Starting phenix.real_space_refine
on Thu Mar 13 10:28:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vn7_21249/03_2025/6vn7_21249.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vn7_21249/03_2025/6vn7_21249.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vn7_21249/03_2025/6vn7_21249.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vn7_21249/03_2025/6vn7_21249.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vn7_21249/03_2025/6vn7_21249.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vn7_21249/03_2025/6vn7_21249.cif"
  }
  resolution = 3.2
  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=   0.004
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      51      5.16       5
     C    5561      2.51       5
     N    1459      2.21       5
     O    1549      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8620
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 2171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 2171
          Classifications: {'peptide': 263}
          Link IDs: {'PTRANS': 8, 'TRANS': 254}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 221
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "A"
      Number of atoms: 1981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1981
          Classifications: {'peptide': 239}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 232}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2610
          Classifications: {'peptide': 340}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 240
          Unusual residues: {'CLR': 6, 'PLM': 4}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
  Time building chain proxies: 5.32, per 1000 atoms: 0.62
  Number of scatterers: 8620
  At special positions: 0
  Unit cell: (100.386, 97.344, 131.82, 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      51     16.00
     O    1549      8.00
     N    1459      7.00
     C    5561      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 215 " - pdb=" SG  CYS R 285 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.21
  Conformation dependent library (CDL) restraints added in 959.8 milliseconds
  

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1972

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      43.3% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'R' and resid 129 through 167
      removed outlier: 4.064A  pdb=" N   GLU R 133 " --> pdb=" O   ALA R 129 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   LEU R 154 " --> pdb=" O   TYR R 150 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LEU R 157 " --> pdb=" O   SER R 153 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 201
      removed outlier: 3.603A  pdb=" N   ALA R 198 " --> pdb=" O   ILE R 194 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 213 through 246
      removed outlier: 4.001A  pdb=" N   ALA R 217 " --> pdb=" O   VAL R 213 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   VAL R 226 " --> pdb=" O   PHE R 222 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   MET R 227 " --> pdb=" O   GLN R 223 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 250 through 281
      removed outlier: 3.929A  pdb=" N   TYR R 254 " --> pdb=" O   SER R 250 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   TRP R 256 " --> pdb=" O   ARG R 252 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   GLY R 257 " --> pdb=" O   LYS R 253 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU R 260 " --> pdb=" O   TRP R 256 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ILE R 261 " --> pdb=" O   GLY R 257 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   VAL R 265 " --> pdb=" O   ILE R 261 " (cutoff:3.500A)
      Proline residue:  R 266  - end of helix
      removed outlier: 3.665A  pdb=" N   GLU R 281 " --> pdb=" O   ARG R 277 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 290 through 295
    Processing helix  chain 'R' and resid 298 through 324
      removed outlier: 4.198A  pdb=" N   LEU R 319 " --> pdb=" O   ILE R 315 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LEU R 320 " --> pdb=" O   ILE R 316 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 336 through 345
    Processing helix  chain 'R' and resid 346 through 351
    Processing helix  chain 'R' and resid 352 through 357
    Processing helix  chain 'R' and resid 365 through 389
      removed outlier: 4.359A  pdb=" N   LYS R 369 " --> pdb=" O   LYS R 365 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   MET R 370 " --> pdb=" O   PRO R 366 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE R 372 " --> pdb=" O   VAL R 368 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   GLY R 381 " --> pdb=" O   GLY R 377 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   PHE R 382 " --> pdb=" O   SER R 378 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 392 through 409
    Processing helix  chain 'L' and resid 2 through 27
    Processing helix  chain 'A' and resid 10 through 40
      removed outlier: 4.062A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
      removed outlier: 3.525A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE A  62 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 264 through 279
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 301 through 304
      removed outlier: 4.351A  pdb=" N   GLY A 304 " --> pdb=" O   VAL A 301 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 301 through 304'
    Processing helix  chain 'A' and resid 306 through 312
      removed outlier: 3.755A  pdb=" N   ASP A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 4.291A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 4.039A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.721A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   MET G  38 " --> pdb=" O   ALA G  34 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.605A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 4.022A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.447A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.856A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.685A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51
      removed outlier: 6.902A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.187A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.226A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.228A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.838A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.641A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.804A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.559A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.790A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 7.006A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    431 hydrogen bonds defined for protein.
    1236 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: 2.51

  Time building geometry restraints manager: 2.62 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2704
        1.34 -     1.46: 1975
        1.46 -     1.58: 4063
        1.58 -     1.70: 0
        1.70 -     1.82: 73
  Bond restraints: 8815
  Sorted by residual:
  bond pdb=" C   VAL R 265 "
       pdb=" N   PRO R 266 "
    ideal  model  delta    sigma   weight residual
    1.335  1.363 -0.027 1.36e-02 5.41e+03 4.02e+00
  bond pdb=" C   PRO R 325 "
       pdb=" N   PRO R 326 "
    ideal  model  delta    sigma   weight residual
    1.341  1.372 -0.031 1.60e-02 3.91e+03 3.86e+00
  bond pdb=" C5  CLR R 602 "
       pdb=" C6  CLR R 602 "
    ideal  model  delta    sigma   weight residual
    1.332  1.301  0.031 2.00e-02 2.50e+03 2.47e+00
  bond pdb=" C   ARG R 324 "
       pdb=" N   PRO R 325 "
    ideal  model  delta    sigma   weight residual
    1.329  1.348 -0.018 1.18e-02 7.18e+03 2.45e+00
  bond pdb=" C5  CLR R 601 "
       pdb=" C6  CLR R 601 "
    ideal  model  delta    sigma   weight residual
    1.332  1.301  0.031 2.00e-02 2.50e+03 2.44e+00
  ... (remaining 8810 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 11480
        2.13 -     4.26: 395
        4.26 -     6.38: 41
        6.38 -     8.51: 13
        8.51 -    10.64: 5
  Bond angle restraints: 11934
  Sorted by residual:
  angle pdb=" CA  TYR R 146 "
        pdb=" CB  TYR R 146 "
        pdb=" CG  TYR R 146 "
      ideal   model   delta    sigma   weight residual
     113.90  121.11   -7.21 1.80e+00 3.09e-01 1.60e+01
  angle pdb=" C   ASP B 195 "
        pdb=" N   THR B 196 "
        pdb=" CA  THR B 196 "
      ideal   model   delta    sigma   weight residual
     122.07  127.37   -5.30 1.43e+00 4.89e-01 1.37e+01
  angle pdb=" N   GLY R 299 "
        pdb=" CA  GLY R 299 "
        pdb=" C   GLY R 299 "
      ideal   model   delta    sigma   weight residual
     112.34  119.31   -6.97 2.04e+00 2.40e-01 1.17e+01
  angle pdb=" C   MET R 137 "
        pdb=" N   PHE R 138 "
        pdb=" CA  PHE R 138 "
      ideal   model   delta    sigma   weight residual
     120.79  125.30   -4.51 1.39e+00 5.18e-01 1.05e+01
  angle pdb=" C   GLY R 214 "
        pdb=" N   CYS R 215 "
        pdb=" CA  CYS R 215 "
      ideal   model   delta    sigma   weight residual
     120.82  125.60   -4.78 1.50e+00 4.44e-01 1.02e+01
  ... (remaining 11929 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.88: 5277
       14.88 -    29.75: 191
       29.75 -    44.63: 41
       44.63 -    59.51: 8
       59.51 -    74.38: 2
  Dihedral angle restraints: 5519
    sinusoidal: 2465
      harmonic: 3054
  Sorted by residual:
  dihedral pdb=" CA  ILE R 315 "
           pdb=" C   ILE R 315 "
           pdb=" N   ILE R 316 "
           pdb=" CA  ILE R 316 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.95   23.05     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  TRP B 169 "
           pdb=" C   TRP B 169 "
           pdb=" N   ASP B 170 "
           pdb=" CA  ASP B 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.75   20.25     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.07   18.93     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 5516 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 1172
       0.088 -    0.176: 127
       0.176 -    0.263: 17
       0.263 -    0.351: 6
       0.351 -    0.439: 6
  Chirality restraints: 1328
  Sorted by residual:
  chirality pdb=" C14 CLR R 606 "
            pdb=" C13 CLR R 606 "
            pdb=" C15 CLR R 606 "
            pdb=" C8  CLR R 606 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.76    0.44 2.00e-01 2.50e+01 4.82e+00
  chirality pdb=" C14 CLR R 603 "
            pdb=" C13 CLR R 603 "
            pdb=" C15 CLR R 603 "
            pdb=" C8  CLR R 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.75    0.43 2.00e-01 2.50e+01 4.67e+00
  chirality pdb=" C14 CLR R 604 "
            pdb=" C13 CLR R 604 "
            pdb=" C15 CLR R 604 "
            pdb=" C8  CLR R 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.74    0.42 2.00e-01 2.50e+01 4.39e+00
  ... (remaining 1325 not shown)

  Planarity restraints: 1476
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 156 "   -0.015 2.00e-02 2.50e+03   2.90e-02 8.43e+00
        pdb=" C   THR R 156 "    0.050 2.00e-02 2.50e+03
        pdb=" O   THR R 156 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LEU R 157 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "   -0.046 5.00e-02 4.00e+02   7.01e-02 7.86e+00
        pdb=" N   PRO G  49 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS R 143 "    0.014 2.00e-02 2.50e+03   2.73e-02 7.45e+00
        pdb=" C   LYS R 143 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   LYS R 143 "    0.018 2.00e-02 2.50e+03
        pdb=" N   THR R 144 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1473 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1570
        2.78 -     3.31: 7564
        3.31 -     3.84: 13488
        3.84 -     4.37: 15647
        4.37 -     4.90: 27482
  Nonbonded interactions: 65751
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OH  TYR A 360 "
            pdb=" OD2 ASP A 381 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OG1 THR R 136 "
            pdb=" OH  TYR L  13 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.313 3.040
  ... (remaining 65746 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.750
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
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   0.053   8815  Z= 0.265
  Angle     :  0.904  10.641  11934  Z= 0.498
  Chirality :  0.066   0.439   1328
  Planarity :  0.007   0.070   1476
  Dihedral  :  8.803  74.384   3538
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  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: -2.38 (0.22), residues: 1032
  helix: -1.35 (0.21), residues: 400
  sheet: -1.06 (0.32), residues: 217
  loop : -1.94 (0.27), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 281 
 HIS   0.016   0.002   HIS A 220 
 PHE   0.021   0.002   PHE A 246 
 TYR   0.022   0.002   TYR R 146 
 ARG   0.006   0.000   ARG N 118 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  346 LEU cc_start: 0.7925 (tp) cc_final: 0.7593 (mt)
REVERT: A  278 ASN cc_start: 0.7809 (m-40) cc_final: 0.7490 (m110)
REVERT: A  344 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8455 (mm-30)
REVERT: A  378 ASP cc_start: 0.8226 (m-30) cc_final: 0.7950 (m-30)
REVERT: B  256 ARG cc_start: 0.7535 (mmm160) cc_final: 0.7247 (mtm-85)
REVERT: N   80 TYR cc_start: 0.8375 (m-80) cc_final: 0.7815 (m-80)
REVERT: N   95 TYR cc_start: 0.8904 (m-10) cc_final: 0.8699 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.3074
  time to fit residues: 81.5201
Evaluate side-chains
  132 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 77 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 79 optimal weight:    0.4980
   chunk 30 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 59 optimal weight:    0.4980
   chunk 92 optimal weight:    4.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
R 134 GLN
** R 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 229 ASN
R 279 HIS
R 363 ASN
** L   1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  59 GLN
A 220 HIS
A 254 ASN
B  91 HIS
B 259 GLN
B 266 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.213372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.176552 restraints weight = 9360.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.4076 rms_B_bonded: 2.27
r_work: 0.3930 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8815  Z= 0.192
  Angle     :  0.550  12.360  11934  Z= 0.282
  Chirality :  0.042   0.160   1328
  Planarity :  0.005   0.060   1476
  Dihedral  :  6.462  58.362   1597
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  :  6.99 %
    Favored  : 90.79 %
  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: -0.21 (0.25), residues: 1032
  helix:  1.35 (0.24), residues: 407
  sheet: -0.55 (0.33), residues: 207
  loop : -1.40 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.018   0.002   PHE A 315 
 TYR   0.026   0.001   TYR R 146 
 ARG   0.004   0.000   ARG L  12 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  137 MET cc_start: 0.7371 (ttt) cc_final: 0.7095 (ttt)
REVERT: R  227 MET cc_start: 0.7638 (ttm) cc_final: 0.7388 (mtt)
REVERT: A   33 ASP cc_start: 0.7382 (t70) cc_final: 0.7069 (t70)
REVERT: A  309 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7621 (pm20)
REVERT: G   21 MET cc_start: 0.6304 (tmm) cc_final: 0.5399 (tpp)
REVERT: N   80 TYR cc_start: 0.8314 (m-80) cc_final: 0.7249 (m-80)
  outliers start: 20
  outliers final: 15
  residues processed: 162
  average time/residue: 0.2417
  time to fit residues: 51.8262
Evaluate side-chains
  146 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 SER
Chi-restraints excluded: chain R residue  161 THR
Chi-restraints excluded: chain R residue  296 ILE
Chi-restraints excluded: chain R residue  319 LEU
Chi-restraints excluded: chain R residue  323 LEU
Chi-restraints excluded: chain R residue  368 VAL
Chi-restraints excluded: chain R residue  407 HIS
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  309 GLU
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain N residue  110 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 98 optimal weight:   10.0000
   chunk 74 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 71 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   chunk 47 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
R 363 ASN
L   1 HIS
B  32 GLN
B 220 GLN
B 259 GLN
N  74 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.209032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.173204 restraints weight = 9560.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.4034 rms_B_bonded: 2.12
r_work: 0.3893 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3744 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8815  Z= 0.168
  Angle     :  0.506  10.872  11934  Z= 0.259
  Chirality :  0.041   0.141   1328
  Planarity :  0.004   0.053   1476
  Dihedral  :  6.188  59.449   1597
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  9.21 %
    Favored  : 88.79 %
  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 (0.26), residues: 1032
  helix:  2.33 (0.25), residues: 406
  sheet: -0.37 (0.33), residues: 225
  loop : -1.17 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.016   0.001   PHE A 315 
 TYR   0.023   0.001   TYR R 146 
 ARG   0.005   0.000   ARG G  27 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
REVERT: R  137 MET cc_start: 0.7512 (ttt) cc_final: 0.7244 (ttt)
REVERT: R  321 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7982 (tt0)
REVERT: A   33 ASP cc_start: 0.7571 (t70) cc_final: 0.7223 (t70)
REVERT: A  309 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7696 (pm20)
REVERT: G   21 MET cc_start: 0.6364 (tmm) cc_final: 0.5450 (tpp)
REVERT: N   80 TYR cc_start: 0.8622 (m-80) cc_final: 0.7384 (m-80)
  outliers start: 18
  outliers final: 13
  residues processed: 143
  average time/residue: 0.2661
  time to fit residues: 50.0812
Evaluate side-chains
  137 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 SER
Chi-restraints excluded: chain R residue  296 ILE
Chi-restraints excluded: chain R residue  319 LEU
Chi-restraints excluded: chain R residue  321 GLN
Chi-restraints excluded: chain R residue  323 LEU
Chi-restraints excluded: chain R residue  407 HIS
Chi-restraints excluded: chain A residue  309 GLU
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue  110 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 99 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 21 optimal weight:    8.9990
   chunk 55 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 17 optimal weight:    0.2980
   chunk 58 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 36 optimal weight:    0.8980
   chunk 66 optimal weight:    0.3980
   chunk 97 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B 220 GLN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.210639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.175404 restraints weight = 9504.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.4055 rms_B_bonded: 2.10
r_work: 0.3939 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3787 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8815  Z= 0.145
  Angle     :  0.477   9.804  11934  Z= 0.244
  Chirality :  0.040   0.137   1328
  Planarity :  0.004   0.051   1476
  Dihedral  :  5.955  58.183   1597
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  :  9.21 %
    Favored  : 88.12 %
  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:  0.96 (0.27), residues: 1032
  helix:  2.69 (0.25), residues: 410
  sheet: -0.32 (0.33), residues: 217
  loop : -1.00 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.012   0.001   PHE A 315 
 TYR   0.021   0.001   TYR R 146 
 ARG   0.005   0.000   ARG G  27 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  137 MET cc_start: 0.7445 (ttt) cc_final: 0.7164 (ttt)
REVERT: A  317 ARG cc_start: 0.7704 (ttp-170) cc_final: 0.7355 (mpp-170)
REVERT: B  169 TRP cc_start: 0.8754 (m100) cc_final: 0.8542 (m100)
REVERT: G   21 MET cc_start: 0.6251 (tmm) cc_final: 0.5338 (tpp)
REVERT: N   80 TYR cc_start: 0.8653 (m-80) cc_final: 0.7412 (m-80)
  outliers start: 24
  outliers final: 19
  residues processed: 142
  average time/residue: 0.2488
  time to fit residues: 46.9769
Evaluate side-chains
  148 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 SER
Chi-restraints excluded: chain R residue  296 ILE
Chi-restraints excluded: chain R residue  319 LEU
Chi-restraints excluded: chain R residue  323 LEU
Chi-restraints excluded: chain R residue  407 HIS
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain N residue  122 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 67 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 91 optimal weight:   20.0000
   chunk 5 optimal weight:    0.8980
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
R 290 ASN
A  14 ASN
A 371 ASN
B  32 GLN
B 156 GLN
B 259 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.204075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.168351 restraints weight = 9485.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.4004 rms_B_bonded: 2.08
r_work: 0.3887 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3736 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.3704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8815  Z= 0.214
  Angle     :  0.522  10.082  11934  Z= 0.267
  Chirality :  0.041   0.135   1328
  Planarity :  0.004   0.056   1476
  Dihedral  :  6.146  53.884   1597
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  :  9.66 %
    Favored  : 87.24 %
  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:  1.02 (0.27), residues: 1032
  helix:  2.86 (0.25), residues: 399
  sheet: -0.30 (0.33), residues: 216
  loop : -1.00 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 339 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.012   0.001   PHE N 108 
 TYR   0.022   0.001   TYR R 146 
 ARG   0.004   0.000   ARG B 219 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 138
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
REVERT: R  137 MET cc_start: 0.7557 (ttt) cc_final: 0.7324 (ttt)
REVERT: A  224 VAL cc_start: 0.8310 (t) cc_final: 0.7945 (m)
REVERT: G   21 MET cc_start: 0.6258 (tmm) cc_final: 0.5311 (tpp)
REVERT: N   95 TYR cc_start: 0.9114 (m-80) cc_final: 0.8692 (m-80)
  outliers start: 28
  outliers final: 24
  residues processed: 151
  average time/residue: 0.2445
  time to fit residues: 49.2370
Evaluate side-chains
  151 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 SER
Chi-restraints excluded: chain R residue  293 LEU
Chi-restraints excluded: chain R residue  296 ILE
Chi-restraints excluded: chain R residue  319 LEU
Chi-restraints excluded: chain R residue  323 LEU
Chi-restraints excluded: chain R residue  363 ASN
Chi-restraints excluded: chain R residue  407 HIS
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  122 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 38 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 89 optimal weight:    0.0470
   chunk 66 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.207584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.172360 restraints weight = 9408.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.4027 rms_B_bonded: 2.05
r_work: 0.3909 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3766 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.3844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8815  Z= 0.143
  Angle     :  0.478   9.284  11934  Z= 0.244
  Chirality :  0.040   0.138   1328
  Planarity :  0.003   0.049   1476
  Dihedral  :  5.888  51.530   1597
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 11.54 %
    Favored  : 86.24 %
  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:  1.22 (0.27), residues: 1032
  helix:  3.09 (0.25), residues: 398
  sheet: -0.24 (0.34), residues: 217
  loop : -0.91 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 232 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.010   0.001   PHE A 222 
 TYR   0.019   0.001   TYR R 146 
 ARG   0.008   0.000   ARG L  12 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 1.399 
Fit side-chains
   revert: symmetry clash
REVERT: R  137 MET cc_start: 0.7514 (ttt) cc_final: 0.7256 (ttt)
REVERT: A  224 VAL cc_start: 0.8211 (t) cc_final: 0.7859 (m)
REVERT: A  307 LYS cc_start: 0.4387 (tmtt) cc_final: 0.2977 (mttm)
REVERT: G   21 MET cc_start: 0.6322 (tmm) cc_final: 0.5278 (tpp)
REVERT: N   95 TYR cc_start: 0.9052 (m-80) cc_final: 0.8719 (m-80)
  outliers start: 20
  outliers final: 16
  residues processed: 146
  average time/residue: 0.2523
  time to fit residues: 48.6612
Evaluate side-chains
  143 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 SER
Chi-restraints excluded: chain R residue  323 LEU
Chi-restraints excluded: chain R residue  407 HIS
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain N residue  122 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 100 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0980
   chunk 49 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0040
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
B  32 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.208210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.173053 restraints weight = 9458.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.4052 rms_B_bonded: 2.06
r_work: 0.3925 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3783 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.3946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8815  Z= 0.137
  Angle     :  0.479   9.877  11934  Z= 0.244
  Chirality :  0.040   0.136   1328
  Planarity :  0.003   0.049   1476
  Dihedral  :  5.688  49.529   1597
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.10 %
    Favored  : 85.24 %
  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:  1.34 (0.27), residues: 1032
  helix:  3.21 (0.25), residues: 399
  sheet: -0.29 (0.33), residues: 228
  loop : -0.81 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 232 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.009   0.001   PHE A 222 
 TYR   0.018   0.001   TYR R 146 
 ARG   0.005   0.000   ARG L  12 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  137 MET cc_start: 0.7623 (ttt) cc_final: 0.7355 (ttt)
REVERT: A  224 VAL cc_start: 0.8116 (t) cc_final: 0.7799 (m)
REVERT: A  307 LYS cc_start: 0.4594 (tmtt) cc_final: 0.3165 (mttm)
REVERT: G   21 MET cc_start: 0.6347 (tmm) cc_final: 0.5375 (tpp)
REVERT: N   95 TYR cc_start: 0.9057 (m-80) cc_final: 0.8797 (m-80)
  outliers start: 15
  outliers final: 15
  residues processed: 137
  average time/residue: 0.2677
  time to fit residues: 48.8144
Evaluate side-chains
  144 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 SER
Chi-restraints excluded: chain R residue  293 LEU
Chi-restraints excluded: chain R residue  323 LEU
Chi-restraints excluded: chain R residue  363 ASN
Chi-restraints excluded: chain R residue  407 HIS
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain N residue  122 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 81 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0050
   chunk 16 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.207723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.172056 restraints weight = 9590.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.4033 rms_B_bonded: 2.08
r_work: 0.3921 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3774 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.4077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8815  Z= 0.148
  Angle     :  0.478   9.347  11934  Z= 0.244
  Chirality :  0.040   0.134   1328
  Planarity :  0.003   0.050   1476
  Dihedral  :  5.646  49.206   1597
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.43 %
    Favored  : 85.24 %
  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:  1.42 (0.27), residues: 1032
  helix:  3.24 (0.25), residues: 400
  sheet: -0.21 (0.32), residues: 239
  loop : -0.78 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 232 
 HIS   0.003   0.001   HIS B 311 
 PHE   0.009   0.001   PHE A 222 
 TYR   0.019   0.001   TYR R 146 
 ARG   0.005   0.000   ARG L  12 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 1.455 
Fit side-chains
   revert: symmetry clash
REVERT: R  137 MET cc_start: 0.7529 (ttt) cc_final: 0.7238 (ttt)
REVERT: A  224 VAL cc_start: 0.8219 (t) cc_final: 0.7887 (m)
REVERT: A  307 LYS cc_start: 0.4493 (tmtt) cc_final: 0.3188 (mttm)
REVERT: A  370 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7195 (mt-10)
REVERT: B   44 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7856 (mp10)
REVERT: B  134 ARG cc_start: 0.6634 (ptt-90) cc_final: 0.6014 (mmp80)
REVERT: B  234 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8586 (m-80)
REVERT: G   21 MET cc_start: 0.6304 (tmm) cc_final: 0.5358 (tpp)
REVERT: N   95 TYR cc_start: 0.9063 (m-80) cc_final: 0.8820 (m-80)
  outliers start: 21
  outliers final: 16
  residues processed: 136
  average time/residue: 0.2527
  time to fit residues: 46.3484
Evaluate side-chains
  141 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 SER
Chi-restraints excluded: chain R residue  293 LEU
Chi-restraints excluded: chain R residue  319 LEU
Chi-restraints excluded: chain R residue  323 LEU
Chi-restraints excluded: chain R residue  363 ASN
Chi-restraints excluded: chain R residue  407 HIS
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  122 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 94 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 86 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 82 optimal weight:    0.2980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
B  32 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.206986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.172408 restraints weight = 9543.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.4029 rms_B_bonded: 2.02
r_work: 0.3922 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3779 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.4181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8815  Z= 0.162
  Angle     :  0.487   9.401  11934  Z= 0.250
  Chirality :  0.040   0.135   1328
  Planarity :  0.003   0.051   1476
  Dihedral  :  5.713  57.744   1597
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 12.32 %
    Favored  : 85.13 %
  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:  1.36 (0.27), residues: 1032
  helix:  3.17 (0.25), residues: 400
  sheet: -0.23 (0.33), residues: 240
  loop : -0.80 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.009   0.001   PHE N 108 
 TYR   0.019   0.001   TYR R 146 
 ARG   0.005   0.000   ARG L  12 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
REVERT: R  137 MET cc_start: 0.7501 (ttt) cc_final: 0.7229 (ttt)
REVERT: R  271 MET cc_start: 0.5801 (mmt) cc_final: 0.5537 (mmp)
REVERT: A  224 VAL cc_start: 0.8303 (t) cc_final: 0.7967 (m)
REVERT: B   44 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7975 (mp10)
REVERT: B  134 ARG cc_start: 0.6627 (ptt-90) cc_final: 0.5972 (mmp80)
REVERT: B  234 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8506 (m-80)
REVERT: G   21 MET cc_start: 0.6320 (tmm) cc_final: 0.5351 (tpp)
  outliers start: 23
  outliers final: 20
  residues processed: 133
  average time/residue: 0.2588
  time to fit residues: 45.2865
Evaluate side-chains
  141 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 SER
Chi-restraints excluded: chain R residue  293 LEU
Chi-restraints excluded: chain R residue  319 LEU
Chi-restraints excluded: chain R residue  321 GLN
Chi-restraints excluded: chain R residue  323 LEU
Chi-restraints excluded: chain R residue  363 ASN
Chi-restraints excluded: chain R residue  407 HIS
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  122 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 86 optimal weight:   10.0000
   chunk 70 optimal weight:    0.8980
   chunk 75 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0770
   chunk 6 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 100 optimal weight:    0.3980
   chunk 94 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.8742

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
N  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.206006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.170882 restraints weight = 9473.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.4020 rms_B_bonded: 2.04
r_work: 0.3905 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3759 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.4286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8815  Z= 0.173
  Angle     :  0.500   9.418  11934  Z= 0.258
  Chirality :  0.041   0.154   1328
  Planarity :  0.003   0.051   1476
  Dihedral  :  5.743  51.557   1597
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 12.32 %
    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:  1.31 (0.27), residues: 1032
  helix:  3.04 (0.25), residues: 404
  sheet: -0.23 (0.32), residues: 240
  loop : -0.78 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 339 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.009   0.001   PHE N 108 
 TYR   0.019   0.001   TYR R 146 
 ARG   0.005   0.000   ARG L  12 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 0.965 
Fit side-chains
REVERT: R  137 MET cc_start: 0.7517 (ttt) cc_final: 0.7257 (ttt)
REVERT: A  224 VAL cc_start: 0.8250 (t) cc_final: 0.7898 (m)
REVERT: A  307 LYS cc_start: 0.4518 (tmtt) cc_final: 0.3217 (mttm)
REVERT: B   32 GLN cc_start: 0.7349 (mt0) cc_final: 0.7003 (tt0)
REVERT: B   44 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7983 (mp10)
REVERT: B  234 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8525 (m-80)
REVERT: G   21 MET cc_start: 0.6335 (tmm) cc_final: 0.5351 (tpp)
  outliers start: 24
  outliers final: 19
  residues processed: 134
  average time/residue: 0.2380
  time to fit residues: 43.0039
Evaluate side-chains
  139 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 SER
Chi-restraints excluded: chain R residue  293 LEU
Chi-restraints excluded: chain R residue  319 LEU
Chi-restraints excluded: chain R residue  321 GLN
Chi-restraints excluded: chain R residue  323 LEU
Chi-restraints excluded: chain R residue  407 HIS
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  343 ASP
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  122 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 101 optimal weight:    0.0000
   chunk 75 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 89 optimal weight:    0.0030
   chunk 44 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.7596

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.207569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.172555 restraints weight = 9626.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.4026 rms_B_bonded: 2.05
r_work: 0.3905 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3760 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.4349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   8815  Z= 0.161
  Angle     :  0.489   9.362  11934  Z= 0.253
  Chirality :  0.041   0.216   1328
  Planarity :  0.003   0.050   1476
  Dihedral  :  5.666  48.542   1597
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 12.43 %
    Favored  : 85.35 %
  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:  1.32 (0.27), residues: 1032
  helix:  3.06 (0.25), residues: 404
  sheet: -0.17 (0.32), residues: 239
  loop : -0.83 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 339 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.008   0.001   PHE B 199 
 TYR   0.019   0.001   TYR R 146 
 ARG   0.006   0.000   ARG B  52 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5232.88 seconds
wall clock time: 91 minutes 20.11 seconds (5480.11 seconds total)