Starting phenix.real_space_refine
on Sun May  3 14:41:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wdb_65888/05_2026/9wdb_65888_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wdb_65888/05_2026/9wdb_65888.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wdb_65888/05_2026/9wdb_65888_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wdb_65888/05_2026/9wdb_65888_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wdb_65888/05_2026/9wdb_65888.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wdb_65888/05_2026/9wdb_65888.map"
  }
  resolution = 2.39
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.039
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: 7
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      49      5.16       5
     C    4321      2.51       5
     N    1161      2.21       5
     O    1326      1.98       5
     H    6526      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13391
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "a"
      Number of atoms: 6684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 433, 6684
          Classifications: {'peptide': 433}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412}
          Chain breaks: 1
    Chain: "b"
      Number of atoms: 6579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 6579
          Classifications: {'peptide': 426}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406}
    Chain: "a"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "b"
      Number of atoms: 95
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 95
          Unusual residues: {' MG': 1, 'G2P': 1, 'TA1': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.51, per 1000 atoms: 0.19
  Number of scatterers: 13391
  At special positions: 0
  Unit cell: (74.5446, 73.5889, 113.728, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      49     16.00
     P       6     15.00
     Mg      2     11.99
     O    1326      8.00
     N    1161      7.00
     C    4321      6.00
     H    6526      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.03
  Conformation dependent library (CDL) restraints added in 362.9 milliseconds
  

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1588

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 5 sheets defined
      50.4% alpha, 14.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'a' and resid 10 through 28
      removed outlier: 3.666A  pdb=" N   ALA a  19 " --> pdb=" O   GLN a  15 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 72 through 80
      removed outlier: 3.565A  pdb=" N   GLU a  77 " --> pdb=" O   THR a  73 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   VAL a  78 " --> pdb=" O   VAL a  74 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 88 through 90
      No H-bonds generated for 'chain 'a' and resid 88 through 90'
    Processing helix  chain 'a' and resid 102 through 108
    Processing helix  chain 'a' and resid 110 through 113
    Processing helix  chain 'a' and resid 114 through 127
    Processing helix  chain 'a' and resid 144 through 161
      removed outlier: 4.387A  pdb=" N   THR a 150 " --> pdb=" O   GLY a 146 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLU a 155 " --> pdb=" O   SER a 151 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   VAL a 159 " --> pdb=" O   GLU a 155 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ASP a 160 " --> pdb=" O   ARG a 156 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 182 through 190
    Processing helix  chain 'a' and resid 192 through 197
    Processing helix  chain 'a' and resid 206 through 216
    Processing helix  chain 'a' and resid 223 through 239
      removed outlier: 3.643A  pdb=" N   LEU a 230 " --> pdb=" O   ASN a 226 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 239 through 244
      removed outlier: 3.748A  pdb=" N   ARG a 243 " --> pdb=" O   THR a 239 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 251 through 258
    Processing helix  chain 'a' and resid 290 through 295
    Processing helix  chain 'a' and resid 296 through 301
      removed outlier: 6.145A  pdb=" N   ALA a 299 " --> pdb=" O   PHE a 296 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLN a 301 " --> pdb=" O   PRO a 298 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 306 through 310
    Processing helix  chain 'a' and resid 324 through 336
    Processing helix  chain 'a' and resid 384 through 401
      removed outlier: 3.753A  pdb=" N   TRP a 388 " --> pdb=" O   ILE a 384 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU a 391 " --> pdb=" O   ALA a 387 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LYS a 394 " --> pdb=" O   ARG a 390 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   LYS a 401 " --> pdb=" O   LEU a 397 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 404 through 410
      removed outlier: 4.093A  pdb=" N   TYR a 408 " --> pdb=" O   PHE a 404 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 415 through 435
      removed outlier: 3.890A  pdb=" N   SER a 419 " --> pdb=" O   GLU a 415 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLU a 433 " --> pdb=" O   GLU a 429 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 10 through 29
    Processing helix  chain 'b' and resid 40 through 45
      removed outlier: 4.376A  pdb=" N   LEU b  44 " --> pdb=" O   SER b  40 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLU b  45 " --> pdb=" O   ASP b  41 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'b' and resid 40 through 45'
    Processing helix  chain 'b' and resid 46 through 49
    Processing helix  chain 'b' and resid 70 through 77
      removed outlier: 3.741A  pdb=" N   SER b  75 " --> pdb=" O   GLY b  71 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL b  76 " --> pdb=" O   THR b  72 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 86 through 88
      No H-bonds generated for 'chain 'b' and resid 86 through 88'
    Processing helix  chain 'b' and resid 100 through 106
    Processing helix  chain 'b' and resid 107 through 125
      removed outlier: 4.100A  pdb=" N   GLU b 111 " --> pdb=" O   THR b 107 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU b 112 " --> pdb=" O   GLU b 108 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ASP b 114 " --> pdb=" O   ALA b 110 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   SER b 115 " --> pdb=" O   GLU b 111 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL b 119 " --> pdb=" O   SER b 115 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 145 through 159
      removed outlier: 3.593A  pdb=" N   THR b 149 " --> pdb=" O   SER b 145 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLU b 158 " --> pdb=" O   LYS b 154 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 180 through 196
      removed outlier: 3.507A  pdb=" N   ASN b 184 " --> pdb=" O   VAL b 180 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   HIS b 190 " --> pdb=" O   THR b 186 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   GLN b 191 " --> pdb=" O   LEU b 187 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR b 196 " --> pdb=" O   LEU b 192 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 203 through 214
    Processing helix  chain 'b' and resid 221 through 237
      removed outlier: 3.640A  pdb=" N   THR b 237 " --> pdb=" O   MET b 233 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 238 through 241
    Processing helix  chain 'b' and resid 249 through 258
    Processing helix  chain 'b' and resid 277 through 282
      removed outlier: 4.040A  pdb=" N   GLN b 280 " --> pdb=" O   GLY b 277 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ARG b 282 " --> pdb=" O   GLN b 279 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 285 through 294
    Processing helix  chain 'b' and resid 295 through 299
      removed outlier: 4.016A  pdb=" N   MET b 299 " --> pdb=" O   ALA b 296 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 304 through 308
    Processing helix  chain 'b' and resid 322 through 335
    Processing helix  chain 'b' and resid 374 through 390
      removed outlier: 3.770A  pdb=" N   PHE b 378 " --> pdb=" O   ILE b 374 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE b 381 " --> pdb=" O   LEU b 377 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 395 through 400
    Processing helix  chain 'b' and resid 405 through 425
      removed outlier: 3.777A  pdb=" N   THR b 409 " --> pdb=" O   GLU b 405 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   TYR b 425 " --> pdb=" O   GLU b 421 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'a' and resid 92 through 94
      removed outlier: 8.239A  pdb=" N   ILE a  93 " --> pdb=" O   ALA a  65 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   PHE a  67 " --> pdb=" O   ILE a  93 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   GLU a   3 " --> pdb=" O   GLY a 134 " (cutoff:3.500A)
      removed outlier: 8.228A  pdb=" N   LEU a 136 " --> pdb=" O   GLU a   3 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ILE a   5 " --> pdb=" O   LEU a 136 " (cutoff:3.500A)
      removed outlier: 8.002A  pdb=" N   PHE a 138 " --> pdb=" O   ILE a   5 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE a   7 " --> pdb=" O   PHE a 138 " (cutoff:3.500A)
      removed outlier: 8.869A  pdb=" N   SER a 140 " --> pdb=" O   ILE a   7 " (cutoff:3.500A)
      removed outlier: 8.792A  pdb=" N   VAL a   9 " --> pdb=" O   SER a 140 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   GLN a 133 " --> pdb=" O   SER a 165 " (cutoff:3.500A)
      removed outlier: 8.041A  pdb=" N   LEU a 167 " --> pdb=" O   GLN a 133 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   PHE a 135 " --> pdb=" O   LEU a 167 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   PHE a 169 " --> pdb=" O   PHE a 135 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL a 137 " --> pdb=" O   PHE a 169 " (cutoff:3.500A)
      removed outlier: 7.828A  pdb=" N   ILE a 171 " --> pdb=" O   VAL a 137 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   HIS a 139 " --> pdb=" O   ILE a 171 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   LYS a 166 " --> pdb=" O   CYS a 200 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   PHE a 202 " --> pdb=" O   LYS a 166 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   GLU a 168 " --> pdb=" O   PHE a 202 " (cutoff:3.500A)
      removed outlier: 7.769A  pdb=" N   VAL a 204 " --> pdb=" O   GLU a 168 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   SER a 170 " --> pdb=" O   VAL a 204 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'a' and resid 53 through 55
    Processing sheet with id=AA3, first strand: chain 'a' and resid 269 through 273
      removed outlier: 3.824A  pdb=" N   ALA a 314 " --> pdb=" O   ASN a 380 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'b' and resid 90 through 92
      removed outlier: 8.344A  pdb=" N   ILE b  91 " --> pdb=" O   ALA b  63 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   LEU b  65 " --> pdb=" O   ILE b  91 " (cutoff:3.500A)
      removed outlier: 8.541A  pdb=" N   ILE b  64 " --> pdb=" O   ILE b   4 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   HIS b   6 " --> pdb=" O   ILE b  64 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   VAL b  66 " --> pdb=" O   HIS b   6 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   GLN b   8 " --> pdb=" O   VAL b  66 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   GLU b   3 " --> pdb=" O   GLY b 132 " (cutoff:3.500A)
      removed outlier: 8.252A  pdb=" N   GLN b 134 " --> pdb=" O   GLU b   3 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   VAL b   5 " --> pdb=" O   GLN b 134 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   THR b 136 " --> pdb=" O   VAL b   5 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   ILE b   7 " --> pdb=" O   THR b 136 " (cutoff:3.500A)
      removed outlier: 9.005A  pdb=" N   SER b 138 " --> pdb=" O   ILE b   7 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   ALA b   9 " --> pdb=" O   SER b 138 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   GLN b 131 " --> pdb=" O   ILE b 163 " (cutoff:3.500A)
      removed outlier: 8.135A  pdb=" N   ASN b 165 " --> pdb=" O   GLN b 131 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   PHE b 133 " --> pdb=" O   ASN b 165 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   PHE b 167 " --> pdb=" O   PHE b 133 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   LEU b 135 " --> pdb=" O   PHE b 167 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   VAL b 169 " --> pdb=" O   LEU b 135 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   HIS b 137 " --> pdb=" O   VAL b 169 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   MET b 164 " --> pdb=" O   GLU b 198 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   TYR b 200 " --> pdb=" O   MET b 164 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   THR b 166 " --> pdb=" O   TYR b 200 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   ILE b 202 " --> pdb=" O   THR b 166 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   SER b 168 " --> pdb=" O   ILE b 202 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   THR b 199 " --> pdb=" O   PHE b 266 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   CYS b 201 " --> pdb=" O   PRO b 268 " (cutoff:3.500A)
      removed outlier: 10.813A  pdb=" N   PHE b 270 " --> pdb=" O   CYS b 201 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   PHE b 265 " --> pdb=" O   SER b 371 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   SER b 371 " --> pdb=" O   PHE b 265 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   SER b 364 " --> pdb=" O   PHE b 317 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   PHE b 317 " --> pdb=" O   SER b 364 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   THR b 366 " --> pdb=" O   THR b 315 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   THR b 315 " --> pdb=" O   THR b 366 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   ILE b 368 " --> pdb=" O   VAL b 313 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   VAL b 313 " --> pdb=" O   ILE b 368 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   ASN b 370 " --> pdb=" O   LEU b 311 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'b' and resid 51 through 53

    276 hydrogen bonds defined for protein.
    795 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: 2.87

  Time building geometry restraints manager: 1.48 seconds

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

  Histogram of bond lengths:
        0.84 -     1.07: 6506
        1.07 -     1.30: 1174
        1.30 -     1.53: 5512
        1.53 -     1.76: 279
        1.76 -     2.00: 80
  Bond restraints: 13551
  Sorted by residual:
  bond pdb=" O5' G2P b 503 "
       pdb=" PA  G2P b 503 "
    ideal  model  delta    sigma   weight residual
    1.656  1.886 -0.230 2.00e-02 2.50e+03 1.32e+02
  bond pdb=" C3A G2P b 503 "
       pdb=" PB  G2P b 503 "
    ideal  model  delta    sigma   weight residual
    1.850  1.995 -0.145 2.00e-02 2.50e+03 5.28e+01
  bond pdb=" O3B G2P b 503 "
       pdb=" PG  G2P b 503 "
    ideal  model  delta    sigma   weight residual
    1.716  1.842 -0.126 2.00e-02 2.50e+03 3.96e+01
  bond pdb=" C3A G2P b 503 "
       pdb=" PA  G2P b 503 "
    ideal  model  delta    sigma   weight residual
    1.818  1.695  0.123 2.00e-02 2.50e+03 3.81e+01
  bond pdb=" C4' G2P b 503 "
       pdb=" C5' G2P b 503 "
    ideal  model  delta    sigma   weight residual
    1.518  1.612 -0.094 2.00e-02 2.50e+03 2.21e+01
  ... (remaining 13546 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.13: 24342
        7.13 -    14.27: 19
       14.27 -    21.40: 4
       21.40 -    28.53: 0
       28.53 -    35.66: 3
  Bond angle restraints: 24368
  Sorted by residual:
  angle pdb=" N   ILE b 202 "
        pdb=" CA  ILE b 202 "
        pdb=" HA  ILE b 202 "
      ideal   model   delta    sigma   weight residual
     110.00   74.34   35.66 3.00e+00 1.11e-01 1.41e+02
  angle pdb=" C   ILE b 202 "
        pdb=" CA  ILE b 202 "
        pdb=" HA  ILE b 202 "
      ideal   model   delta    sigma   weight residual
     109.00   74.30   34.70 3.00e+00 1.11e-01 1.34e+02
  angle pdb=" CB  ILE b 202 "
        pdb=" CA  ILE b 202 "
        pdb=" HA  ILE b 202 "
      ideal   model   delta    sigma   weight residual
     109.00   75.31   33.69 3.00e+00 1.11e-01 1.26e+02
  angle pdb=" O1A G2P b 503 "
        pdb=" PA  G2P b 503 "
        pdb=" O5' G2P b 503 "
      ideal   model   delta    sigma   weight residual
     109.23   88.90   20.33 3.00e+00 1.11e-01 4.59e+01
  angle pdb=" C3A G2P b 503 "
        pdb=" PB  G2P b 503 "
        pdb=" O3B G2P b 503 "
      ideal   model   delta    sigma   weight residual
      99.71  116.74  -17.03 3.00e+00 1.11e-01 3.22e+01
  ... (remaining 24363 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.53: 6155
       31.53 -    63.05: 324
       63.05 -    94.58: 25
       94.58 -   126.10: 10
      126.10 -   157.63: 10
  Dihedral angle restraints: 6524
    sinusoidal: 3580
      harmonic: 2944
  Sorted by residual:
  dihedral pdb=" C4' GTP a 501 "
           pdb=" C5' GTP a 501 "
           pdb=" O5' GTP a 501 "
           pdb=" PA  GTP a 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     260.87  103.25  157.63     1      2.00e+01 2.50e-03 4.62e+01
  dihedral pdb=" C8  GTP a 501 "
           pdb=" C1' GTP a 501 "
           pdb=" N9  GTP a 501 "
           pdb=" O4' GTP a 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -46.22  150.81     1      2.00e+01 2.50e-03 4.50e+01
  dihedral pdb=" O3B GTP a 501 "
           pdb=" O3A GTP a 501 "
           pdb=" PB  GTP a 501 "
           pdb=" PA  GTP a 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -68.92   79.21 -148.13     1      2.00e+01 2.50e-03 4.44e+01
  ... (remaining 6521 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.101: 990
       0.101 -    0.203: 47
       0.203 -    0.304: 4
       0.304 -    0.406: 0
       0.406 -    0.507: 1
  Chirality restraints: 1042
  Sorted by residual:
  chirality pdb=" C18 TA1 b 501 "
            pdb=" C10 TA1 b 501 "
            pdb=" C17 TA1 b 501 "
            pdb=" C20 TA1 b 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -3.16   -2.66   -0.51 2.00e-01 2.50e+01 6.43e+00
  chirality pdb=" C2' G2P b 503 "
            pdb=" C1' G2P b 503 "
            pdb=" C3' G2P b 503 "
            pdb=" O2' G2P b 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.76    0.28 2.00e-01 2.50e+01 2.01e+00
  chirality pdb=" C4' G2P b 503 "
            pdb=" C3' G2P b 503 "
            pdb=" C5' G2P b 503 "
            pdb=" O4' G2P b 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.75    0.26 2.00e-01 2.50e+01 1.66e+00
  ... (remaining 1039 not shown)

  Planarity restraints: 2052
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C29 TA1 b 501 "   -0.029 2.00e-02 2.50e+03   2.44e-02 7.43e+00
        pdb=" C30 TA1 b 501 "    0.022 2.00e-02 2.50e+03
        pdb=" C31 TA1 b 501 "   -0.026 2.00e-02 2.50e+03
        pdb=" N01 TA1 b 501 "    0.032 2.00e-02 2.50e+03
        pdb=" O14 TA1 b 501 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP a 322 "   -0.011 2.00e-02 2.50e+03   2.20e-02 4.83e+00
        pdb=" CG  ASP a 322 "    0.038 2.00e-02 2.50e+03
        pdb=" OD1 ASP a 322 "   -0.014 2.00e-02 2.50e+03
        pdb=" OD2 ASP a 322 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL a 324 "   -0.025 5.00e-02 4.00e+02   3.73e-02 2.23e+00
        pdb=" N   PRO a 325 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO a 325 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO a 325 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 2049 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 433
        2.17 -     2.78: 25289
        2.78 -     3.38: 35742
        3.38 -     3.99: 48494
        3.99 -     4.60: 76238
  Nonbonded interactions: 186196
  Sorted by model distance:
  nonbonded pdb=" H   ILE b 202 "
            pdb=" HA  ILE b 202 "
     model   vdw
     1.560 1.816
  nonbonded pdb=" HG3 GLU a 414 "
            pdb=" H   GLY a 416 "
     model   vdw
     1.705 2.270
  nonbonded pdb=" HE2 LYS a 311 "
            pdb="HE22 GLN a 342 "
     model   vdw
     1.764 2.270
  nonbonded pdb=" H   LYS a 163 "
            pdb=" HD3 LYS a 163 "
     model   vdw
     1.840 2.270
  nonbonded pdb=" HA  ASN a 293 "
            pdb="HD22 ASN a 293 "
     model   vdw
     1.881 2.270
  ... (remaining 186191 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:             11.750
  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:             0.090
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.280
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:6.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
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      :  0.006   0.230   7025  Z= 0.275
  Angle     :  0.822  20.328   9553  Z= 0.337
  Chirality :  0.047   0.507   1042
  Planarity :  0.004   0.037   1237
  Dihedral  : 21.371 157.626   2671
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 22.30 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.28), residues: 853
  helix: -0.78 (0.27), residues: 345
  sheet:  0.19 (0.43), residues: 157
  loop : -1.04 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG b 162 
 TYR   0.006   0.001   TYR b  59 
 PHE   0.016   0.001   PHE a  49 
 TRP   0.009   0.001   TRP b  21 
 HIS   0.004   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 ( 7025)
  covalent geometry    : angle       0.82219 ( 9553)
  hydrogen bonds       : bond        0.29697 (  276)
  hydrogen bonds       : angle       7.72821 (  795)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: b    1 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.6746 (ttp)
REVERT: b   86 ARG cc_start: 0.8393 (ttm170) cc_final: 0.7247 (tpt170)
REVERT: b  118 ASP cc_start: 0.8376 (t0) cc_final: 0.8051 (m-30)
REVERT: b  209 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7810 (t0)
REVERT: b  213 ARG cc_start: 0.8695 (ttm110) cc_final: 0.8477 (ttm170)
REVERT: b  280 GLN cc_start: 0.8347 (pt0) cc_final: 0.7909 (pm20)
REVERT: b  320 ARG cc_start: 0.7837 (ttm-80) cc_final: 0.7626 (mtt90)
REVERT: b  359 ARG cc_start: 0.7924 (mtp-110) cc_final: 0.7652 (mtp-110)
REVERT: b  362 LYS cc_start: 0.8376 (mmtp) cc_final: 0.8134 (mmtm)
REVERT: b  416 ASN cc_start: 0.8345 (m110) cc_final: 0.8105 (m110)
  outliers start: 3
  outliers final: 1
  residues processed: 101
  average time/residue: 1.3675
  time to fit residues: 144.3689
Evaluate side-chains
  95 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   49 PHE
Chi-restraints excluded: chain b residue    1 MET
Chi-restraints excluded: chain b residue  209 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 74 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  28 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.120294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.100053 restraints weight = 23728.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 2.18
r_work: 0.3471 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3359 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.1022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7025  Z= 0.125
  Angle     :  0.555   8.406   9553  Z= 0.290
  Chirality :  0.044   0.242   1042
  Planarity :  0.004   0.036   1237
  Dihedral  : 14.954 162.960   1093
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 20.93 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.28), residues: 853
  helix:  0.59 (0.27), residues: 360
  sheet:  0.51 (0.45), residues: 151
  loop : -0.99 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG b 162 
 TYR   0.006   0.001   TYR a 224 
 PHE   0.016   0.001   PHE a  49 
 TRP   0.015   0.002   TRP a  21 
 HIS   0.003   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7025)
  covalent geometry    : angle       0.55534 ( 9553)
  hydrogen bonds       : bond        0.06654 (  276)
  hydrogen bonds       : angle       4.77617 (  795)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: a   49 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7311 (p90)
REVERT: a  113 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7163 (mt-10)
REVERT: a  120 ASP cc_start: 0.7931 (t70) cc_final: 0.7561 (t0)
REVERT: a  128 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8160 (mt0)
REVERT: a  255 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7567 (p90)
REVERT: b    1 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.6557 (ttp)
REVERT: b   86 ARG cc_start: 0.8182 (ttm170) cc_final: 0.7020 (tpt170)
REVERT: b  118 ASP cc_start: 0.8022 (t0) cc_final: 0.7577 (m-30)
REVERT: b  280 GLN cc_start: 0.8258 (pt0) cc_final: 0.7864 (pm20)
REVERT: b  320 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7587 (mtt90)
REVERT: b  359 ARG cc_start: 0.7875 (mtp-110) cc_final: 0.7607 (mtp-110)
REVERT: b  379 LYS cc_start: 0.8158 (mmpt) cc_final: 0.7862 (mtpt)
REVERT: b  416 ASN cc_start: 0.8173 (m110) cc_final: 0.7858 (m110)
  outliers start: 16
  outliers final: 5
  residues processed: 109
  average time/residue: 1.2909
  time to fit residues: 147.5579
Evaluate side-chains
  100 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   49 PHE
Chi-restraints excluded: chain a residue  255 PHE
Chi-restraints excluded: chain a residue  414 GLU
Chi-restraints excluded: chain a residue  423 GLU
Chi-restraints excluded: chain b residue    1 MET
Chi-restraints excluded: chain b residue  172 SER
Chi-restraints excluded: chain b residue  316 VAL
Chi-restraints excluded: chain b residue  335 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 7 optimal weight:    0.4980
   chunk 70 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** a 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 414 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.118961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.098646 restraints weight = 23980.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 2.17
r_work: 0.3445 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.1160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7025  Z= 0.160
  Angle     :  0.550   5.457   9553  Z= 0.289
  Chirality :  0.045   0.236   1042
  Planarity :  0.004   0.041   1237
  Dihedral  : 13.107 171.380   1091
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 2.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 20.11 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.28), residues: 853
  helix:  0.91 (0.27), residues: 361
  sheet:  0.53 (0.43), residues: 157
  loop : -1.02 (0.31), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG b 162 
 TYR   0.007   0.001   TYR b  59 
 PHE   0.016   0.001   PHE a  49 
 TRP   0.014   0.002   TRP a  21 
 HIS   0.004   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 7025)
  covalent geometry    : angle       0.54967 ( 9553)
  hydrogen bonds       : bond        0.06903 (  276)
  hydrogen bonds       : angle       4.53646 (  795)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a  120 ASP cc_start: 0.7948 (t70) cc_final: 0.7621 (t0)
REVERT: a  255 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7615 (p90)
REVERT: b    1 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6568 (ttp)
REVERT: b   86 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7058 (tpm170)
REVERT: b  118 ASP cc_start: 0.8073 (t0) cc_final: 0.7610 (m-30)
REVERT: b  280 GLN cc_start: 0.8316 (pt0) cc_final: 0.7921 (pm20)
REVERT: b  320 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.7516 (mtt90)
REVERT: b  359 ARG cc_start: 0.7840 (mtp-110) cc_final: 0.7557 (mtp-110)
REVERT: b  362 LYS cc_start: 0.8363 (mmtp) cc_final: 0.8143 (mmtt)
REVERT: b  379 LYS cc_start: 0.8225 (mmpt) cc_final: 0.7933 (mtpt)
REVERT: b  416 ASN cc_start: 0.8172 (m110) cc_final: 0.7846 (m110)
  outliers start: 22
  outliers final: 9
  residues processed: 109
  average time/residue: 1.3063
  time to fit residues: 149.3856
Evaluate side-chains
  101 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   49 PHE
Chi-restraints excluded: chain a residue  158 SER
Chi-restraints excluded: chain a residue  255 PHE
Chi-restraints excluded: chain a residue  414 GLU
Chi-restraints excluded: chain a residue  423 GLU
Chi-restraints excluded: chain b residue    1 MET
Chi-restraints excluded: chain b residue   88 ASP
Chi-restraints excluded: chain b residue  172 SER
Chi-restraints excluded: chain b residue  316 VAL
Chi-restraints excluded: chain b residue  335 SER
Chi-restraints excluded: chain b residue  339 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 16 optimal weight:    0.2980
   chunk 31 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0060
   chunk 33 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.7798

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

Flipped N/Q/H residues before XYZ refinement:
** a 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 292 GLN
b 414 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.121680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.101298 restraints weight = 23598.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 2.17
r_work: 0.3487 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   7025  Z= 0.104
  Angle     :  0.486   5.562   9553  Z= 0.257
  Chirality :  0.042   0.236   1042
  Planarity :  0.004   0.042   1237
  Dihedral  : 12.506 169.382   1091
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 2.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 21.20 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.29), residues: 853
  helix:  1.31 (0.27), residues: 362
  sheet:  0.56 (0.44), residues: 151
  loop : -1.01 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG b 162 
 TYR   0.006   0.001   TYR a 319 
 PHE   0.016   0.001   PHE a  49 
 TRP   0.012   0.001   TRP a  21 
 HIS   0.003   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 7025)
  covalent geometry    : angle       0.48649 ( 9553)
  hydrogen bonds       : bond        0.05050 (  276)
  hydrogen bonds       : angle       4.18135 (  795)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: a   49 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7301 (p90)
REVERT: a  120 ASP cc_start: 0.7898 (t70) cc_final: 0.7615 (t0)
REVERT: a  255 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7524 (p90)
REVERT: b    1 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6328 (ttp)
REVERT: b   86 ARG cc_start: 0.8164 (ttm170) cc_final: 0.7044 (tpm170)
REVERT: b  118 ASP cc_start: 0.8034 (t0) cc_final: 0.7592 (m-30)
REVERT: b  280 GLN cc_start: 0.8257 (pt0) cc_final: 0.7865 (pm20)
REVERT: b  320 ARG cc_start: 0.7719 (ttm-80) cc_final: 0.7516 (mtt90)
REVERT: b  379 LYS cc_start: 0.8169 (mmpt) cc_final: 0.7822 (mttm)
REVERT: b  416 ASN cc_start: 0.8154 (m110) cc_final: 0.7837 (m110)
  outliers start: 10
  outliers final: 5
  residues processed: 102
  average time/residue: 1.3397
  time to fit residues: 143.0838
Evaluate side-chains
  101 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   49 PHE
Chi-restraints excluded: chain a residue  255 PHE
Chi-restraints excluded: chain a residue  414 GLU
Chi-restraints excluded: chain a residue  423 GLU
Chi-restraints excluded: chain b residue    1 MET
Chi-restraints excluded: chain b residue  172 SER
Chi-restraints excluded: chain b residue  316 VAL
Chi-restraints excluded: chain b residue  335 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 81 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0370
   chunk 58 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.5062

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

Flipped N/Q/H residues before XYZ refinement:
** a 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 414 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.119734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.099283 restraints weight = 23860.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.19
r_work: 0.3457 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3345 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7025  Z= 0.146
  Angle     :  0.519   5.310   9553  Z= 0.273
  Chirality :  0.044   0.233   1042
  Planarity :  0.004   0.042   1237
  Dihedral  : 12.601 169.234   1091
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 2.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 20.52 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.28), residues: 853
  helix:  1.31 (0.27), residues: 361
  sheet:  0.67 (0.43), residues: 150
  loop : -0.94 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG b 162 
 TYR   0.007   0.001   TYR b  59 
 PHE   0.016   0.001   PHE a  49 
 TRP   0.013   0.002   TRP a  21 
 HIS   0.004   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 7025)
  covalent geometry    : angle       0.51862 ( 9553)
  hydrogen bonds       : bond        0.05874 (  276)
  hydrogen bonds       : angle       4.23507 (  795)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a  120 ASP cc_start: 0.7942 (t70) cc_final: 0.7646 (t0)
REVERT: a  255 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7556 (p90)
REVERT: b   86 ARG cc_start: 0.8188 (ttm170) cc_final: 0.7051 (tpm170)
REVERT: b  118 ASP cc_start: 0.8076 (t0) cc_final: 0.7599 (m-30)
REVERT: b  280 GLN cc_start: 0.8305 (pt0) cc_final: 0.7892 (pm20)
REVERT: b  320 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.7503 (mtt90)
REVERT: b  379 LYS cc_start: 0.8205 (mmpt) cc_final: 0.7952 (mtpt)
REVERT: b  416 ASN cc_start: 0.8180 (m110) cc_final: 0.7862 (m110)
  outliers start: 19
  outliers final: 10
  residues processed: 107
  average time/residue: 1.3546
  time to fit residues: 152.1088
Evaluate side-chains
  105 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   49 PHE
Chi-restraints excluded: chain a residue  158 SER
Chi-restraints excluded: chain a residue  255 PHE
Chi-restraints excluded: chain a residue  414 GLU
Chi-restraints excluded: chain a residue  423 GLU
Chi-restraints excluded: chain a residue  435 VAL
Chi-restraints excluded: chain b residue    1 MET
Chi-restraints excluded: chain b residue   88 ASP
Chi-restraints excluded: chain b residue  172 SER
Chi-restraints excluded: chain b residue  335 SER
Chi-restraints excluded: chain b residue  339 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** a 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.120994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.100556 restraints weight = 23675.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 2.18
r_work: 0.3479 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.1514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7025  Z= 0.114
  Angle     :  0.491   5.634   9553  Z= 0.258
  Chirality :  0.042   0.234   1042
  Planarity :  0.004   0.041   1237
  Dihedral  : 12.400 169.285   1091
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 20.79 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.29), residues: 853
  helix:  1.46 (0.28), residues: 361
  sheet:  0.66 (0.43), residues: 150
  loop : -0.87 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG b 162 
 TYR   0.006   0.001   TYR a 319 
 PHE   0.016   0.001   PHE a  49 
 TRP   0.013   0.001   TRP a  21 
 HIS   0.004   0.001   HIS a  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7025)
  covalent geometry    : angle       0.49111 ( 9553)
  hydrogen bonds       : bond        0.05158 (  276)
  hydrogen bonds       : angle       4.08870 (  795)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
REVERT: a   49 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.7354 (p90)
REVERT: a  120 ASP cc_start: 0.7931 (t70) cc_final: 0.7655 (t0)
REVERT: a  255 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7533 (p90)
REVERT: b   86 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7062 (tpm170)
REVERT: b  118 ASP cc_start: 0.8051 (t0) cc_final: 0.7601 (m-30)
REVERT: b  280 GLN cc_start: 0.8298 (pt0) cc_final: 0.7888 (pm20)
REVERT: b  320 ARG cc_start: 0.7707 (ttm-80) cc_final: 0.7487 (mtt90)
REVERT: b  379 LYS cc_start: 0.8193 (mmpt) cc_final: 0.7938 (mtpt)
REVERT: b  416 ASN cc_start: 0.8178 (m110) cc_final: 0.7877 (m110)
  outliers start: 14
  outliers final: 8
  residues processed: 106
  average time/residue: 1.3322
  time to fit residues: 148.6610
Evaluate side-chains
  104 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   49 PHE
Chi-restraints excluded: chain a residue  158 SER
Chi-restraints excluded: chain a residue  255 PHE
Chi-restraints excluded: chain a residue  342 GLN
Chi-restraints excluded: chain a residue  414 GLU
Chi-restraints excluded: chain a residue  435 VAL
Chi-restraints excluded: chain b residue    1 MET
Chi-restraints excluded: chain b residue  172 SER
Chi-restraints excluded: chain b residue  335 SER
Chi-restraints excluded: chain b residue  339 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 82 optimal weight:    0.6980
   chunk 75 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** a 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.121879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.100055 restraints weight = 24170.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 2.19
r_work: 0.3460 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3349 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.1536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7025  Z= 0.142
  Angle     :  0.513   5.408   9553  Z= 0.269
  Chirality :  0.044   0.233   1042
  Planarity :  0.004   0.039   1237
  Dihedral  : 12.532 177.089   1091
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 2.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 20.38 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.28), residues: 853
  helix:  1.39 (0.27), residues: 361
  sheet:  0.67 (0.43), residues: 150
  loop : -0.90 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG b 162 
 TYR   0.007   0.001   TYR a 161 
 PHE   0.016   0.001   PHE a  49 
 TRP   0.013   0.002   TRP a  21 
 HIS   0.004   0.001   HIS a  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 7025)
  covalent geometry    : angle       0.51340 ( 9553)
  hydrogen bonds       : bond        0.05686 (  276)
  hydrogen bonds       : angle       4.14845 (  795)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a  120 ASP cc_start: 0.7935 (t70) cc_final: 0.7655 (t0)
REVERT: a  255 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7524 (p90)
REVERT: b   86 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7059 (tpm170)
REVERT: b  118 ASP cc_start: 0.8069 (t0) cc_final: 0.7569 (m-30)
REVERT: b  147 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8061 (ttt)
REVERT: b  280 GLN cc_start: 0.8319 (pt0) cc_final: 0.7923 (pm20)
REVERT: b  320 ARG cc_start: 0.7691 (ttm-80) cc_final: 0.7472 (mtt90)
REVERT: b  379 LYS cc_start: 0.8207 (mmpt) cc_final: 0.7959 (mtpt)
REVERT: b  416 ASN cc_start: 0.8201 (m110) cc_final: 0.7896 (m110)
  outliers start: 15
  outliers final: 9
  residues processed: 103
  average time/residue: 1.3489
  time to fit residues: 145.9147
Evaluate side-chains
  102 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   49 PHE
Chi-restraints excluded: chain a residue  158 SER
Chi-restraints excluded: chain a residue  255 PHE
Chi-restraints excluded: chain a residue  342 GLN
Chi-restraints excluded: chain a residue  414 GLU
Chi-restraints excluded: chain a residue  435 VAL
Chi-restraints excluded: chain b residue    1 MET
Chi-restraints excluded: chain b residue  147 MET
Chi-restraints excluded: chain b residue  172 SER
Chi-restraints excluded: chain b residue  335 SER
Chi-restraints excluded: chain b residue  339 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 71 optimal weight:    0.4980
   chunk 0 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** a 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.121398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.100812 restraints weight = 23414.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 2.18
r_work: 0.3488 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7025  Z= 0.106
  Angle     :  0.483   5.756   9553  Z= 0.253
  Chirality :  0.042   0.233   1042
  Planarity :  0.004   0.040   1237
  Dihedral  : 12.039 169.712   1091
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 20.93 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.29), residues: 853
  helix:  1.59 (0.28), residues: 361
  sheet:  0.59 (0.43), residues: 152
  loop : -0.79 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG b 162 
 TYR   0.006   0.001   TYR a 319 
 PHE   0.016   0.001   PHE a  49 
 TRP   0.012   0.001   TRP a  21 
 HIS   0.003   0.001   HIS a  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 7025)
  covalent geometry    : angle       0.48312 ( 9553)
  hydrogen bonds       : bond        0.04851 (  276)
  hydrogen bonds       : angle       3.98970 (  795)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: a   49 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7345 (p90)
REVERT: a  120 ASP cc_start: 0.7906 (t70) cc_final: 0.7648 (t0)
REVERT: a  255 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7505 (p90)
REVERT: b   86 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7056 (tpm170)
REVERT: b  118 ASP cc_start: 0.8065 (t0) cc_final: 0.7594 (m-30)
REVERT: b  280 GLN cc_start: 0.8346 (pt0) cc_final: 0.7958 (pm20)
REVERT: b  320 ARG cc_start: 0.7630 (ttm-80) cc_final: 0.7416 (mtt90)
REVERT: b  379 LYS cc_start: 0.8180 (mmpt) cc_final: 0.7838 (mttm)
REVERT: b  416 ASN cc_start: 0.8166 (m110) cc_final: 0.7844 (m110)
  outliers start: 13
  outliers final: 7
  residues processed: 103
  average time/residue: 1.3628
  time to fit residues: 147.7556
Evaluate side-chains
  101 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   49 PHE
Chi-restraints excluded: chain a residue  158 SER
Chi-restraints excluded: chain a residue  255 PHE
Chi-restraints excluded: chain a residue  414 GLU
Chi-restraints excluded: chain a residue  435 VAL
Chi-restraints excluded: chain b residue    1 MET
Chi-restraints excluded: chain b residue  172 SER
Chi-restraints excluded: chain b residue  335 SER
Chi-restraints excluded: chain b residue  339 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 82 optimal weight:    0.0000
   chunk 19 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 70 optimal weight:    0.4980
   chunk 22 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
** a 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.122016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.101493 restraints weight = 23672.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.19
r_work: 0.3489 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3378 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7025  Z= 0.105
  Angle     :  0.482   5.807   9553  Z= 0.252
  Chirality :  0.042   0.234   1042
  Planarity :  0.004   0.040   1237
  Dihedral  : 11.623 170.228   1091
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 21.34 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.29), residues: 853
  helix:  1.64 (0.28), residues: 364
  sheet:  0.54 (0.44), residues: 153
  loop : -0.83 (0.32), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG b 162 
 TYR   0.005   0.001   TYR b 310 
 PHE   0.015   0.001   PHE a  49 
 TRP   0.012   0.001   TRP a  21 
 HIS   0.003   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 7025)
  covalent geometry    : angle       0.48214 ( 9553)
  hydrogen bonds       : bond        0.04719 (  276)
  hydrogen bonds       : angle       3.93697 (  795)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   49 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7336 (p90)
REVERT: a  120 ASP cc_start: 0.7896 (t70) cc_final: 0.7645 (t0)
REVERT: a  255 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7497 (p90)
REVERT: b   86 ARG cc_start: 0.8166 (ttm170) cc_final: 0.7050 (tpm170)
REVERT: b  118 ASP cc_start: 0.8072 (t0) cc_final: 0.7580 (m-30)
REVERT: b  280 GLN cc_start: 0.8332 (pt0) cc_final: 0.7928 (pm20)
REVERT: b  320 ARG cc_start: 0.7603 (ttm-80) cc_final: 0.7385 (mtt90)
REVERT: b  379 LYS cc_start: 0.8182 (mmpt) cc_final: 0.7840 (mttm)
REVERT: b  416 ASN cc_start: 0.8161 (m110) cc_final: 0.7859 (m110)
  outliers start: 10
  outliers final: 7
  residues processed: 104
  average time/residue: 1.3532
  time to fit residues: 148.0140
Evaluate side-chains
  102 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   49 PHE
Chi-restraints excluded: chain a residue  158 SER
Chi-restraints excluded: chain a residue  255 PHE
Chi-restraints excluded: chain a residue  342 GLN
Chi-restraints excluded: chain a residue  414 GLU
Chi-restraints excluded: chain a residue  435 VAL
Chi-restraints excluded: chain b residue    1 MET
Chi-restraints excluded: chain b residue  172 SER
Chi-restraints excluded: chain b residue  335 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   chunk 69 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 28 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** a 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.122833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.102156 restraints weight = 23599.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 2.20
r_work: 0.3489 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3377 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.1812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   7025  Z= 0.095
  Angle     :  0.475   5.912   9553  Z= 0.246
  Chirality :  0.042   0.236   1042
  Planarity :  0.004   0.039   1237
  Dihedral  : 11.241 170.926   1091
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 2.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 21.34 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.29), residues: 853
  helix:  1.75 (0.28), residues: 364
  sheet:  0.53 (0.44), residues: 153
  loop : -0.77 (0.32), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG b 162 
 TYR   0.005   0.001   TYR a 319 
 PHE   0.015   0.001   PHE a  49 
 TRP   0.011   0.001   TRP a  21 
 HIS   0.003   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 7025)
  covalent geometry    : angle       0.47501 ( 9553)
  hydrogen bonds       : bond        0.04373 (  276)
  hydrogen bonds       : angle       3.84165 (  795)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
REVERT: a   49 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7259 (p90)
REVERT: a  120 ASP cc_start: 0.7841 (t70) cc_final: 0.7614 (t0)
REVERT: a  255 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7356 (p90)
REVERT: b   86 ARG cc_start: 0.8141 (ttm170) cc_final: 0.6930 (tpm170)
REVERT: b  118 ASP cc_start: 0.8037 (t0) cc_final: 0.7522 (m-30)
REVERT: b  280 GLN cc_start: 0.8347 (pt0) cc_final: 0.7928 (pm20)
REVERT: b  320 ARG cc_start: 0.7595 (ttm-80) cc_final: 0.7376 (mtt90)
REVERT: b  379 LYS cc_start: 0.8139 (mmpt) cc_final: 0.7792 (mttm)
REVERT: b  416 ASN cc_start: 0.8150 (m110) cc_final: 0.7842 (m110)
  outliers start: 9
  outliers final: 6
  residues processed: 104
  average time/residue: 1.3065
  time to fit residues: 143.1857
Evaluate side-chains
  103 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   49 PHE
Chi-restraints excluded: chain a residue  158 SER
Chi-restraints excluded: chain a residue  255 PHE
Chi-restraints excluded: chain a residue  342 GLN
Chi-restraints excluded: chain a residue  414 GLU
Chi-restraints excluded: chain b residue    1 MET
Chi-restraints excluded: chain b residue  172 SER
Chi-restraints excluded: chain b residue  335 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0980
   chunk 10 optimal weight:    4.9990
   chunk 51 optimal weight:    0.3980
   chunk 28 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** a 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b  15 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.121581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.100964 restraints weight = 23835.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 2.21
r_work: 0.3491 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7025  Z= 0.117
  Angle     :  0.493   5.690   9553  Z= 0.258
  Chirality :  0.043   0.234   1042
  Planarity :  0.004   0.039   1237
  Dihedral  : 11.325 170.898   1091
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 21.61 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.29), residues: 853
  helix:  1.68 (0.28), residues: 362
  sheet:  0.54 (0.44), residues: 153
  loop : -0.81 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG b 162 
 TYR   0.005   0.001   TYR b  59 
 PHE   0.015   0.001   PHE a  49 
 TRP   0.012   0.001   TRP a  21 
 HIS   0.003   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7025)
  covalent geometry    : angle       0.49294 ( 9553)
  hydrogen bonds       : bond        0.04885 (  276)
  hydrogen bonds       : angle       3.92588 (  795)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5252.11 seconds
wall clock time: 89 minutes 36.08 seconds (5376.08 seconds total)