Starting phenix.real_space_refine
on Sat Aug 23 15:45:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uoy_42441/08_2025/8uoy_42441.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uoy_42441/08_2025/8uoy_42441.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uoy_42441/08_2025/8uoy_42441.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uoy_42441/08_2025/8uoy_42441.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uoy_42441/08_2025/8uoy_42441.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uoy_42441/08_2025/8uoy_42441.cif"
  }
  resolution = 3.4
  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=  -0.000 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    4182      2.51       5
     N    1122      2.21       5
     O    1318      1.98       5
     H    6544      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13188
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 6594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 436, 6594
          Classifications: {'peptide': 436}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 424}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "C"
      Number of atoms: 6594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 436, 6594
          Classifications: {'peptide': 436}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 424}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 21
  Time building chain proxies: 2.88, per 1000 atoms: 0.22
  Number of scatterers: 13188
  At special positions: 0
  Unit cell: (119.658, 76.538, 86.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      22     16.00
     O    1318      8.00
     N    1122      7.00
     C    4182      6.00
     H    6544      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: 1.21
  Conformation dependent library (CDL) restraints added in 429.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1564

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 7 sheets defined
      43.2% alpha, 11.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'B' and resid 66 through 71
    Processing helix  chain 'B' and resid 75 through 80
      removed outlier: 3.562A  pdb=" N   ALA B  78 " --> pdb=" O   ILE B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 99
      removed outlier: 3.944A  pdb=" N   ALA B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 127
      removed outlier: 3.516A  pdb=" N   ALA B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 135
    Processing helix  chain 'B' and resid 152 through 156
      removed outlier: 4.281A  pdb=" N   HIS B 155 " --> pdb=" O   GLY B 152 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   SER B 156 " --> pdb=" O   GLY B 153 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 152 through 156'
    Processing helix  chain 'B' and resid 174 through 179
    Processing helix  chain 'B' and resid 180 through 182
      No H-bonds generated for 'chain 'B' and resid 180 through 182'
    Processing helix  chain 'B' and resid 183 through 197
      removed outlier: 3.660A  pdb=" N   HIS B 187 " --> pdb=" O   ALA B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 229
      removed outlier: 4.156A  pdb=" N   ILE B 222 " --> pdb=" O   GLY B 218 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   ILE B 226 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   GLU B 227 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 249
    Processing helix  chain 'B' and resid 259 through 262
    Processing helix  chain 'B' and resid 273 through 280
      removed outlier: 3.866A  pdb=" N   ASP B 277 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 310
      removed outlier: 4.261A  pdb=" N   GLU B 308 " --> pdb=" O   LYS B 304 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU B 310 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 335
    Processing helix  chain 'B' and resid 346 through 349
      removed outlier: 3.785A  pdb=" N   GLY B 349 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 346 through 349'
    Processing helix  chain 'B' and resid 350 through 364
    Processing helix  chain 'B' and resid 380 through 390
      removed outlier: 4.170A  pdb=" N   ALA B 386 " --> pdb=" O   ILE B 382 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   VAL B 387 " --> pdb=" O   ALA B 383 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   THR B 389 " --> pdb=" O   ILE B 385 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   ASN B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 401 through 406
    Processing helix  chain 'B' and resid 407 through 416
      removed outlier: 4.413A  pdb=" N   ARG B 413 " --> pdb=" O   ASN B 409 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 62
    Processing helix  chain 'C' and resid 64 through 79
      removed outlier: 5.887A  pdb=" N   ASN C  73 " --> pdb=" O   ASP C  69 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ILE C  74 " --> pdb=" O   ASN C  70 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ALA C  76 " --> pdb=" O   ASN C  72 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLU C  77 " --> pdb=" O   ASN C  73 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ALA C  78 " --> pdb=" O   ILE C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 99
      removed outlier: 3.581A  pdb=" N   ILE C  95 " --> pdb=" O   ASP C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 119
    Processing helix  chain 'C' and resid 122 through 127
    Processing helix  chain 'C' and resid 129 through 136
    Processing helix  chain 'C' and resid 153 through 156
      removed outlier: 3.521A  pdb=" N   SER C 156 " --> pdb=" O   GLY C 153 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 153 through 156'
    Processing helix  chain 'C' and resid 174 through 179
    Processing helix  chain 'C' and resid 184 through 197
      removed outlier: 3.953A  pdb=" N   ALA C 188 " --> pdb=" O   GLU C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 215 through 229
      removed outlier: 3.936A  pdb=" N   VAL C 219 " --> pdb=" O   THR C 215 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLU C 220 " --> pdb=" O   GLU C 216 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE C 222 " --> pdb=" O   GLY C 218 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   LEU C 223 " --> pdb=" O   VAL C 219 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 249
    Processing helix  chain 'C' and resid 260 through 262
      No H-bonds generated for 'chain 'C' and resid 260 through 262'
    Processing helix  chain 'C' and resid 271 through 280
      removed outlier: 3.507A  pdb=" N   GLU C 280 " --> pdb=" O   VAL C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 281 through 284
    Processing helix  chain 'C' and resid 299 through 311
      removed outlier: 4.415A  pdb=" N   THR C 307 " --> pdb=" O   TRP C 303 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   GLU C 308 " --> pdb=" O   LYS C 304 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   ARG C 309 " --> pdb=" O   VAL C 305 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 325 through 335
      removed outlier: 3.685A  pdb=" N   LYS C 334 " --> pdb=" O   ALA C 330 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 346 through 348
      No H-bonds generated for 'chain 'C' and resid 346 through 348'
    Processing helix  chain 'C' and resid 350 through 365
      removed outlier: 3.705A  pdb=" N   ALA C 364 " --> pdb=" O   MET C 360 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 380 through 385
      removed outlier: 3.690A  pdb=" N   ASP C 384 " --> pdb=" O   SER C 380 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 401 through 409
      removed outlier: 4.674A  pdb=" N   LYS C 407 " --> pdb=" O   ASP C 403 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 409 through 419
      removed outlier: 5.245A  pdb=" N   GLU C 415 " --> pdb=" O   LEU C 411 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 420 through 422
      No H-bonds generated for 'chain 'C' and resid 420 through 422'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 14
      removed outlier: 4.036A  pdb=" N   ASP B   6 " --> pdb=" O   TYR B  26 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL B  12 " --> pdb=" O   THR B  20 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASN B  18 " --> pdb=" O   ASP B  14 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 144 through 145
      removed outlier: 6.252A  pdb=" N   THR B 144 " --> pdb=" O   ILE B 394 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 169
      removed outlier: 3.836A  pdb=" N   GLU B 164 " --> pdb=" O   ASP B 243 " (cutoff:3.500A)
      removed outlier: 8.653A  pdb=" N   ILE B 288 " --> pdb=" O   ILE B 238 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ILE B 240 " --> pdb=" O   ILE B 288 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   ILE B 289 " --> pdb=" O   GLN B 315 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   VAL B 317 " --> pdb=" O   ILE B 289 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ILE B 291 " --> pdb=" O   VAL B 317 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   LEU B 316 " --> pdb=" O   SER B 340 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   LEU B 342 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   GLY B 318 " --> pdb=" O   LEU B 342 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   LYS B 344 " --> pdb=" O   GLY B 318 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ILE B 341 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   SER B 371 " --> pdb=" O   ILE B 341 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   ILE B 343 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 250 through 251
    Processing sheet with id=AA5, first strand: chain 'C' and resid 8 through 10
      removed outlier: 4.227A  pdb=" N   TYR C   8 " --> pdb=" O   GLU C  24 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 144 through 151
      removed outlier: 5.462A  pdb=" N   ASN C 148 " --> pdb=" O   ILE C 167 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   ILE C 167 " --> pdb=" O   ASN C 148 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ILE C 150 " --> pdb=" O   PHE C 165 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ILE C 240 " --> pdb=" O   THR C 290 " (cutoff:3.500A)
      removed outlier: 8.427A  pdb=" N   GLU C 292 " --> pdb=" O   ILE C 240 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   PHE C 242 " --> pdb=" O   GLU C 292 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ALA C 368 " --> pdb=" O   GLN C 393 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   LYS C 395 " --> pdb=" O   ALA C 368 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL C 370 " --> pdb=" O   LYS C 395 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   THR C 144 " --> pdb=" O   ILE C 394 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 250 through 251

    228 hydrogen bonds defined for protein.
    648 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: 3.09

  Time building geometry restraints manager: 1.73 seconds

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

  Histogram of bond lengths:
        0.90 -     1.08: 1954
        1.08 -     1.27: 5778
        1.27 -     1.46: 1743
        1.46 -     1.65: 3777
        1.65 -     1.83: 42
  Bond restraints: 13294
  Sorted by residual:
  bond pdb=" CG  ASP B 301 "
       pdb=" OD1 ASP B 301 "
    ideal  model  delta    sigma   weight residual
    1.249  1.080  0.169 1.90e-02 2.77e+03 7.93e+01
  bond pdb=" CB  ASP B 301 "
       pdb=" CG  ASP B 301 "
    ideal  model  delta    sigma   weight residual
    1.516  1.322  0.194 2.50e-02 1.60e+03 6.01e+01
  bond pdb=" CE1 TYR C  59 "
       pdb=" HE1 TYR C  59 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" N   LEU C 351 "
       pdb=" H   LEU C 351 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" N   LEU B  51 "
       pdb=" H   LEU B  51 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.66e+01
  ... (remaining 13289 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 18171
        2.30 -     4.60: 4437
        4.60 -     6.91: 987
        6.91 -     9.21: 393
        9.21 -    11.51: 34
  Bond angle restraints: 24022
  Sorted by residual:
  angle pdb=" CA  PHE C 249 "
        pdb=" CB  PHE C 249 "
        pdb=" CG  PHE C 249 "
      ideal   model   delta    sigma   weight residual
     113.80  122.09   -8.29 1.00e+00 1.00e+00 6.87e+01
  angle pdb=" CA  ASN C 236 "
        pdb=" CB  ASN C 236 "
        pdb=" CG  ASN C 236 "
      ideal   model   delta    sigma   weight residual
     112.60  120.58   -7.98 1.00e+00 1.00e+00 6.36e+01
  angle pdb=" C   LEU B  62 "
        pdb=" N   GLY B  63 "
        pdb=" CA  GLY B  63 "
      ideal   model   delta    sigma   weight residual
     120.31  128.40   -8.09 1.02e+00 9.61e-01 6.30e+01
  angle pdb=" CA  ASN C 284 "
        pdb=" CB  ASN C 284 "
        pdb=" CG  ASN C 284 "
      ideal   model   delta    sigma   weight residual
     112.60  120.24   -7.64 1.00e+00 1.00e+00 5.83e+01
  angle pdb=" CA  ASP B 301 "
        pdb=" CB  ASP B 301 "
        pdb=" CG  ASP B 301 "
      ideal   model   delta    sigma   weight residual
     112.60  120.21   -7.61 1.00e+00 1.00e+00 5.79e+01
  ... (remaining 24017 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.79: 5349
       16.79 -    33.59: 568
       33.59 -    50.38: 182
       50.38 -    67.17: 97
       67.17 -    83.97: 16
  Dihedral angle restraints: 6212
    sinusoidal: 3390
      harmonic: 2822
  Sorted by residual:
  dihedral pdb=" C   ILE B 222 "
           pdb=" N   ILE B 222 "
           pdb=" CA  ILE B 222 "
           pdb=" CB  ILE B 222 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -140.12   18.12     0      2.50e+00 1.60e-01 5.25e+01
  dihedral pdb=" CA  MET B 239 "
           pdb=" C   MET B 239 "
           pdb=" N   ILE B 240 "
           pdb=" CA  ILE B 240 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.43  -29.57     0      5.00e+00 4.00e-02 3.50e+01
  dihedral pdb=" CA  HIS C 372 "
           pdb=" C   HIS C 372 "
           pdb=" N   ARG C 373 "
           pdb=" CA  ARG C 373 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.43   29.57     0      5.00e+00 4.00e-02 3.50e+01
  ... (remaining 6209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 703
       0.106 -    0.213: 258
       0.213 -    0.319: 54
       0.319 -    0.425: 7
       0.425 -    0.532: 4
  Chirality restraints: 1026
  Sorted by residual:
  chirality pdb=" CA  THR B  64 "
            pdb=" N   THR B  64 "
            pdb=" C   THR B  64 "
            pdb=" CB  THR B  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.99    0.53 2.00e-01 2.50e+01 7.06e+00
  chirality pdb=" CA  ILE B 222 "
            pdb=" N   ILE B 222 "
            pdb=" C   ILE B 222 "
            pdb=" CB  ILE B 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.91    0.52 2.00e-01 2.50e+01 6.79e+00
  chirality pdb=" CA  LYS C 434 "
            pdb=" N   LYS C 434 "
            pdb=" C   LYS C 434 "
            pdb=" CB  LYS C 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.49e+00
  ... (remaining 1023 not shown)

  Planarity restraints: 2046
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 181 "   -0.316 2.00e-02 2.50e+03   1.10e-01 4.81e+02
        pdb=" CG  TRP C 181 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 181 "    0.072 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 181 "    0.066 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 181 "    0.116 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 181 "    0.043 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 181 "    0.092 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 181 "   -0.053 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 181 "    0.042 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 181 "   -0.059 2.00e-02 2.50e+03
        pdb=" HD1 TRP C 181 "   -0.012 2.00e-02 2.50e+03
        pdb=" HE1 TRP C 181 "    0.075 2.00e-02 2.50e+03
        pdb=" HE3 TRP C 181 "    0.126 2.00e-02 2.50e+03
        pdb=" HZ2 TRP C 181 "   -0.107 2.00e-02 2.50e+03
        pdb=" HZ3 TRP C 181 "    0.044 2.00e-02 2.50e+03
        pdb=" HH2 TRP C 181 "   -0.126 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  82 "   -0.267 2.00e-02 2.50e+03   1.09e-01 3.55e+02
        pdb=" CG  TYR B  82 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  82 "    0.074 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  82 "    0.086 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  82 "    0.051 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  82 "    0.049 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  82 "   -0.016 2.00e-02 2.50e+03
        pdb=" OH  TYR B  82 "   -0.201 2.00e-02 2.50e+03
        pdb=" HD1 TYR B  82 "    0.066 2.00e-02 2.50e+03
        pdb=" HD2 TYR B  82 "    0.074 2.00e-02 2.50e+03
        pdb=" HE1 TYR B  82 "    0.031 2.00e-02 2.50e+03
        pdb=" HE2 TYR B  82 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  34 "   -0.679 9.50e-02 1.11e+02   2.47e-01 2.71e+02
        pdb=" NE  ARG B  34 "   -0.084 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  34 "   -0.057 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  34 "   -0.059 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  34 "   -0.026 2.00e-02 2.50e+03
        pdb="HH11 ARG B  34 "    0.208 2.00e-02 2.50e+03
        pdb="HH12 ARG B  34 "   -0.072 2.00e-02 2.50e+03
        pdb="HH21 ARG B  34 "    0.154 2.00e-02 2.50e+03
        pdb="HH22 ARG B  34 "   -0.034 2.00e-02 2.50e+03
  ... (remaining 2043 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 925
        2.18 -     2.79: 23119
        2.79 -     3.39: 37363
        3.39 -     4.00: 47978
        4.00 -     4.60: 71199
  Nonbonded interactions: 180584
  Sorted by model distance:
  nonbonded pdb=" HG  SER C 246 "
            pdb=" O   ASP C 293 "
     model   vdw
     1.575 2.450
  nonbonded pdb=" HG  SER B 247 "
            pdb=" OD1 ASP B 296 "
     model   vdw
     1.590 2.450
  nonbonded pdb=" OD1 ASP C  98 "
            pdb=" HG1 THR C 100 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" HH  TYR B 257 "
            pdb=" OD2 ASP B 299 "
     model   vdw
     1.601 2.450
  nonbonded pdb=" HG1 THR C 271 "
            pdb=" OE1 GLU C 274 "
     model   vdw
     1.603 2.450
  ... (remaining 180579 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

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:             0.780
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.650
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2472
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      :  0.016   0.194   6750  Z= 0.975
  Angle     :  2.246  11.081   9128  Z= 1.461
  Chirality :  0.113   0.532   1026
  Planarity :  0.019   0.226   1198
  Dihedral  : 17.124  83.965   2470
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 0.83
  Ramachandran Plot:
    Outliers :  2.65 %
    Allowed  : 12.10 %
    Favored  : 85.25 %
  Rotamer:
    Outliers :  6.89 %
    Allowed  :  9.24 %
    Favored  : 83.87 %
  Cbeta Deviations :  1.28 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.89 (0.24), residues: 868
  helix: -3.32 (0.20), residues: 303
  sheet: -1.58 (0.76), residues: 45
  loop : -2.27 (0.25), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  85 
 TYR   0.229   0.028   TYR B  82 
 PHE   0.128   0.019   PHE C 249 
 TRP   0.209   0.039   TRP C 181 
 HIS   0.013   0.004   HIS C 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.01568 ( 6750)
  covalent geometry    : angle       2.24587 ( 9128)
  hydrogen bonds       : bond        0.17939 (  228)
  hydrogen bonds       : angle      10.47586 (  648)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 76
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    6 ASP cc_start: 0.6247 (p0) cc_final: 0.4794 (m-30)
REVERT: B   36 MET cc_start: -0.0763 (OUTLIER) cc_final: -0.2787 (pmt)
REVERT: B   65 GLN cc_start: 0.3000 (tp40) cc_final: 0.1919 (tp40)
REVERT: B  124 ASP cc_start: 0.2300 (OUTLIER) cc_final: 0.2038 (m-30)
REVERT: B  147 MET cc_start: 0.1162 (ptp) cc_final: 0.0918 (ptt)
REVERT: B  213 GLU cc_start: 0.3711 (OUTLIER) cc_final: 0.2465 (tp30)
REVERT: B  274 GLU cc_start: 0.2338 (OUTLIER) cc_final: 0.1550 (mt-10)
REVERT: B  282 LEU cc_start: 0.1614 (OUTLIER) cc_final: 0.0893 (tt)
REVERT: B  284 ASN cc_start: 0.3150 (OUTLIER) cc_final: 0.0099 (m-40)
REVERT: B  301 ASP cc_start: 0.2824 (OUTLIER) cc_final: 0.2156 (t0)
REVERT: B  309 ARG cc_start: 0.4183 (OUTLIER) cc_final: 0.2286 (tpt170)
REVERT: C    1 MET cc_start: 0.2811 (mmt) cc_final: 0.2413 (mmt)
REVERT: C   77 GLU cc_start: 0.0585 (OUTLIER) cc_final: -0.0529 (pp20)
REVERT: C   85 ARG cc_start: 0.3713 (mtm180) cc_final: 0.0636 (ttp80)
REVERT: C  181 TRP cc_start: 0.2747 (OUTLIER) cc_final: 0.2024 (m-10)
REVERT: C  261 LYS cc_start: 0.3104 (tptt) cc_final: 0.2753 (tptp)
REVERT: C  362 LYS cc_start: 0.2445 (OUTLIER) cc_final: 0.0412 (tmmt)
  outliers start: 47
  outliers final: 25
  residues processed: 119
  average time/residue: 0.2160
  time to fit residues: 33.8144
Evaluate side-chains
  97 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 61
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  124 ASP
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  222 ILE
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  301 ASP
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   68 VAL
Chi-restraints excluded: chain C residue   72 ASN
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  156 SER
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  249 PHE
Chi-restraints excluded: chain C residue  309 ARG
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  372 HIS
Chi-restraints excluded: chain C residue  424 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
C  18 ASN
C  72 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5410 r_free = 0.5410 target = 0.360004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.5403 r_free = 0.5403 target = 0.359093 restraints weight = 26583.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.5403 rms_B_bonded: 0.18
r_work: 0.5394 rms_B_bonded: 0.32 restraints_weight: 0.5000
r_work: 0.5368 rms_B_bonded: 1.01 restraints_weight: 0.2500
r_work (final): 0.5368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2394
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.092   6750  Z= 0.194
  Angle     :  0.867  11.219   9128  Z= 0.473
  Chirality :  0.047   0.170   1026
  Planarity :  0.006   0.069   1198
  Dihedral  : 12.442  71.601   1029
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  9.91 %
    Favored  : 89.63 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 12.76 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.59 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.35 (0.26), residues: 868
  helix: -2.22 (0.26), residues: 304
  sheet: -2.97 (0.44), residues: 112
  loop : -1.96 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 270 
 TYR   0.023   0.002   TYR B 408 
 PHE   0.026   0.002   PHE B 249 
 TRP   0.006   0.001   TRP B 181 
 HIS   0.004   0.002   HIS C 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 6750)
  covalent geometry    : angle       0.86742 ( 9128)
  hydrogen bonds       : bond        0.05798 (  228)
  hydrogen bonds       : angle       8.13319 (  648)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 61
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 ASP cc_start: 0.0839 (OUTLIER) cc_final: 0.0496 (m-30)
REVERT: B  126 LEU cc_start: 0.0195 (OUTLIER) cc_final: -0.1443 (mt)
REVERT: B  132 THR cc_start: 0.3059 (OUTLIER) cc_final: 0.2438 (p)
REVERT: B  147 MET cc_start: 0.0993 (ptp) cc_final: 0.0767 (ptt)
REVERT: B  274 GLU cc_start: 0.2484 (OUTLIER) cc_final: 0.1455 (mt-10)
REVERT: B  284 ASN cc_start: 0.2790 (OUTLIER) cc_final: -0.0646 (m110)
REVERT: B  309 ARG cc_start: 0.4218 (OUTLIER) cc_final: 0.1518 (mmm160)
REVERT: C    1 MET cc_start: 0.2561 (mmt) cc_final: 0.0835 (ttp)
REVERT: C   36 MET cc_start: 0.2451 (OUTLIER) cc_final: 0.1923 (tpp)
REVERT: C   77 GLU cc_start: 0.0615 (OUTLIER) cc_final: -0.0004 (pp20)
REVERT: C   85 ARG cc_start: 0.3476 (mtm180) cc_final: 0.1978 (ttt180)
REVERT: C  146 MET cc_start: 0.0373 (ptm) cc_final: 0.0039 (ptm)
REVERT: C  181 TRP cc_start: 0.2431 (OUTLIER) cc_final: 0.1860 (m-10)
REVERT: C  261 LYS cc_start: 0.3447 (tptt) cc_final: 0.2914 (tptp)
REVERT: C  276 VAL cc_start: 0.0836 (OUTLIER) cc_final: -0.0039 (t)
REVERT: C  362 LYS cc_start: 0.2058 (OUTLIER) cc_final: -0.0165 (tmmt)
  outliers start: 38
  outliers final: 22
  residues processed: 95
  average time/residue: 0.2052
  time to fit residues: 26.0481
Evaluate side-chains
  84 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 51
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  124 ASP
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  429 SER
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   68 VAL
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  249 PHE
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  372 HIS
Chi-restraints excluded: chain C residue  389 THR
Chi-restraints excluded: chain C residue  424 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 37 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 78 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
B 284 ASN
C 155 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5399 r_free = 0.5399 target = 0.359041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5317 r_free = 0.5317 target = 0.348834 restraints weight = 273906.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.5293 rms_B_bonded: 6.82
r_work (final): 0.5293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2561
moved from start:          0.3385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.108   6750  Z= 0.203
  Angle     :  0.800  10.771   9128  Z= 0.435
  Chirality :  0.046   0.158   1026
  Planarity :  0.006   0.073   1198
  Dihedral  : 11.279  73.264   1003
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 11.06 %
    Favored  : 88.82 %
  Rotamer:
    Outliers :  6.45 %
    Allowed  : 14.37 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.59 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.19 (0.26), residues: 868
  helix: -1.74 (0.28), residues: 299
  sheet: -3.04 (0.43), residues: 112
  loop : -2.10 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  58 
 TYR   0.022   0.002   TYR B 408 
 PHE   0.035   0.002   PHE C 249 
 TRP   0.009   0.002   TRP C 181 
 HIS   0.004   0.001   HIS B   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 6750)
  covalent geometry    : angle       0.79983 ( 9128)
  hydrogen bonds       : bond        0.04897 (  228)
  hydrogen bonds       : angle       7.64240 (  648)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 56
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 ASP cc_start: 0.0472 (OUTLIER) cc_final: 0.0120 (m-30)
REVERT: B  126 LEU cc_start: -0.0039 (OUTLIER) cc_final: -0.1642 (mt)
REVERT: B  132 THR cc_start: 0.2995 (OUTLIER) cc_final: 0.2442 (p)
REVERT: B  133 TYR cc_start: 0.2099 (OUTLIER) cc_final: 0.1657 (t80)
REVERT: B  149 ILE cc_start: 0.2321 (pt) cc_final: 0.2055 (tt)
REVERT: B  213 GLU cc_start: 0.3487 (OUTLIER) cc_final: 0.3158 (tp30)
REVERT: B  263 GLU cc_start: 0.3130 (OUTLIER) cc_final: 0.2481 (tt0)
REVERT: B  274 GLU cc_start: 0.2363 (OUTLIER) cc_final: 0.1454 (mt-10)
REVERT: B  284 ASN cc_start: 0.3248 (OUTLIER) cc_final: -0.0276 (p0)
REVERT: B  309 ARG cc_start: 0.4460 (OUTLIER) cc_final: 0.2437 (mmm160)
REVERT: B  360 MET cc_start: 0.2051 (ptt) cc_final: 0.0583 (mmt)
REVERT: C    1 MET cc_start: 0.2667 (mmt) cc_final: 0.0511 (ttp)
REVERT: C   36 MET cc_start: 0.2468 (OUTLIER) cc_final: 0.1984 (tpt)
REVERT: C   85 ARG cc_start: 0.3535 (mtm180) cc_final: 0.1597 (ttt180)
REVERT: C  181 TRP cc_start: 0.2293 (OUTLIER) cc_final: 0.1679 (m-10)
REVERT: C  276 VAL cc_start: 0.0582 (OUTLIER) cc_final: -0.0525 (m)
REVERT: C  362 LYS cc_start: 0.1985 (OUTLIER) cc_final: 0.0103 (tmmt)
  outliers start: 44
  outliers final: 24
  residues processed: 97
  average time/residue: 0.2077
  time to fit residues: 26.8979
Evaluate side-chains
  90 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 53
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   66 LYS
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  124 ASP
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  429 SER
Chi-restraints excluded: chain B residue  430 PHE
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   68 VAL
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  367 THR
Chi-restraints excluded: chain C residue  372 HIS
Chi-restraints excluded: chain C residue  389 THR
Chi-restraints excluded: chain C residue  424 TYR
Chi-restraints excluded: chain C residue  432 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 82 optimal weight:    6.9990
   chunk 33 optimal weight:    8.9990
   chunk 38 optimal weight:    6.9990
   chunk 71 optimal weight:    3.9990
   chunk 28 optimal weight:    0.4980
   chunk 4 optimal weight:    0.0970
   chunk 19 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5437 r_free = 0.5437 target = 0.362851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5359 r_free = 0.5359 target = 0.353297 restraints weight = 271241.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.5339 rms_B_bonded: 6.72
r_work (final): 0.5339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2372
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6750  Z= 0.122
  Angle     :  0.630   6.257   9128  Z= 0.341
  Chirality :  0.043   0.148   1026
  Planarity :  0.005   0.068   1198
  Dihedral  : 10.226  78.458    993
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.95 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 15.84 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.83 (0.27), residues: 868
  helix: -1.28 (0.30), residues: 302
  sheet: -2.65 (0.49), residues: 100
  loop : -2.11 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  85 
 TYR   0.017   0.001   TYR B 408 
 PHE   0.019   0.002   PHE B 249 
 TRP   0.006   0.001   TRP B 300 
 HIS   0.002   0.001   HIS C   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6750)
  covalent geometry    : angle       0.62965 ( 9128)
  hydrogen bonds       : bond        0.04050 (  228)
  hydrogen bonds       : angle       6.86483 (  648)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 49
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 ASP cc_start: 0.0537 (OUTLIER) cc_final: 0.0116 (m-30)
REVERT: B  126 LEU cc_start: -0.0048 (OUTLIER) cc_final: -0.1667 (mt)
REVERT: B  132 THR cc_start: 0.2460 (OUTLIER) cc_final: 0.1836 (p)
REVERT: B  147 MET cc_start: 0.0665 (ptt) cc_final: 0.0249 (ptt)
REVERT: B  263 GLU cc_start: 0.2999 (OUTLIER) cc_final: 0.2757 (tt0)
REVERT: B  274 GLU cc_start: 0.1505 (OUTLIER) cc_final: 0.0913 (mt-10)
REVERT: B  284 ASN cc_start: 0.2726 (OUTLIER) cc_final: -0.0928 (p0)
REVERT: B  309 ARG cc_start: 0.3756 (OUTLIER) cc_final: 0.1777 (mmm160)
REVERT: B  360 MET cc_start: 0.2188 (ptt) cc_final: 0.0645 (mmt)
REVERT: C    1 MET cc_start: 0.2370 (mmt) cc_final: 0.0307 (ttp)
REVERT: C   36 MET cc_start: 0.1987 (OUTLIER) cc_final: 0.1646 (tpt)
REVERT: C  155 HIS cc_start: 0.4600 (OUTLIER) cc_final: 0.3285 (m90)
REVERT: C  181 TRP cc_start: 0.2479 (OUTLIER) cc_final: 0.1789 (m-10)
REVERT: C  362 LYS cc_start: 0.1870 (OUTLIER) cc_final: -0.0049 (tmmt)
  outliers start: 38
  outliers final: 22
  residues processed: 82
  average time/residue: 0.2030
  time to fit residues: 22.5915
Evaluate side-chains
  79 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 46
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   66 LYS
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  124 ASP
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  239 MET
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  429 SER
Chi-restraints excluded: chain B residue  430 PHE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  155 HIS
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  367 THR
Chi-restraints excluded: chain C residue  372 HIS
Chi-restraints excluded: chain C residue  390 ASN
Chi-restraints excluded: chain C residue  424 TYR
Chi-restraints excluded: chain C residue  432 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 11 optimal weight:    9.9990
   chunk 54 optimal weight:    7.9990
   chunk 14 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   chunk 81 optimal weight:   10.0000
   chunk 5 optimal weight:    0.8980
   chunk 47 optimal weight:    9.9990
   chunk 53 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
C 236 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5404 r_free = 0.5404 target = 0.359369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.5334 r_free = 0.5334 target = 0.350438 restraints weight = 270899.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.5310 rms_B_bonded: 6.35
r_work (final): 0.5310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2490
moved from start:          0.4248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   6750  Z= 0.157
  Angle     :  0.653   6.369   9128  Z= 0.354
  Chirality :  0.043   0.151   1026
  Planarity :  0.005   0.071   1198
  Dihedral  : 10.077  74.843    992
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.68 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 16.72 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.77 (0.27), residues: 868
  helix: -1.13 (0.30), residues: 294
  sheet: -2.84 (0.45), residues: 114
  loop : -2.03 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  58 
 TYR   0.016   0.002   TYR B 408 
 PHE   0.020   0.002   PHE B 249 
 TRP   0.007   0.001   TRP B 300 
 HIS   0.004   0.001   HIS B   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 6750)
  covalent geometry    : angle       0.65340 ( 9128)
  hydrogen bonds       : bond        0.03946 (  228)
  hydrogen bonds       : angle       6.81674 (  648)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 49
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 ASP cc_start: 0.0376 (OUTLIER) cc_final: 0.0161 (m-30)
REVERT: B  126 LEU cc_start: -0.0188 (OUTLIER) cc_final: -0.0486 (tp)
REVERT: B  132 THR cc_start: 0.2785 (OUTLIER) cc_final: 0.2232 (p)
REVERT: B  133 TYR cc_start: 0.2077 (OUTLIER) cc_final: 0.1494 (t80)
REVERT: B  147 MET cc_start: 0.0592 (ptt) cc_final: 0.0105 (ptt)
REVERT: B  155 HIS cc_start: 0.5594 (OUTLIER) cc_final: 0.3686 (m90)
REVERT: B  263 GLU cc_start: 0.2949 (OUTLIER) cc_final: 0.2430 (tt0)
REVERT: B  274 GLU cc_start: 0.2170 (OUTLIER) cc_final: 0.1480 (mt-10)
REVERT: B  284 ASN cc_start: 0.2929 (OUTLIER) cc_final: -0.0878 (p0)
REVERT: B  309 ARG cc_start: 0.4340 (OUTLIER) cc_final: 0.2389 (mmm160)
REVERT: B  360 MET cc_start: 0.2148 (ptt) cc_final: 0.0490 (mmt)
REVERT: C    1 MET cc_start: 0.2433 (mmt) cc_final: 0.0415 (ttp)
REVERT: C   36 MET cc_start: 0.2316 (OUTLIER) cc_final: 0.1798 (tpt)
REVERT: C  146 MET cc_start: 0.1752 (OUTLIER) cc_final: 0.1446 (ptp)
REVERT: C  155 HIS cc_start: 0.4695 (OUTLIER) cc_final: 0.3570 (m90)
REVERT: C  181 TRP cc_start: 0.2154 (OUTLIER) cc_final: 0.1529 (m-10)
REVERT: C  236 ASN cc_start: 0.4098 (m110) cc_final: 0.2603 (m-40)
REVERT: C  362 LYS cc_start: 0.1998 (OUTLIER) cc_final: 0.0218 (tmmt)
REVERT: C  372 HIS cc_start: 0.1185 (OUTLIER) cc_final: 0.0877 (p90)
REVERT: C  378 GLU cc_start: 0.5457 (tm-30) cc_final: 0.5128 (tm-30)
  outliers start: 40
  outliers final: 22
  residues processed: 84
  average time/residue: 0.1638
  time to fit residues: 19.1488
Evaluate side-chains
  85 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 48
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 LYS
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  124 ASP
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  155 HIS
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  429 SER
Chi-restraints excluded: chain B residue  430 PHE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  155 HIS
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  367 THR
Chi-restraints excluded: chain C residue  372 HIS
Chi-restraints excluded: chain C residue  390 ASN
Chi-restraints excluded: chain C residue  424 TYR
Chi-restraints excluded: chain C residue  432 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 19 optimal weight:    7.9990
   chunk 70 optimal weight:    0.7980
   chunk 55 optimal weight:    6.9990
   chunk 58 optimal weight:    0.6980
   chunk 34 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.2384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5409 r_free = 0.5409 target = 0.359839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.5406 r_free = 0.5406 target = 0.359329 restraints weight = 26994.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.5407 rms_B_bonded: 0.10
r_work: 0.5403 rms_B_bonded: 0.15 restraints_weight: 0.5000
r_work: 0.5394 rms_B_bonded: 0.41 restraints_weight: 0.2500
r_work: 0.5305 rms_B_bonded: 3.62 restraints_weight: 0.1250
r_work (final): 0.5305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2451
moved from start:          0.4600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6750  Z= 0.129
  Angle     :  0.595   5.713   9128  Z= 0.322
  Chirality :  0.042   0.148   1026
  Planarity :  0.004   0.068   1198
  Dihedral  :  9.662  76.525    991
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.53 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 17.60 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.72 (0.27), residues: 868
  helix: -1.07 (0.30), residues: 301
  sheet: -2.59 (0.48), residues: 100
  loop : -2.13 (0.26), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  58 
 TYR   0.015   0.001   TYR B 408 
 PHE   0.022   0.001   PHE B 249 
 TRP   0.007   0.001   TRP B 303 
 HIS   0.003   0.001   HIS B   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6750)
  covalent geometry    : angle       0.59516 ( 9128)
  hydrogen bonds       : bond        0.03614 (  228)
  hydrogen bonds       : angle       6.56765 (  648)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 52
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  126 LEU cc_start: 0.0331 (OUTLIER) cc_final: -0.0093 (tp)
REVERT: B  132 THR cc_start: 0.2821 (OUTLIER) cc_final: 0.2185 (p)
REVERT: B  147 MET cc_start: 0.1437 (ptt) cc_final: 0.0946 (ptt)
REVERT: B  155 HIS cc_start: 0.5882 (OUTLIER) cc_final: 0.3816 (m90)
REVERT: B  263 GLU cc_start: 0.3362 (OUTLIER) cc_final: 0.2839 (tt0)
REVERT: B  274 GLU cc_start: 0.1826 (OUTLIER) cc_final: 0.0941 (tp30)
REVERT: B  284 ASN cc_start: 0.3055 (OUTLIER) cc_final: -0.0668 (m110)
REVERT: B  309 ARG cc_start: 0.4246 (OUTLIER) cc_final: 0.2310 (mmm160)
REVERT: B  360 MET cc_start: 0.2233 (ptt) cc_final: 0.0737 (mmt)
REVERT: C    1 MET cc_start: 0.1823 (mmt) cc_final: 0.0107 (ttp)
REVERT: C   36 MET cc_start: 0.2149 (OUTLIER) cc_final: 0.1681 (tpt)
REVERT: C  155 HIS cc_start: 0.5051 (OUTLIER) cc_final: 0.4069 (m90)
REVERT: C  181 TRP cc_start: 0.2564 (OUTLIER) cc_final: 0.1877 (m-10)
REVERT: C  274 GLU cc_start: 0.1957 (OUTLIER) cc_final: 0.1171 (mm-30)
REVERT: C  362 LYS cc_start: 0.2264 (OUTLIER) cc_final: 0.0544 (tmmt)
REVERT: C  372 HIS cc_start: 0.1399 (OUTLIER) cc_final: 0.1199 (p90)
  outliers start: 37
  outliers final: 23
  residues processed: 83
  average time/residue: 0.1822
  time to fit residues: 20.7714
Evaluate side-chains
  88 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 52
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   66 LYS
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  155 HIS
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  239 MET
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  429 SER
Chi-restraints excluded: chain B residue  430 PHE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  155 HIS
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  274 GLU
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  367 THR
Chi-restraints excluded: chain C residue  372 HIS
Chi-restraints excluded: chain C residue  389 THR
Chi-restraints excluded: chain C residue  390 ASN
Chi-restraints excluded: chain C residue  424 TYR
Chi-restraints excluded: chain C residue  432 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 79 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 9 optimal weight:   20.0000
   chunk 1 optimal weight:    5.9990
   chunk 62 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 63 optimal weight:    0.2980
   chunk 46 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    3.6588

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

Flipped N/Q/H residues before XYZ refinement:
** C 148 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 = 0.5373 r_free = 0.5373 target = 0.355916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5303 r_free = 0.5303 target = 0.346415 restraints weight = 273978.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.5274 rms_B_bonded: 6.73
r_work (final): 0.5274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2707
moved from start:          0.4814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.146   6750  Z= 0.256
  Angle     :  0.830   7.891   9128  Z= 0.452
  Chirality :  0.047   0.163   1026
  Planarity :  0.007   0.104   1198
  Dihedral  : 10.420  78.607    989
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 16.84
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 13.48 %
    Favored  : 86.29 %
  Rotamer:
    Outliers :  6.45 %
    Allowed  : 17.16 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.33 (0.26), residues: 868
  helix: -1.58 (0.28), residues: 293
  sheet: -3.30 (0.42), residues: 113
  loop : -2.35 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  85 
 TYR   0.027   0.003   TYR C 286 
 PHE   0.023   0.002   PHE B 249 
 TRP   0.012   0.003   TRP C 181 
 HIS   0.006   0.002   HIS B   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 ( 6750)
  covalent geometry    : angle       0.83031 ( 9128)
  hydrogen bonds       : bond        0.04628 (  228)
  hydrogen bonds       : angle       7.41453 (  648)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 53
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  132 THR cc_start: 0.2872 (OUTLIER) cc_final: 0.2319 (p)
REVERT: B  133 TYR cc_start: 0.2407 (OUTLIER) cc_final: 0.1944 (t80)
REVERT: B  147 MET cc_start: 0.1509 (ptt) cc_final: 0.1014 (ptt)
REVERT: B  155 HIS cc_start: 0.5829 (OUTLIER) cc_final: 0.4014 (m90)
REVERT: B  263 GLU cc_start: 0.2869 (OUTLIER) cc_final: 0.2051 (tt0)
REVERT: B  274 GLU cc_start: 0.2259 (OUTLIER) cc_final: 0.1723 (mt-10)
REVERT: B  284 ASN cc_start: 0.3051 (OUTLIER) cc_final: -0.0976 (p0)
REVERT: B  309 ARG cc_start: 0.5099 (OUTLIER) cc_final: 0.0893 (mpt180)
REVERT: C    1 MET cc_start: 0.2751 (mmt) cc_final: 0.0882 (ttp)
REVERT: C   85 ARG cc_start: 0.4047 (mtm180) cc_final: 0.0738 (ttp-170)
REVERT: C  168 MET cc_start: 0.5031 (mtp) cc_final: 0.4804 (mtt)
REVERT: C  181 TRP cc_start: 0.2504 (OUTLIER) cc_final: 0.1820 (m-10)
REVERT: C  216 GLU cc_start: 0.5817 (mp0) cc_final: 0.5356 (mp0)
REVERT: C  274 GLU cc_start: 0.1843 (OUTLIER) cc_final: 0.1370 (mm-30)
REVERT: C  276 VAL cc_start: 0.1093 (OUTLIER) cc_final: -0.0047 (m)
REVERT: C  362 LYS cc_start: 0.2622 (OUTLIER) cc_final: 0.0996 (tmmt)
  outliers start: 44
  outliers final: 32
  residues processed: 91
  average time/residue: 0.1935
  time to fit residues: 23.5335
Evaluate side-chains
  92 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 49
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  155 HIS
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  239 MET
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  372 HIS
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  430 PHE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain C residue  239 MET
Chi-restraints excluded: chain C residue  274 GLU
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  367 THR
Chi-restraints excluded: chain C residue  372 HIS
Chi-restraints excluded: chain C residue  389 THR
Chi-restraints excluded: chain C residue  424 TYR
Chi-restraints excluded: chain C residue  432 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 49 optimal weight:    0.0870
   chunk 63 optimal weight:   20.0000
   chunk 68 optimal weight:    7.9990
   chunk 37 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.9362

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

Flipped N/Q/H residues before XYZ refinement:
C 148 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5401 r_free = 0.5401 target = 0.358854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.5400 r_free = 0.5400 target = 0.358779 restraints weight = 26899.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.5401 rms_B_bonded: 0.01
r_work: 0.5400 rms_B_bonded: 0.02 restraints_weight: 0.5000
r_work: 0.5399 rms_B_bonded: 0.05 restraints_weight: 0.2500
r_work: 0.5385 rms_B_bonded: 0.55 restraints_weight: 0.1250
r_work: 0.5350 rms_B_bonded: 2.27 restraints_weight: 0.0625
r_work (final): 0.5350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2470
moved from start:          0.5063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   6750  Z= 0.127
  Angle     :  0.611   5.942   9128  Z= 0.332
  Chirality :  0.042   0.154   1026
  Planarity :  0.004   0.066   1198
  Dihedral  :  9.507  87.348    987
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.29 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 19.06 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.96 (0.26), residues: 868
  helix: -1.20 (0.29), residues: 305
  sheet: -2.76 (0.47), residues: 98
  loop : -2.34 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 180 
 TYR   0.014   0.001   TYR B 408 
 PHE   0.022   0.002   PHE B 242 
 TRP   0.008   0.001   TRP B 300 
 HIS   0.002   0.001   HIS B   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6750)
  covalent geometry    : angle       0.61064 ( 9128)
  hydrogen bonds       : bond        0.03667 (  228)
  hydrogen bonds       : angle       6.75978 (  648)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 52
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  132 THR cc_start: 0.2672 (OUTLIER) cc_final: 0.2004 (p)
REVERT: B  147 MET cc_start: 0.1373 (ptt) cc_final: 0.0899 (ptt)
REVERT: B  155 HIS cc_start: 0.5905 (OUTLIER) cc_final: 0.3757 (m90)
REVERT: B  239 MET cc_start: 0.2327 (OUTLIER) cc_final: 0.1919 (tpt)
REVERT: B  263 GLU cc_start: 0.3064 (OUTLIER) cc_final: 0.2369 (tt0)
REVERT: B  274 GLU cc_start: 0.2360 (OUTLIER) cc_final: 0.1798 (mt-10)
REVERT: B  284 ASN cc_start: 0.2958 (OUTLIER) cc_final: -0.0789 (p0)
REVERT: B  309 ARG cc_start: 0.4355 (OUTLIER) cc_final: 0.2449 (mmm160)
REVERT: C    1 MET cc_start: 0.2482 (mmt) cc_final: 0.2038 (mmt)
REVERT: C   36 MET cc_start: 0.2286 (OUTLIER) cc_final: 0.1806 (tpt)
REVERT: C   82 TYR cc_start: 0.1580 (m-80) cc_final: 0.0791 (m-80)
REVERT: C   85 ARG cc_start: 0.3611 (mtm180) cc_final: 0.0505 (ttp-170)
REVERT: C  168 MET cc_start: 0.5134 (mtp) cc_final: 0.4859 (mtt)
REVERT: C  181 TRP cc_start: 0.2572 (OUTLIER) cc_final: 0.1887 (m-10)
REVERT: C  261 LYS cc_start: 0.4185 (tptt) cc_final: 0.2498 (tptp)
REVERT: C  278 TYR cc_start: 0.2046 (OUTLIER) cc_final: 0.1572 (t80)
REVERT: C  362 LYS cc_start: 0.2425 (OUTLIER) cc_final: 0.0649 (tmmt)
  outliers start: 34
  outliers final: 21
  residues processed: 82
  average time/residue: 0.2162
  time to fit residues: 23.2324
Evaluate side-chains
  82 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 50
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  155 HIS
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  239 MET
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  372 HIS
Chi-restraints excluded: chain B residue  430 PHE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  278 TYR
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  367 THR
Chi-restraints excluded: chain C residue  389 THR
Chi-restraints excluded: chain C residue  390 ASN
Chi-restraints excluded: chain C residue  424 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 4 optimal weight:    9.9990
   chunk 1 optimal weight:    2.9990
   chunk 47 optimal weight:   10.0000
   chunk 71 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 29 optimal weight:   20.0000
   chunk 10 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 85 optimal weight:    5.9990
   chunk 9 optimal weight:    9.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
B  65 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5381 r_free = 0.5381 target = 0.355803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5373 r_free = 0.5373 target = 0.354497 restraints weight = 27146.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.5373 rms_B_bonded: 0.23
r_work: 0.5366 rms_B_bonded: 0.33 restraints_weight: 0.5000
r_work: 0.5350 rms_B_bonded: 0.77 restraints_weight: 0.2500
r_work (final): 0.5350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2641
moved from start:          0.5274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.121   6750  Z= 0.223
  Angle     :  0.762   6.814   9128  Z= 0.413
  Chirality :  0.045   0.156   1026
  Planarity :  0.007   0.083   1198
  Dihedral  : 10.038  86.146    984
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 16.46
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 12.67 %
    Favored  : 87.10 %
  Rotamer:
    Outliers :  5.72 %
    Allowed  : 18.48 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.47 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.27 (0.26), residues: 868
  helix: -1.41 (0.29), residues: 294
  sheet: -3.31 (0.42), residues: 110
  loop : -2.39 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  58 
 TYR   0.025   0.002   TYR C 286 
 PHE   0.022   0.002   PHE B 249 
 TRP   0.011   0.002   TRP B 303 
 HIS   0.007   0.001   HIS B   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 6750)
  covalent geometry    : angle       0.76248 ( 9128)
  hydrogen bonds       : bond        0.04281 (  228)
  hydrogen bonds       : angle       7.22593 (  648)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 51
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 ARG cc_start: 0.3308 (OUTLIER) cc_final: 0.0554 (tpt170)
REVERT: B   58 ARG cc_start: 0.3397 (OUTLIER) cc_final: -0.1426 (mmt-90)
REVERT: B  132 THR cc_start: 0.2956 (OUTLIER) cc_final: 0.2399 (p)
REVERT: B  147 MET cc_start: 0.1551 (ptt) cc_final: 0.1087 (ptt)
REVERT: B  155 HIS cc_start: 0.5484 (OUTLIER) cc_final: 0.3562 (m90)
REVERT: B  263 GLU cc_start: 0.3125 (OUTLIER) cc_final: 0.2426 (tt0)
REVERT: B  274 GLU cc_start: 0.1964 (OUTLIER) cc_final: 0.1342 (mt-10)
REVERT: B  284 ASN cc_start: 0.3016 (OUTLIER) cc_final: -0.1007 (p0)
REVERT: B  309 ARG cc_start: 0.5068 (OUTLIER) cc_final: 0.3538 (mmm-85)
REVERT: C    1 MET cc_start: 0.2588 (mmt) cc_final: 0.2131 (mmt)
REVERT: C   82 TYR cc_start: 0.1810 (m-80) cc_final: 0.0981 (m-80)
REVERT: C   85 ARG cc_start: 0.3714 (mtm180) cc_final: 0.0489 (ttp80)
REVERT: C  181 TRP cc_start: 0.2516 (OUTLIER) cc_final: 0.1785 (m-10)
REVERT: C  216 GLU cc_start: 0.5837 (mp0) cc_final: 0.5424 (mp0)
REVERT: C  261 LYS cc_start: 0.3892 (tptt) cc_final: 0.2338 (tptp)
REVERT: C  362 LYS cc_start: 0.2799 (OUTLIER) cc_final: 0.1035 (tmmt)
  outliers start: 39
  outliers final: 26
  residues processed: 84
  average time/residue: 0.2140
  time to fit residues: 23.6572
Evaluate side-chains
  86 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 50
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 ARG
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  155 HIS
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  239 MET
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  372 HIS
Chi-restraints excluded: chain B residue  430 PHE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  239 MET
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  367 THR
Chi-restraints excluded: chain C residue  389 THR
Chi-restraints excluded: chain C residue  424 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 34 optimal weight:    9.9990
   chunk 80 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 67 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 81 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    2.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5385 r_free = 0.5385 target = 0.356417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5377 r_free = 0.5377 target = 0.354934 restraints weight = 26855.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.5377 rms_B_bonded: 0.29
r_work: 0.5348 rms_B_bonded: 0.93 restraints_weight: 0.5000
r_work: 0.5302 rms_B_bonded: 2.51 restraints_weight: 0.2500
r_work (final): 0.5302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2654
moved from start:          0.5462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.096   6750  Z= 0.191
  Angle     :  0.702   6.477   9128  Z= 0.381
  Chirality :  0.044   0.157   1026
  Planarity :  0.006   0.068   1198
  Dihedral  :  9.880  90.794    984
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 11.98 %
    Favored  : 87.79 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 18.62 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.38 (0.26), residues: 868
  helix: -1.56 (0.28), residues: 307
  sheet: -3.17 (0.45), residues: 98
  loop : -2.54 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  85 
 TYR   0.022   0.002   TYR C 286 
 PHE   0.026   0.002   PHE B 242 
 TRP   0.011   0.002   TRP B 303 
 HIS   0.005   0.001   HIS B   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 6750)
  covalent geometry    : angle       0.70195 ( 9128)
  hydrogen bonds       : bond        0.04031 (  228)
  hydrogen bonds       : angle       7.15133 (  648)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 50
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    8 TYR cc_start: 0.4117 (OUTLIER) cc_final: 0.1914 (t80)
REVERT: B   10 ARG cc_start: 0.3257 (OUTLIER) cc_final: -0.0150 (tpt170)
REVERT: B   28 GLU cc_start: 0.4099 (tp30) cc_final: 0.3811 (tp30)
REVERT: B  132 THR cc_start: 0.2885 (OUTLIER) cc_final: 0.2286 (p)
REVERT: B  147 MET cc_start: 0.1517 (ptt) cc_final: 0.1063 (ptt)
REVERT: B  155 HIS cc_start: 0.5691 (OUTLIER) cc_final: 0.3633 (m90)
REVERT: B  263 GLU cc_start: 0.3190 (OUTLIER) cc_final: 0.2257 (tt0)
REVERT: B  284 ASN cc_start: 0.2938 (OUTLIER) cc_final: -0.1027 (p0)
REVERT: B  309 ARG cc_start: 0.4807 (OUTLIER) cc_final: 0.3788 (mmm-85)
REVERT: C    1 MET cc_start: 0.2646 (mmt) cc_final: 0.2188 (mmt)
REVERT: C   82 TYR cc_start: 0.1923 (m-80) cc_final: 0.1090 (m-80)
REVERT: C   85 ARG cc_start: 0.3779 (mtm180) cc_final: 0.0619 (ttp80)
REVERT: C  168 MET cc_start: 0.5298 (mtp) cc_final: 0.4975 (mtp)
REVERT: C  181 TRP cc_start: 0.2180 (OUTLIER) cc_final: 0.1504 (m-10)
REVERT: C  216 GLU cc_start: 0.5822 (mp0) cc_final: 0.5390 (mp0)
REVERT: C  261 LYS cc_start: 0.3804 (tptt) cc_final: 0.2276 (tptp)
REVERT: C  362 LYS cc_start: 0.2852 (OUTLIER) cc_final: 0.0889 (tmmt)
  outliers start: 37
  outliers final: 27
  residues processed: 82
  average time/residue: 0.2232
  time to fit residues: 24.0881
Evaluate side-chains
  85 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 49
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 TYR
Chi-restraints excluded: chain B residue   10 ARG
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  155 HIS
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  372 HIS
Chi-restraints excluded: chain B residue  430 PHE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  239 MET
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  278 TYR
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  367 THR
Chi-restraints excluded: chain C residue  389 THR
Chi-restraints excluded: chain C residue  424 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 82 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 73 optimal weight:    7.9990
   chunk 81 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 77 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    1.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5393 r_free = 0.5393 target = 0.357307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.5383 r_free = 0.5383 target = 0.355461 restraints weight = 26854.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.5383 rms_B_bonded: 0.38
r_work: 0.5350 rms_B_bonded: 1.11 restraints_weight: 0.5000
r_work: 0.5290 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.5290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2629
moved from start:          0.5654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   6750  Z= 0.163
  Angle     :  0.655   6.149   9128  Z= 0.355
  Chirality :  0.043   0.162   1026
  Planarity :  0.005   0.070   1198
  Dihedral  :  9.490  93.113    981
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 11.75 %
    Favored  : 88.13 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 19.65 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.27 (0.26), residues: 868
  helix: -1.36 (0.29), residues: 306
  sheet: -3.14 (0.46), residues: 98
  loop : -2.55 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  34 
 TYR   0.019   0.001   TYR C 286 
 PHE   0.026   0.002   PHE B 165 
 TRP   0.014   0.002   TRP B 303 
 HIS   0.005   0.001   HIS B   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 6750)
  covalent geometry    : angle       0.65515 ( 9128)
  hydrogen bonds       : bond        0.03775 (  228)
  hydrogen bonds       : angle       6.89979 (  648)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2577.61 seconds
wall clock time: 44 minutes 38.22 seconds (2678.22 seconds total)