LEU
Chi-restraints excluded: chain R residue  238 ASN
Chi-restraints excluded: chain R residue  295 VAL
Chi-restraints excluded: chain R residue  316 ILE
Chi-restraints excluded: chain R residue  357 THR
Chi-restraints excluded: chain R residue  367 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 64 optimal weight:   10.0000
   chunk 35 optimal weight:    0.0870
   chunk 73 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 43 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0980
   chunk 21 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    1.5962

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

Flipped N/Q/H residues before XYZ refinement:
D 230 ASN
D 295 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6564
moved from start:          0.3898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6754  Z= 0.274
  Angle     :  0.503   4.354   9252  Z= 0.278
  Chirality :  0.038   0.141   1141
  Planarity :  0.003   0.041   1155
  Dihedral  :  4.393  54.333   1074
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.32 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.29), residues: 892
  helix:  2.17 (0.27), residues: 376
  sheet: -1.27 (0.41), residues: 155
  loop : -1.30 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D  99 
 HIS   0.005   0.001   HIS D  54 
 PHE   0.012   0.002   PHE C 189 
 TYR   0.011   0.001   TYR R 313 
 ARG   0.003   0.000   ARG D 314 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue LYS   54 is missing expected H atoms. Skipping.
Residue LYS  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue TYR  287 is missing expected H atoms. Skipping.
Residue LYS  330 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue MET  217 is missing expected H atoms. Skipping.
Residue MET  262 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue MET  325 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   32 is missing expected H atoms. Skipping.
Residue MET   38 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS    7 is missing expected H atoms. Skipping.
Residue MET   15 is missing expected H atoms. Skipping.
Residue LYS   18 is missing expected H atoms. Skipping.
Residue ILE   19 is missing expected H atoms. Skipping.
Residue LEU   23 is missing expected H atoms. Skipping.
Residue SER   33 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   59 is missing expected H atoms. Skipping.
Residue MET   62 is missing expected H atoms. Skipping.
Residue TYR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  152 is missing expected H atoms. Skipping.
Residue LYS  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue LYS  165 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue TYR  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  203 is missing expected H atoms. Skipping.
Residue LYS  205 is missing expected H atoms. Skipping.
Residue MET  268 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue TYR  281 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue LYS  324 is missing expected H atoms. Skipping.
Residue LYS  327 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue LYS  359 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue TYR  361 is missing expected H atoms. Skipping.
Residue MET  369 is missing expected H atoms. Skipping.
Residue LYS  371 is missing expected H atoms. Skipping.
Residue SER  386 is missing expected H atoms. Skipping.
Residue LEU  390 is missing expected H atoms. Skipping.
Residue LEU  393 is missing expected H atoms. Skipping.
Evaluate side-chains
  159 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  297 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8039 (mp0)
REVERT: D  105 TYR cc_start: 0.7648 (t80) cc_final: 0.6585 (t80)
REVERT: D  196 THR cc_start: 0.6582 (p) cc_final: 0.6307 (p)
  outliers start: 20
  outliers final: 16
  residues processed: 152
  average time/residue: 0.2994
  time to fit residues: 63.9849
Evaluate side-chains
  149 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  306 GLN
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain D residue   88 ASN
Chi-restraints excluded: chain D residue  298 ASP
Chi-restraints excluded: chain R residue   13 SER
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue  173 LEU
Chi-restraints excluded: chain R residue  238 ASN
Chi-restraints excluded: chain R residue  295 VAL
Chi-restraints excluded: chain R residue  316 ILE
Chi-restraints excluded: chain R residue  357 THR
Chi-restraints excluded: chain R residue  367 CYS
Chi-restraints excluded: chain R residue  378 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 86 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
D 230 ASN
D 259 GLN
R 350 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6597
moved from start:          0.4373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6754  Z= 0.269
  Angle     :  0.502   4.269   9252  Z= 0.277
  Chirality :  0.038   0.141   1141
  Planarity :  0.003   0.041   1155
  Dihedral  :  4.234  31.545   1074
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 19.03 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.29), residues: 892
  helix:  2.09 (0.27), residues: 376
  sheet: -1.38 (0.40), residues: 160
  loop : -1.36 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  99 
 HIS   0.005   0.001   HIS C 322 
 PHE   0.011   0.001   PHE C 196 
 TYR   0.010   0.002   TYR D 105 
 ARG   0.002   0.000   ARG C 313 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue LYS   54 is missing expected H atoms. Skipping.
Residue LYS  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue TYR  287 is missing expected H atoms. Skipping.
Residue LYS  330 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue MET  217 is missing expected H atoms. Skipping.
Residue MET  262 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue MET  325 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   32 is missing expected H atoms. Skipping.
Residue MET   38 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS    7 is missing expected H atoms. Skipping.
Residue MET   15 is missing expected H atoms. Skipping.
Residue LYS   18 is missing expected H atoms. Skipping.
Residue ILE   19 is missing expected H atoms. Skipping.
Residue LEU   23 is missing expected H atoms. Skipping.
Residue SER   33 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   59 is missing expected H atoms. Skipping.
Residue MET   62 is missing expected H atoms. Skipping.
Residue TYR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  152 is missing expected H atoms. Skipping.
Residue LYS  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue LYS  165 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue TYR  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  203 is missing expected H atoms. Skipping.
Residue LYS  205 is missing expected H atoms. Skipping.
Residue MET  268 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue TYR  281 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue LYS  324 is missing expected H atoms. Skipping.
Residue LYS  327 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue LYS  359 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue TYR  361 is missing expected H atoms. Skipping.
Residue MET  369 is missing expected H atoms. Skipping.
Residue LYS  371 is missing expected H atoms. Skipping.
Residue SER  386 is missing expected H atoms. Skipping.
Residue LEU  390 is missing expected H atoms. Skipping.
Residue LEU  393 is missing expected H atoms. Skipping.
Evaluate side-chains
  166 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   33 GLU cc_start: 0.7460 (tt0) cc_final: 0.7236 (tt0)
REVERT: D  196 THR cc_start: 0.6644 (p) cc_final: 0.6373 (p)
REVERT: D  211 TRP cc_start: 0.6347 (m-10) cc_final: 0.6082 (m-10)
  outliers start: 22
  outliers final: 21
  residues processed: 158
  average time/residue: 0.2894
  time to fit residues: 66.0269
Evaluate side-chains
  155 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  247 MET
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  306 GLN
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain D residue   88 ASN
Chi-restraints excluded: chain D residue  230 ASN
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  233 CYS
Chi-restraints excluded: chain D residue  298 ASP
Chi-restraints excluded: chain R residue   13 SER
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  173 LEU
Chi-restraints excluded: chain R residue  212 PHE
Chi-restraints excluded: chain R residue  238 ASN
Chi-restraints excluded: chain R residue  295 VAL
Chi-restraints excluded: chain R residue  316 ILE
Chi-restraints excluded: chain R residue  357 THR
Chi-restraints excluded: chain R residue  367 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 62 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 85 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
D 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6620
moved from start:          0.4642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6754  Z= 0.288
  Angle     :  0.518   4.459   9252  Z= 0.287
  Chirality :  0.039   0.142   1141
  Planarity :  0.004   0.049   1155
  Dihedral  :  4.256  33.053   1074
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 20.28 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.28), residues: 892
  helix:  1.98 (0.27), residues: 382
  sheet: -1.58 (0.40), residues: 155
  loop : -1.41 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D  63 
 HIS   0.005   0.001   HIS C 322 
 PHE   0.011   0.001   PHE C 196 
 TYR   0.010   0.002   TYR R 395 
 ARG   0.008   0.000   ARG D 314 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue LYS   54 is missing expected H atoms. Skipping.
Residue LYS  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue TYR  287 is missing expected H atoms. Skipping.
Residue LYS  330 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue MET  217 is missing expected H atoms. Skipping.
Residue MET  262 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue MET  325 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   32 is missing expected H atoms. Skipping.
Residue MET   38 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS    7 is missing expected H atoms. Skipping.
Residue MET   15 is missing expected H atoms. Skipping.
Residue LYS   18 is missing expected H atoms. Skipping.
Residue ILE   19 is missing expected H atoms. Skipping.
Residue LEU   23 is missing expected H atoms. Skipping.
Residue SER   33 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   59 is missing expected H atoms. Skipping.
Residue MET   62 is missing expected H atoms. Skipping.
Residue TYR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  152 is missing expected H atoms. Skipping.
Residue LYS  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue LYS  165 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue TYR  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  203 is missing expected H atoms. Skipping.
Residue LYS  205 is missing expected H atoms. Skipping.
Residue MET  268 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue TYR  281 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue LYS  324 is missing expected H atoms. Skipping.
Residue LYS  327 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue LYS  359 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue TYR  361 is missing expected H atoms. Skipping.
Residue MET  369 is missing expected H atoms. Skipping.
Residue LYS  371 is missing expected H atoms. Skipping.
Residue SER  386 is missing expected H atoms. Skipping.
Residue LEU  390 is missing expected H atoms. Skipping.
Residue LEU  393 is missing expected H atoms. Skipping.
Evaluate side-chains
  162 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  345 LYS cc_start: 0.7540 (mtmt) cc_final: 0.7303 (mtpp)
REVERT: D  196 THR cc_start: 0.6695 (p) cc_final: 0.6400 (p)
  outliers start: 21
  outliers final: 19
  residues processed: 155
  average time/residue: 0.2762
  time to fit residues: 61.6073
Evaluate side-chains
  154 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  247 MET
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  306 GLN
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain D residue   88 ASN
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  233 CYS
Chi-restraints excluded: chain D residue  298 ASP
Chi-restraints excluded: chain R residue   13 SER
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue  173 LEU
Chi-restraints excluded: chain R residue  212 PHE
Chi-restraints excluded: chain R residue  238 ASN
Chi-restraints excluded: chain R residue  295 VAL
Chi-restraints excluded: chain R residue  316 ILE
Chi-restraints excluded: chain R residue  357 THR
Chi-restraints excluded: chain R residue  367 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0770
   chunk 58 optimal weight:    0.1980
   chunk 42 optimal weight:    0.9990
   chunk 7 optimal weight:    0.4980
   chunk 67 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 79 optimal weight:    0.4980
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6537
moved from start:          0.4596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6754  Z= 0.157
  Angle     :  0.473   4.156   9252  Z= 0.257
  Chirality :  0.038   0.145   1141
  Planarity :  0.003   0.041   1155
  Dihedral  :  3.756  27.474   1074
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 20.90 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.29), residues: 892
  helix:  2.34 (0.27), residues: 381
  sheet: -1.55 (0.41), residues: 143
  loop : -1.27 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  63 
 HIS   0.005   0.001   HIS C 322 
 PHE   0.011   0.001   PHE R 212 
 TYR   0.013   0.001   TYR R 349 
 ARG   0.005   0.000   ARG D 314 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue LYS   54 is missing expected H atoms. Skipping.
Residue LYS  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue TYR  287 is missing expected H atoms. Skipping.
Residue LYS  330 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue MET  217 is missing expected H atoms. Skipping.
Residue MET  262 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue MET  325 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   32 is missing expected H atoms. Skipping.
Residue MET   38 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS    7 is missing expected H atoms. Skipping.
Residue MET   15 is missing expected H atoms. Skipping.
Residue LYS   18 is missing expected H atoms. Skipping.
Residue ILE   19 is missing expected H atoms. Skipping.
Residue LEU   23 is missing expected H atoms. Skipping.
Residue SER   33 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   59 is missing expected H atoms. Skipping.
Residue MET   62 is missing expected H atoms. Skipping.
Residue TYR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  152 is missing expected H atoms. Skipping.
Residue LYS  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue LYS  165 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue TYR  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  203 is missing expected H atoms. Skipping.
Residue LYS  205 is missing expected H atoms. Skipping.
Residue MET  268 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue TYR  281 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue LYS  324 is missing expected H atoms. Skipping.
Residue LYS  327 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue LYS  359 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue TYR  361 is missing expected H atoms. Skipping.
Residue MET  369 is missing expected H atoms. Skipping.
Residue LYS  371 is missing expected H atoms. Skipping.
Residue SER  386 is missing expected H atoms. Skipping.
Residue LEU  390 is missing expected H atoms. Skipping.
Residue LEU  393 is missing expected H atoms. Skipping.
Evaluate side-chains
  160 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  105 TYR cc_start: 0.7623 (t80) cc_final: 0.6823 (t80)
REVERT: D  196 THR cc_start: 0.6409 (p) cc_final: 0.6101 (p)
  outliers start: 17
  outliers final: 15
  residues processed: 155
  average time/residue: 0.2682
  time to fit residues: 60.6724
Evaluate side-chains
  150 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 GLU
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  247 MET
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  283 LEU
Chi-restraints excluded: chain C residue  306 GLN
Chi-restraints excluded: chain D residue   88 ASN
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  233 CYS
Chi-restraints excluded: chain R residue   13 SER
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue  173 LEU
Chi-restraints excluded: chain R residue  212 PHE
Chi-restraints excluded: chain R residue  295 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 62 optimal weight:    9.9990
   chunk 24 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 79 optimal weight:    0.5980
   chunk 52 optimal weight:    3.9990
   chunk 84 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0980
   chunk 40 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6595
moved from start:          0.4811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6754  Z= 0.226
  Angle     :  0.498   4.280   9252  Z= 0.274
  Chirality :  0.038   0.151   1141
  Planarity :  0.004   0.060   1155
  Dihedral  :  3.951  29.049   1074
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 21.22 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.29), residues: 892
  helix:  2.40 (0.27), residues: 374
  sheet: -1.64 (0.38), residues: 160
  loop : -1.17 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP D  63 
 HIS   0.005   0.001   HIS C 322 
 PHE   0.011   0.001   PHE R 342 
 TYR   0.011   0.001   TYR R 395 
 ARG   0.006   0.000   ARG D 304 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue LYS   54 is missing expected H atoms. Skipping.
Residue LYS  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue TYR  287 is missing expected H atoms. Skipping.
Residue LYS  330 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue MET  217 is missing expected H atoms. Skipping.
Residue MET  262 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue MET  325 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   32 is missing expected H atoms. Skipping.
Residue MET   38 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS    7 is missing expected H atoms. Skipping.
Residue MET   15 is missing expected H atoms. Skipping.
Residue LYS   18 is missing expected H atoms. Skipping.
Residue ILE   19 is missing expected H atoms. Skipping.
Residue LEU   23 is missing expected H atoms. Skipping.
Residue SER   33 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   59 is missing expected H atoms. Skipping.
Residue MET   62 is missing expected H atoms. Skipping.
Residue TYR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  152 is missing expected H atoms. Skipping.
Residue LYS  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue LYS  165 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue TYR  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  203 is missing expected H atoms. Skipping.
Residue LYS  205 is missing expected H atoms. Skipping.
Residue MET  268 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue TYR  281 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue LYS  324 is missing expected H atoms. Skipping.
Residue LYS  327 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue LYS  359 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue TYR  361 is missing expected H atoms. Skipping.
Residue MET  369 is missing expected H atoms. Skipping.
Residue LYS  371 is missing expected H atoms. Skipping.
Residue SER  386 is missing expected H atoms. Skipping.
Residue LEU  390 is missing expected H atoms. Skipping.
Residue LEU  393 is missing expected H atoms. Skipping.
Evaluate side-chains
  155 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  196 THR cc_start: 0.6542 (p) cc_final: 0.6261 (p)
  outliers start: 19
  outliers final: 18
  residues processed: 149
  average time/residue: 0.2628
  time to fit residues: 57.4763
Evaluate side-chains
  153 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  247 MET
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  283 LEU
Chi-restraints excluded: chain C residue  294 ASN
Chi-restraints excluded: chain C residue  306 GLN
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   88 ASN
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  233 CYS
Chi-restraints excluded: chain D residue  298 ASP
Chi-restraints excluded: chain R residue   13 SER
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue  173 LEU
Chi-restraints excluded: chain R residue  212 PHE
Chi-restraints excluded: chain R residue  295 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 70 optimal weight:    0.3980
   chunk 7 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 75 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 65 optimal weight:    0.1980
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6552
moved from start:          0.4795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6754  Z= 0.164
  Angle     :  0.479   4.139   9252  Z= 0.260
  Chirality :  0.038   0.153   1141
  Planarity :  0.004   0.041   1155
  Dihedral  :  3.737  26.075   1074
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 21.22 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.30), residues: 892
  helix:  2.50 (0.27), residues: 374
  sheet: -1.57 (0.41), residues: 143
  loop : -1.12 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D  63 
 HIS   0.005   0.001   HIS C 322 
 PHE   0.010   0.001   PHE R 212 
 TYR   0.012   0.001   TYR R 395 
 ARG   0.005   0.001   ARG D 304 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue LYS   54 is missing expected H atoms. Skipping.
Residue LYS  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue SER  206 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue TYR  287 is missing expected H atoms. Skipping.
Residue LYS  330 is missing expected H atoms. Skipping.
Residue LYS  127 is missing expected H atoms. Skipping.
Residue MET  217 is missing expected H atoms. Skipping.
Residue MET  262 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue LYS  301 is missing expected H atoms. Skipping.
Residue MET  325 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Residue LYS   32 is missing expected H atoms. Skipping.
Residue MET   38 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue LYS    7 is missing expected H atoms. Skipping.
Residue MET   15 is missing expected H atoms. Skipping.
Residue LYS   18 is missing expected H atoms. Skipping.
Residue ILE   19 is missing expected H atoms. Skipping.
Residue LEU   23 is missing expected H atoms. Skipping.
Residue SER   33 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   59 is missing expected H atoms. Skipping.
Residue MET   62 is missing expected H atoms. Skipping.
Residue TYR  124 is missing expected H atoms. Skipping.
Residue ILE  125 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue LEU  148 is missing expected H atoms. Skipping.
Residue LEU  152 is missing expected H atoms. Skipping.
Residue LYS  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue LYS  165 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue TYR  192 is missing expected H atoms. Skipping.
Residue LYS  197 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  203 is missing expected H atoms. Skipping.
Residue LYS  205 is missing expected H atoms. Skipping.
Residue MET  268 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue TYR  281 is missing expected H atoms. Skipping.
Residue ILE  288 is missing expected H atoms. Skipping.
Residue LYS  324 is missing expected H atoms. Skipping.
Residue LYS  327 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue LYS  359 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue TYR  361 is missing expected H atoms. Skipping.
Residue MET  369 is missing expected H atoms. Skipping.
Residue LYS  371 is missing expected H atoms. Skipping.
Residue SER  386 is missing expected H atoms. Skipping.
Residue LEU  390 is missing expected H atoms. Skipping.
Residue LEU  393 is missing expected H atoms. Skipping.
Evaluate side-chains
  155 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 138
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   33 GLU cc_start: 0.7413 (tt0) cc_final: 0.7189 (tt0)
REVERT: D  196 THR cc_start: 0.6485 (p) cc_final: 0.6182 (p)
  outliers start: 17
  outliers final: 16
  residues processed: 150
  average time/residue: 0.2778
  time to fit residues: 61.3165
Evaluate side-chains
  153 residues out of total 789 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 GLU
Chi-restraints excluded: chain C residue  247 MET
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  283 LEU
Chi-restraints excluded: chain C residue  294 ASN
Chi-restraints excluded: chain C residue  306 GLN
Chi-restraints excluded: chain D residue   88 ASN
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  233 CYS
Chi-restraints excluded: chain D residue  298 ASP
Chi-restraints excluded: chain R residue   13 SER
Chi-restraints excluded: chain R residue   50 CYS
Chi-restraints excluded: chain R residue  173 LEU
Chi-restraints excluded: chain R residue  212 PHE
Chi-restraints excluded: chain R residue  295 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 29 optimal weight:    0.4980
   chunk 72 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0870
   chunk 51 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.170204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.133029 restraints weight = 25264.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 3.05
r_work: 0.3794 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6661
moved from start:          0.4812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6754  Z= 0.156
  Angle     :  0.470   4.163   9252  Z= 0.255
  Chirality :  0.037   0.154   1141
  Planarity :  0.004   0.042   1155
  Dihedral  :  3.607  23.534   1074
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 21.06 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.30), residues: 892
  helix:  2.56 (0.27), residues: 374
  sheet: -1.51 (0.40), residues: 151
  loop : -1.06 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP D  63 
 HIS   0.005   0.001   HIS C 322 
 PHE   0.009   0.001   PHE R 212 
 TYR   0.010   0.001   TYR R 395 
 ARG   0.005   0.000   ARG D 304 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3586.14 seconds
wall clock time: 63 minutes 5.31 seconds (3785.31 seconds total)