Starting phenix.real_space_refine (version: 1.21rc1)
on Fri Apr 21 07:57:56 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq3_32698/04_2023/7wq3_32698_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq3_32698/04_2023/7wq3_32698.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq3_32698/04_2023/7wq3_32698.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq3_32698/04_2023/7wq3_32698.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq3_32698/04_2023/7wq3_32698_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq3_32698/04_2023/7wq3_32698_updated.pdb"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      61      5.16       5
     C    5915      2.51       5
     N    1548      2.21       5
     O    1685      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 9209
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 2303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2303
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 13, 'TRANS': 275}
    Chain: "A"
      Number of atoms: 1811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1811
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "S"
      Number of atoms: 1787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1787
          Classifications: {'peptide': 233}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 117
          Classifications: {'peptide': 16}
          Link IDs: {'PTRANS': 1, 'TRANS': 14}
    Chain: "R"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 140
          Unusual residues: {'CLR': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 5.13, per 1000 atoms: 0.56
  Number of scatterers: 9209
  At special positions: 0
  Unit cell: (110.16, 125.46, 123.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      61     16.00
     O    1685      8.00
     N    1548      7.00
     C    5915      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 108 " - pdb=" SG  CYS R 187 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 3.37
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2172

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      31 helices and 13 sheets defined
      35.0% alpha, 22.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'R' and resid 33 through 60
      removed outlier: 4.618A  pdb=" N   VAL R  38 " --> pdb=" O   PHE R  34 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 69 through 97
      removed outlier: 3.754A  pdb=" N   ILE R  89 " --> pdb=" O   LEU R  85 " (cutoff:3.500A)
      Proline residue:  R  90  - end of helix
      removed outlier: 4.257A  pdb=" N   THR R  94 " --> pdb=" O   PRO R  90 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL R  95 " --> pdb=" O   PHE R  91 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   TYR R  96 " --> pdb=" O   GLN R  92 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 104 through 135
      removed outlier: 4.149A  pdb=" N   HIS R 112 " --> pdb=" O   CYS R 108 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   TYR R 113 " --> pdb=" O   LYS R 109 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   THR R 116 " --> pdb=" O   HIS R 112 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 143 through 146
      No H-bonds generated for 'chain 'R' and resid 143 through 146'
    Processing helix  chain 'R' and resid 149 through 166
    Processing helix  chain 'R' and resid 168 through 173
    Processing helix  chain 'R' and resid 194 through 208
      removed outlier: 3.715A  pdb=" N   ALA R 199 " --> pdb=" O   ARG R 195 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 210 through 230
    Processing helix  chain 'R' and resid 236 through 259
    Processing helix  chain 'R' and resid 261 through 271
    Processing helix  chain 'R' and resid 279 through 302
      removed outlier: 3.780A  pdb=" N   SER R 296 " --> pdb=" O   ALA R 292 " (cutoff:3.500A)
      Proline residue:  R 300  - end of helix
    Processing helix  chain 'R' and resid 308 through 317
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 4.215A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 52
    Processing helix  chain 'A' and resid 208 through 210
      No H-bonds generated for 'chain 'A' and resid 208 through 210'
    Processing helix  chain 'A' and resid 212 through 215
    Processing helix  chain 'A' and resid 227 through 231
      removed outlier: 4.166A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 254
    Processing helix  chain 'A' and resid 271 through 277
      removed outlier: 4.360A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 285
      No H-bonds generated for 'chain 'A' and resid 283 through 285'
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 3.884A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 350
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.627A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 36
      removed outlier: 3.942A  pdb=" N   ASN B  35 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   ASN B  36 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 30 through 43
      removed outlier: 3.605A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 29 through 31
      No H-bonds generated for 'chain 'S' and resid 29 through 31'
    Processing helix  chain 'S' and resid 53 through 55
      No H-bonds generated for 'chain 'S' and resid 53 through 55'
    Processing helix  chain 'S' and resid 88 through 90
      No H-bonds generated for 'chain 'S' and resid 88 through 90'
    Processing helix  chain 'S' and resid 221 through 223
      No H-bonds generated for 'chain 'S' and resid 221 through 223'
    Processing helix  chain 'L' and resid 4 through 11
    Processing sheet with id=  A, first strand: chain 'R' and resid 175 through 178
    Processing sheet with id=  B, first strand: chain 'A' and resid 319 through 323
      removed outlier: 6.591A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.033A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.010A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.864A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.431A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.177A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.902A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.939A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.620A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.575A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   TYR B 289 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.973A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=  K, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.864A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.111A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   ALA S  40 " --> pdb=" O   LEU S  45 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   LEU S  45 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'S' and resid 146 through 148
      removed outlier: 7.287A  pdb=" N   LYS S 244 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.058A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'S' and resid 155 through 160

    418 hydrogen bonds defined for protein.
    1200 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.48

  Time building geometry restraints manager: 3.68 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2915
        1.34 -     1.46: 2281
        1.46 -     1.58: 4113
        1.58 -     1.70: 25
        1.70 -     1.81: 91
  Bond restraints: 9425
  Sorted by residual:
  bond pdb=" C5  CLR R 401 "
       pdb=" C6  CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.652 -0.320 2.00e-02 2.50e+03 2.56e+02
  bond pdb=" C5  CLR R 402 "
       pdb=" C6  CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.332  1.651 -0.319 2.00e-02 2.50e+03 2.54e+02
  bond pdb=" C5  CLR R 405 "
       pdb=" C6  CLR R 405 "
    ideal  model  delta    sigma   weight residual
    1.332  1.651 -0.319 2.00e-02 2.50e+03 2.54e+02
  bond pdb=" C5  CLR R 403 "
       pdb=" C6  CLR R 403 "
    ideal  model  delta    sigma   weight residual
    1.332  1.651 -0.319 2.00e-02 2.50e+03 2.54e+02
  bond pdb=" C5  CLR R 404 "
       pdb=" C6  CLR R 404 "
    ideal  model  delta    sigma   weight residual
    1.332  1.650 -0.318 2.00e-02 2.50e+03 2.53e+02
  ... (remaining 9420 not shown)

  Histogram of bond angle deviations from ideal:
      100.60 -   107.28: 313
      107.28 -   113.96: 5396
      113.96 -   120.63: 3710
      120.63 -   127.31: 3275
      127.31 -   133.99: 103
  Bond angle restraints: 12797
  Sorted by residual:
  angle pdb=" C5  CLR R 405 "
        pdb=" C6  CLR R 405 "
        pdb=" C7  CLR R 405 "
      ideal   model   delta    sigma   weight residual
     125.11  111.81   13.30 3.00e+00 1.11e-01 1.97e+01
  angle pdb=" C5  CLR R 403 "
        pdb=" C6  CLR R 403 "
        pdb=" C7  CLR R 403 "
      ideal   model   delta    sigma   weight residual
     125.11  111.81   13.30 3.00e+00 1.11e-01 1.97e+01
  angle pdb=" C5  CLR R 402 "
        pdb=" C6  CLR R 402 "
        pdb=" C7  CLR R 402 "
      ideal   model   delta    sigma   weight residual
     125.11  111.81   13.30 3.00e+00 1.11e-01 1.96e+01
  angle pdb=" C5  CLR R 404 "
        pdb=" C6  CLR R 404 "
        pdb=" C7  CLR R 404 "
      ideal   model   delta    sigma   weight residual
     125.11  111.82   13.29 3.00e+00 1.11e-01 1.96e+01
  angle pdb=" C4  CLR R 401 "
        pdb=" C5  CLR R 401 "
        pdb=" C6  CLR R 401 "
      ideal   model   delta    sigma   weight residual
     120.33  107.93   12.40 3.00e+00 1.11e-01 1.71e+01
  ... (remaining 12792 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.56: 5341
       15.56 -    31.12: 150
       31.12 -    46.68: 23
       46.68 -    62.24: 13
       62.24 -    77.79: 1
  Dihedral angle restraints: 5528
    sinusoidal: 2163
      harmonic: 3365
  Sorted by residual:
  dihedral pdb=" N   ARG S 191 "
           pdb=" CA  ARG S 191 "
           pdb=" CB  ARG S 191 "
           pdb=" CG  ARG S 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.85   59.85     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   PHE B 234 "
           pdb=" CA  PHE B 234 "
           pdb=" CB  PHE B 234 "
           pdb=" CG  PHE B 234 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.95  -57.05     3      1.50e+01 4.44e-03 9.43e+00
  dihedral pdb=" N   PHE R 114 "
           pdb=" CA  PHE R 114 "
           pdb=" CB  PHE R 114 "
           pdb=" CG  PHE R 114 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.13   53.13     3      1.50e+01 4.44e-03 9.18e+00
  ... (remaining 5525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 1408
       0.112 -    0.223: 29
       0.223 -    0.335: 11
       0.335 -    0.446: 4
       0.446 -    0.558: 5
  Chirality restraints: 1457
  Sorted by residual:
  chirality pdb=" C13 CLR R 405 "
            pdb=" C12 CLR R 405 "
            pdb=" C14 CLR R 405 "
            pdb=" C17 CLR R 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.37   -0.56 2.00e-01 2.50e+01 7.78e+00
  chirality pdb=" C13 CLR R 404 "
            pdb=" C12 CLR R 404 "
            pdb=" C14 CLR R 404 "
            pdb=" C17 CLR R 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.38   -0.56 2.00e-01 2.50e+01 7.74e+00
  chirality pdb=" C13 CLR R 401 "
            pdb=" C12 CLR R 401 "
            pdb=" C14 CLR R 401 "
            pdb=" C17 CLR R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.38   -0.55 2.00e-01 2.50e+01 7.69e+00
  ... (remaining 1454 not shown)

  Planarity restraints: 1586
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 299 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO R 300 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO R 300 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO R 300 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA S  40 "   -0.020 5.00e-02 4.00e+02   3.05e-02 1.49e+00
        pdb=" N   PRO S  41 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO S  41 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO S  41 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.019 5.00e-02 4.00e+02   2.87e-02 1.32e+00
        pdb=" N   PRO B 236 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1583 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 438
        2.73 -     3.27: 9064
        3.27 -     3.82: 14967
        3.82 -     4.36: 17842
        4.36 -     4.90: 31261
  Nonbonded interactions: 73572
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 248 "
            pdb=" OD1 ASP A 251 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.243 2.440
  nonbonded pdb=" OH  TYR A 230 "
            pdb=" OG  SER A 281 "
     model   vdw
     2.248 2.440
  nonbonded pdb=" O   PHE S  29 "
            pdb=" NH2 ARG S  72 "
     model   vdw
     2.263 2.520
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.269 2.440
  ... (remaining 73567 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          3.280
  Check model and map are aligned:         0.130
  Set scattering table:                    0.080
  Process input model:                     25.680
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4588
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      :  0.011   0.320   9425  Z= 0.680
  Angle     :  0.724  13.301  12797  Z= 0.335
  Chirality :  0.061   0.558   1457
  Planarity :  0.003   0.032   1586
  Dihedral  :  8.044  77.794   3353
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer Outliers :  0.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -1.34 (0.23), residues: 1144
  helix:  0.07 (0.25), residues: 408
  sheet: -1.00 (0.27), residues: 292
  loop : -1.59 (0.26), residues: 444

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 227
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 0
  residues processed: 231
  average time/residue: 1.0323
  time to fit residues: 256.8423
Evaluate side-chains
  131 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.946 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3743
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.3980
   chunk 84 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0040
   chunk 53 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 101 optimal weight:    0.5980
   overall best weight:    0.4792

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

Flipped N/Q/H residues before XYZ refinement:
R 190 GLN
A 204 GLN
B  91 HIS
B 176 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  18 GLN
S  39 GLN
S 142 GLN
S 194 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5964
moved from start:          0.4411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9425  Z= 0.207
  Angle     :  0.629   9.094  12797  Z= 0.317
  Chirality :  0.042   0.173   1457
  Planarity :  0.004   0.048   1586
  Dihedral  :  5.170  55.631   1294
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer Outliers :  3.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 (0.25), residues: 1144
  helix:  1.19 (0.28), residues: 395
  sheet: -0.43 (0.30), residues: 283
  loop : -0.95 (0.27), residues: 466

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 178
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
  outliers start: 33
  outliers final: 10
  residues processed: 194
  average time/residue: 1.0655
  time to fit residues: 223.4777
Evaluate side-chains
  131 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 1.102 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 8
  residues processed: 2
  average time/residue: 0.0914
  time to fit residues: 1.9156
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 28 optimal weight:    0.2980
   chunk 101 optimal weight:    0.0770
   chunk 110 optimal weight:    0.0770
   chunk 90 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.4296

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

Flipped N/Q/H residues before XYZ refinement:
R 190 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
B  16 ASN
B 125 ASN
B 142 HIS
B 156 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 142 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6335
moved from start:          0.6002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9425  Z= 0.150
  Angle     :  0.514   7.493  12797  Z= 0.262
  Chirality :  0.040   0.140   1457
  Planarity :  0.004   0.054   1586
  Dihedral  :  4.514  53.833   1294
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer Outliers :  3.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.36 (0.25), residues: 1144
  helix:  1.65 (0.27), residues: 393
  sheet: -0.06 (0.30), residues: 288
  loop : -0.74 (0.28), residues: 463

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 153
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
  outliers start: 34
  outliers final: 15
  residues processed: 174
  average time/residue: 1.0438
  time to fit residues: 196.0351
Evaluate side-chains
  128 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 1.040 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 11
  residues processed: 4
  average time/residue: 0.3481
  time to fit residues: 3.1666
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 11 optimal weight:    8.9990
   chunk 48 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 102 optimal weight:    6.9990
   chunk 108 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0070
   chunk 96 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.8006

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

Flipped N/Q/H residues before XYZ refinement:
R 190 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
B  32 GLN
B  88 ASN
B 340 ASN
S  39 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6922
moved from start:          1.0038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9425  Z= 0.318
  Angle     :  0.679   8.305  12797  Z= 0.356
  Chirality :  0.046   0.359   1457
  Planarity :  0.004   0.047   1586
  Dihedral  :  5.630  58.029   1294
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer Outliers :  5.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.29 (0.25), residues: 1144
  helix:  1.61 (0.27), residues: 388
  sheet: -0.05 (0.28), residues: 297
  loop : -0.82 (0.28), residues: 459

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 55
    poor density    : 167
  time to evaluate  : 1.978 
Fit side-chains
  outliers start: 55
  outliers final: 17
  residues processed: 206
  average time/residue: 1.2092
  time to fit residues: 266.6202
Evaluate side-chains
  146 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 1.098 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 13
  residues processed: 4
  average time/residue: 0.6342
  time to fit residues: 4.3189
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 55 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
A 269 ASN
S  77 ASN
S 142 GLN
S 171 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
moved from start:          1.0178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9425  Z= 0.157
  Angle     :  0.512   6.010  12797  Z= 0.268
  Chirality :  0.040   0.136   1457
  Planarity :  0.003   0.047   1586
  Dihedral  :  4.908  56.758   1294
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer Outliers :  4.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.66 (0.25), residues: 1144
  helix:  2.14 (0.27), residues: 385
  sheet:  0.05 (0.30), residues: 280
  loop : -0.69 (0.28), residues: 479

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 152
  time to evaluate  : 1.001 
Fit side-chains
  outliers start: 41
  outliers final: 21
  residues processed: 174
  average time/residue: 1.1219
  time to fit residues: 210.3161
Evaluate side-chains
  146 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.985 
Switching outliers to nearest non-outliers
  outliers start: 21
  outliers final: 16
  residues processed: 5
  average time/residue: 0.2865
  time to fit residues: 3.1658
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 97 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 63 optimal weight:    0.2980
   chunk 26 optimal weight:    2.9990
   chunk 108 optimal weight:    6.9990
   chunk 89 optimal weight:    7.9990
   chunk 50 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   chunk 35 optimal weight:   10.0000
   chunk 56 optimal weight:    0.8980
   chunk 104 optimal weight:    0.0770
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 256 ASN
B 176 GLN
B 230 ASN
G  59 ASN
S 142 GLN
S 186 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
moved from start:          1.0359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9425  Z= 0.136
  Angle     :  0.497   7.747  12797  Z= 0.259
  Chirality :  0.040   0.139   1457
  Planarity :  0.003   0.046   1586
  Dihedral  :  4.746  55.889   1294
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer Outliers :  3.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.96 (0.25), residues: 1144
  helix:  2.45 (0.27), residues: 379
  sheet:  0.15 (0.30), residues: 281
  loop : -0.51 (0.28), residues: 484

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 134
  time to evaluate  : 1.065 
Fit side-chains
  outliers start: 38
  outliers final: 25
  residues processed: 159
  average time/residue: 1.2186
  time to fit residues: 207.5572
Evaluate side-chains
  154 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 1.026 
Switching outliers to nearest non-outliers
  outliers start: 25
  outliers final: 21
  residues processed: 5
  average time/residue: 0.7110
  time to fit residues: 5.3580
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 79 optimal weight:    7.9990
   chunk 91 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 107 optimal weight:    5.9990
   chunk 67 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 43 optimal weight:   20.0000
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
A 269 ASN
B  32 GLN
B 340 ASN
S 142 GLN
S 186 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6974
moved from start:          1.0662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.063   9425  Z= 0.189
  Angle     :  0.543   7.117  12797  Z= 0.282
  Chirality :  0.042   0.140   1457
  Planarity :  0.003   0.047   1586
  Dihedral  :  4.921  57.577   1294
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer Outliers :  4.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.90 (0.25), residues: 1144
  helix:  2.40 (0.27), residues: 382
  sheet:  0.00 (0.29), residues: 288
  loop : -0.49 (0.28), residues: 474

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 130
  time to evaluate  : 1.087 
Fit side-chains
  outliers start: 43
  outliers final: 29
  residues processed: 158
  average time/residue: 1.1125
  time to fit residues: 189.6151
Evaluate side-chains
  149 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 120
  time to evaluate  : 0.940 
Switching outliers to nearest non-outliers
  outliers start: 29
  outliers final: 24
  residues processed: 6
  average time/residue: 0.6715
  time to fit residues: 5.8767
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 84 optimal weight:    6.9990
   chunk 98 optimal weight:    0.7980
   chunk 103 optimal weight:    4.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
B  32 GLN
B 340 ASN
S 142 GLN
S 186 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6961
moved from start:          1.0844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.076   9425  Z= 0.166
  Angle     :  0.523   8.279  12797  Z= 0.268
  Chirality :  0.041   0.137   1457
  Planarity :  0.003   0.046   1586
  Dihedral  :  4.830  57.631   1294
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer Outliers :  4.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.96 (0.25), residues: 1144
  helix:  2.48 (0.27), residues: 379
  sheet:  0.06 (0.29), residues: 287
  loop : -0.47 (0.28), residues: 478

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 128
  time to evaluate  : 1.149 
Fit side-chains
  outliers start: 41
  outliers final: 31
  residues processed: 157
  average time/residue: 1.1105
  time to fit residues: 189.0976
Evaluate side-chains
  151 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 120
  time to evaluate  : 1.076 
Switching outliers to nearest non-outliers
  outliers start: 31
  outliers final: 25
  residues processed: 7
  average time/residue: 0.4552
  time to fit residues: 5.3272
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    7.9990
   chunk 100 optimal weight:    1.9990
   chunk 103 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 43 optimal weight:   20.0000
   chunk 78 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 90 optimal weight:    6.9990
   chunk 95 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
B 340 ASN
S 142 GLN
S 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
moved from start:          1.1211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.079   9425  Z= 0.241
  Angle     :  0.588   8.354  12797  Z= 0.304
  Chirality :  0.043   0.148   1457
  Planarity :  0.004   0.049   1586
  Dihedral  :  5.193  58.501   1294
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer Outliers :  3.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.80 (0.25), residues: 1144
  helix:  2.17 (0.27), residues: 388
  sheet:  0.07 (0.29), residues: 294
  loop : -0.54 (0.29), residues: 462

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 131
  time to evaluate  : 1.070 
Fit side-chains
  outliers start: 35
  outliers final: 27
  residues processed: 157
  average time/residue: 1.1595
  time to fit residues: 195.8125
Evaluate side-chains
  156 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 1.036 
Switching outliers to nearest non-outliers
  outliers start: 27
  outliers final: 23
  residues processed: 5
  average time/residue: 0.4349
  time to fit residues: 4.1290
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 50 optimal weight:   10.0000
   chunk 73 optimal weight:    0.7980
   chunk 111 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   chunk 88 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9980
   chunk 68 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 94 optimal weight:    8.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
B 266 HIS
B 340 ASN
G  18 GLN
S  77 ASN
S 142 GLN
S 186 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7047
moved from start:          1.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.078   9425  Z= 0.282
  Angle     :  0.638   9.713  12797  Z= 0.325
  Chirality :  0.044   0.172   1457
  Planarity :  0.004   0.051   1586
  Dihedral  :  5.483  54.963   1294
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer Outliers :  3.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.63 (0.25), residues: 1144
  helix:  2.03 (0.27), residues: 388
  sheet:  0.01 (0.29), residues: 294
  loop : -0.65 (0.28), residues: 462

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 135
  time to evaluate  : 1.117 
Fit side-chains
  outliers start: 36
  outliers final: 26
  residues processed: 160
  average time/residue: 1.1319
  time to fit residues: 194.9908
Evaluate side-chains
  152 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 1.100 
Switching outliers to nearest non-outliers
  outliers start: 26
  outliers final: 21
  residues processed: 5
  average time/residue: 0.5203
  time to fit residues: 4.3711
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 81 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 88 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0970
   chunk 78 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
B  36 ASN
B 340 ASN
G  18 GLN
S  77 ASN
S 142 GLN
S 186 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.167803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.137196 restraints weight = 11203.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 1.85
r_work: 0.3461 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          1.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.067   9425  Z= 0.181
  Angle     :  0.562   9.223  12797  Z= 0.287
  Chirality :  0.041   0.146   1457
  Planarity :  0.004   0.049   1586
  Dihedral  :  5.055  51.558   1294
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer Outliers :  2.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.81 (0.25), residues: 1144
  helix:  2.28 (0.27), residues: 389
  sheet:  0.06 (0.30), residues: 286
  loop : -0.61 (0.28), residues: 469

===============================================================================
Job complete
usr+sys time: 3897.08 seconds
wall clock time: 69 minutes 52.41 seconds (4192.41 seconds total)