Starting phenix.real_space_refine
on Wed Sep 17 08:13:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9izu_61042/09_2025/9izu_61042.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9izu_61042/09_2025/9izu_61042.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9izu_61042/09_2025/9izu_61042.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9izu_61042/09_2025/9izu_61042.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9izu_61042/09_2025/9izu_61042.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9izu_61042/09_2025/9izu_61042.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      47      5.16       5
     C    4513      2.51       5
     N    1224      2.21       5
     O    1321      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7105
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 3581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 470, 3581
          Classifications: {'peptide': 470}
          Link IDs: {'PTRANS': 26, 'TRANS': 443}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3524
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 463, 3524
          Classifications: {'peptide': 463}
          Link IDs: {'PTRANS': 25, 'TRANS': 437}
          Chain breaks: 2
  Time building chain proxies: 2.10, per 1000 atoms: 0.30
  Number of scatterers: 7105
  At special positions: 0
  Unit cell: (62.624, 83.224, 117.008, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      47     16.00
     O    1321      8.00
     N    1224      7.00
     C    4513      6.00
    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: 0.66
  Conformation dependent library (CDL) restraints added in 417.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1702

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 6 sheets defined
      48.6% alpha, 14.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'C' and resid 43 through 64
      Proline residue:  C  59  - end of helix
    Processing helix  chain 'C' and resid 65 through 83
    Processing helix  chain 'C' and resid 83 through 95
    Processing helix  chain 'C' and resid 98 through 118
      removed outlier: 3.690A  pdb=" N   SER C 118 " --> pdb=" O   GLU C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 124
      removed outlier: 3.569A  pdb=" N   MET C 124 " --> pdb=" O   THR C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 157 through 170
      Proline residue:  C 165  - end of helix
    Processing helix  chain 'C' and resid 183 through 196
    Processing helix  chain 'C' and resid 209 through 219
      removed outlier: 3.694A  pdb=" N   VAL C 213 " --> pdb=" O   GLN C 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 230 through 245
    Processing helix  chain 'C' and resid 265 through 278
    Processing helix  chain 'C' and resid 279 through 283
    Processing helix  chain 'C' and resid 296 through 310
      Proline residue:  C 302  - end of helix
    Processing helix  chain 'C' and resid 328 through 345
    Processing helix  chain 'C' and resid 379 through 384
    Processing helix  chain 'C' and resid 398 through 408
    Processing helix  chain 'C' and resid 421 through 432
    Processing helix  chain 'C' and resid 466 through 474
    Processing helix  chain 'D' and resid 43 through 64
      Proline residue:  D  59  - end of helix
    Processing helix  chain 'D' and resid 65 through 83
    Processing helix  chain 'D' and resid 83 through 95
    Processing helix  chain 'D' and resid 98 through 119
      removed outlier: 3.575A  pdb=" N   VAL D 119 " --> pdb=" O   HIS D 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 124
      removed outlier: 4.082A  pdb=" N   MET D 123 " --> pdb=" O   THR D 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 158 through 170
      Proline residue:  D 165  - end of helix
    Processing helix  chain 'D' and resid 182 through 196
      removed outlier: 4.685A  pdb=" N   THR D 186 " --> pdb=" O   VAL D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 219
    Processing helix  chain 'D' and resid 230 through 244
      removed outlier: 3.677A  pdb=" N   HIS D 244 " --> pdb=" O   ARG D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 265 through 278
    Processing helix  chain 'D' and resid 279 through 283
    Processing helix  chain 'D' and resid 296 through 299
    Processing helix  chain 'D' and resid 300 through 311
      removed outlier: 3.536A  pdb=" N   LEU D 311 " --> pdb=" O   HIS D 307 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 328 through 345
    Processing helix  chain 'D' and resid 379 through 384
    Processing helix  chain 'D' and resid 398 through 409
      removed outlier: 3.567A  pdb=" N   ASN D 409 " --> pdb=" O   ILE D 405 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 421 through 432
    Processing helix  chain 'D' and resid 467 through 475
    Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 28
    Processing sheet with id=AA2, first strand: chain 'C' and resid 127 through 132
      removed outlier: 8.413A  pdb=" N   MET C 128 " --> pdb=" O   SER C 139 " (cutoff:3.500A)
      removed outlier: 8.360A  pdb=" N   SER C 139 " --> pdb=" O   MET C 128 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   SER C 130 " --> pdb=" O   LEU C 137 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   LEU C 137 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
      removed outlier: 7.705A  pdb=" N   VAL D 437 " --> pdb=" O   LEU C 477 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   THR C 479 " --> pdb=" O   VAL D 437 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   VAL D 439 " --> pdb=" O   THR C 479 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   THR C 481 " --> pdb=" O   VAL D 439 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   THR D 415 " --> pdb=" O   GLY D 438 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   HIS D 257 " --> pdb=" O   GLY D 414 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   GLY D 258 " --> pdb=" O   VAL D 292 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   VAL D 294 " --> pdb=" O   GLY D 258 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   VAL D 260 " --> pdb=" O   VAL D 294 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   THR D 396 " --> pdb=" O   LEU D 293 " (cutoff:3.500A)
      removed outlier: 8.162A  pdb=" N   LEU D 391 " --> pdb=" O   GLY D 368 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   THR D 370 " --> pdb=" O   LEU D 391 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   VAL D 393 " --> pdb=" O   THR D 370 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   ILE D 372 " --> pdb=" O   VAL D 393 " (cutoff:3.500A)
      removed outlier: 8.127A  pdb=" N   GLU D 395 " --> pdb=" O   ILE D 372 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   GLY D 353 " --> pdb=" O   GLY D 368 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   THR D 370 " --> pdb=" O   LEU D 351 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   LEU D 351 " --> pdb=" O   THR D 370 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   ILE D 372 " --> pdb=" O   ILE D 349 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   ILE D 349 " --> pdb=" O   ILE D 372 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 203 through 205
      removed outlier: 7.505A  pdb=" N   VAL C 146 " --> pdb=" O   LYS C 223 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   ILE C 225 " --> pdb=" O   VAL C 146 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ALA C 148 " --> pdb=" O   ILE C 225 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   PHE C 227 " --> pdb=" O   ALA C 148 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   ILE C 150 " --> pdb=" O   PHE C 227 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASN C 251 " --> pdb=" O   PHE C 227 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 349 through 351
      removed outlier: 5.853A  pdb=" N   ILE C 349 " --> pdb=" O   SER C 373 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   SER C 373 " --> pdb=" O   ILE C 349 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU C 351 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   GLU C 395 " --> pdb=" O   ASN C 374 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   GLY C 258 " --> pdb=" O   VAL C 292 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   VAL C 294 " --> pdb=" O   GLY C 258 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   VAL C 260 " --> pdb=" O   VAL C 294 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   THR C 415 " --> pdb=" O   GLY C 438 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   VAL C 437 " --> pdb=" O   THR D 481 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 24 through 28
      removed outlier: 3.651A  pdb=" N   GLY D  37 " --> pdb=" O   ILE D  27 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 203 through 205
      removed outlier: 6.888A  pdb=" N   VAL D 146 " --> pdb=" O   ILE D 222 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA D 224 " --> pdb=" O   VAL D 146 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL D 228 " --> pdb=" O   ILE D 150 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   LYS D 223 " --> pdb=" O   ARG D 247 " (cutoff:3.500A)
      removed outlier: 8.264A  pdb=" N   GLN D 249 " --> pdb=" O   LYS D 223 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   ILE D 225 " --> pdb=" O   GLN D 249 " (cutoff:3.500A)
      removed outlier: 8.372A  pdb=" N   ASN D 251 " --> pdb=" O   ILE D 225 " (cutoff:3.500A)
      removed outlier: 7.369A  pdb=" N   PHE D 227 " --> pdb=" O   ASN D 251 " (cutoff:3.500A)

    350 hydrogen bonds defined for protein.
    1020 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: 1.17

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2351
        1.34 -     1.46: 1390
        1.46 -     1.58: 3425
        1.58 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 7244
  Sorted by residual:
  bond pdb=" N   SER D   3 "
       pdb=" CA  SER D   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.83e+00
  bond pdb=" N   SER C   3 "
       pdb=" CA  SER C   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.82e+00
  bond pdb=" CA  GLY D 438 "
       pdb=" C   GLY D 438 "
    ideal  model  delta    sigma   weight residual
    1.516  1.525 -0.010 8.10e-03 1.52e+04 1.44e+00
  bond pdb=" N   SER D  30 "
       pdb=" CA  SER D  30 "
    ideal  model  delta    sigma   weight residual
    1.458  1.472 -0.014 1.30e-02 5.92e+03 1.24e+00
  bond pdb=" N   SER C  30 "
       pdb=" CA  SER C  30 "
    ideal  model  delta    sigma   weight residual
    1.458  1.471 -0.014 1.33e-02 5.65e+03 1.09e+00
  ... (remaining 7239 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 9590
        1.14 -     2.29: 162
        2.29 -     3.43: 43
        3.43 -     4.57: 17
        4.57 -     5.71: 1
  Bond angle restraints: 9813
  Sorted by residual:
  angle pdb=" C   ILE D 159 "
        pdb=" CA  ILE D 159 "
        pdb=" CB  ILE D 159 "
      ideal   model   delta    sigma   weight residual
     113.70  110.79    2.91 9.50e-01 1.11e+00 9.37e+00
  angle pdb=" N   VAL C 119 "
        pdb=" CA  VAL C 119 "
        pdb=" C   VAL C 119 "
      ideal   model   delta    sigma   weight residual
     112.29  109.63    2.66 9.40e-01 1.13e+00 8.01e+00
  angle pdb=" N   ILE D  36 "
        pdb=" CA  ILE D  36 "
        pdb=" C   ILE D  36 "
      ideal   model   delta    sigma   weight residual
     113.20  110.55    2.65 9.60e-01 1.09e+00 7.63e+00
  angle pdb=" CA  ASN C  29 "
        pdb=" C   ASN C  29 "
        pdb=" N   SER C  30 "
      ideal   model   delta    sigma   weight residual
     116.21  119.58   -3.37 1.33e+00 5.65e-01 6.43e+00
  angle pdb=" N   ILE D 159 "
        pdb=" CA  ILE D 159 "
        pdb=" C   ILE D 159 "
      ideal   model   delta    sigma   weight residual
     112.67  109.58    3.09 1.25e+00 6.40e-01 6.12e+00
  ... (remaining 9808 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 4253
       16.01 -    32.02: 103
       32.02 -    48.02: 20
       48.02 -    64.03: 5
       64.03 -    80.04: 1
  Dihedral angle restraints: 4382
    sinusoidal: 1732
      harmonic: 2650
  Sorted by residual:
  dihedral pdb=" CA  ARG C 334 "
           pdb=" CB  ARG C 334 "
           pdb=" CG  ARG C 334 "
           pdb=" CD  ARG C 334 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.99  -57.01     3      1.50e+01 4.44e-03 9.42e+00
  dihedral pdb=" CA  LYS D 468 "
           pdb=" CB  LYS D 468 "
           pdb=" CG  LYS D 468 "
           pdb=" CD  LYS D 468 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  103.43  -43.43     3      1.50e+01 4.44e-03 7.81e+00
  dihedral pdb=" N   TRP D 484 "
           pdb=" CA  TRP D 484 "
           pdb=" CB  TRP D 484 "
           pdb=" CG  TRP D 484 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -136.88  -43.12     3      1.50e+01 4.44e-03 7.75e+00
  ... (remaining 4379 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 718
       0.025 -    0.051: 208
       0.051 -    0.076: 69
       0.076 -    0.101: 60
       0.101 -    0.127: 61
  Chirality restraints: 1116
  Sorted by residual:
  chirality pdb=" CA  VAL D  39 "
            pdb=" N   VAL D  39 "
            pdb=" C   VAL D  39 "
            pdb=" CB  VAL D  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.02e-01
  chirality pdb=" CA  ILE C 225 "
            pdb=" N   ILE C 225 "
            pdb=" C   ILE C 225 "
            pdb=" CB  ILE C 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.93e-01
  chirality pdb=" CA  VAL C  39 "
            pdb=" N   VAL C  39 "
            pdb=" C   VAL C  39 "
            pdb=" CB  VAL C  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.89e-01
  ... (remaining 1113 not shown)

  Planarity restraints: 1274
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D 151 "    0.021 5.00e-02 4.00e+02   3.14e-02 1.58e+00
        pdb=" N   PRO D 152 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO D 152 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO D 152 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 301 "    0.018 5.00e-02 4.00e+02   2.68e-02 1.15e+00
        pdb=" N   PRO C 302 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO C 302 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO C 302 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D  39 "   -0.018 5.00e-02 4.00e+02   2.66e-02 1.13e+00
        pdb=" N   PRO D  40 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO D  40 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO D  40 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 1271 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.66: 95
        2.66 -     3.22: 7149
        3.22 -     3.78: 11250
        3.78 -     4.34: 15357
        4.34 -     4.90: 25285
  Nonbonded interactions: 59136
  Sorted by model distance:
  nonbonded pdb=" O   LEU D 193 "
            pdb=" OG  SER D 196 "
     model   vdw
     2.095 3.040
  nonbonded pdb=" OG  SER D 348 "
            pdb=" OD1 ASN D 374 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" NZ  LYS D 255 "
            pdb=" O   TYR D 382 "
     model   vdw
     2.173 3.120
  nonbonded pdb=" ND2 ASN D  33 "
            pdb=" O   ASN D 363 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" OD1 ASP D 340 "
            pdb=" NH1 ARG D 354 "
     model   vdw
     2.238 3.120
  ... (remaining 59131 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'C' and (resid 3 through 125 or resid 134 through 450 or resid 466 throug \ 
h 486))
  selection = (chain 'D' and (resid 3 through 450 or resid 466 through 486))
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.040
  Find NCS groups from input model:        0.120
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1532
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      :  0.002   0.032   7244  Z= 0.111
  Angle     :  0.447   5.714   9813  Z= 0.258
  Chirality :  0.041   0.127   1116
  Planarity :  0.002   0.031   1274
  Dihedral  :  7.952  80.041   2680
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.14 %
    Favored  : 96.73 %
  Cbeta Deviations :  0.00 %
  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: -0.47 (0.26), residues: 923
  helix:  1.13 (0.25), residues: 402
  sheet: -0.82 (0.35), residues: 173
  loop : -1.75 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 312 
 TYR   0.006   0.001   TYR C 411 
 PHE   0.013   0.001   PHE C 164 
 TRP   0.005   0.001   TRP C 484 
 HIS   0.002   0.000   HIS C 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 ( 7244)
  covalent geometry    : angle       0.44709 ( 9813)
  hydrogen bonds       : bond        0.17534 (  350)
  hydrogen bonds       : angle       6.07296 ( 1020)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  124 MET cc_start: -0.1731 (mtt) cc_final: -0.2546 (mtt)
REVERT: D   54 CYS cc_start: 0.4254 (m) cc_final: 0.3867 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1191
  time to fit residues: 19.9496
Evaluate side-chains
  75 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:   20.0000
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:   20.0000
   overall best weight:    7.5990

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

Flipped N/Q/H residues before XYZ refinement:
C  95 GLN
C 115 HIS
C 207 HIS
C 272 GLN
C 310 ASN
C 318 GLN
C 365 ASN
C 421 ASN
** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 204 ASN
** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 378 ASN
** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 483 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5436 r_free = 0.5436 target = 0.220318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.5246 r_free = 0.5246 target = 0.183622 restraints weight = 21638.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.5225 r_free = 0.5225 target = 0.181679 restraints weight = 24794.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5225 r_free = 0.5225 target = 0.181679 restraints weight = 26813.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5225 r_free = 0.5225 target = 0.181679 restraints weight = 26813.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5225 r_free = 0.5225 target = 0.181679 restraints weight = 26813.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.5126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4870
moved from start:          0.5898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.190   7244  Z= 0.353
  Angle     :  1.030  13.683   9813  Z= 0.541
  Chirality :  0.060   0.402   1116
  Planarity :  0.008   0.079   1274
  Dihedral  :  5.888  26.424    978
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 29.32
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.96 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  :  7.19 %
    Favored  : 89.15 %
  Cbeta Deviations :  0.00 %
  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: -1.43 (0.25), residues: 923
  helix: -0.10 (0.24), residues: 407
  sheet: -0.74 (0.41), residues: 152
  loop : -1.96 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.025   0.002   ARG D 108 
 TYR   0.042   0.004   TYR D 428 
 PHE   0.036   0.004   PHE D  58 
 TRP   0.022   0.004   TRP C 300 
 HIS   0.015   0.003   HIS D 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00796 ( 7244)
  covalent geometry    : angle       1.02986 ( 9813)
  hydrogen bonds       : bond        0.05615 (  350)
  hydrogen bonds       : angle       6.23606 ( 1020)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 95
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  252 MET cc_start: 0.7236 (mpp) cc_final: 0.6032 (mpp)
REVERT: C  306 GLU cc_start: 0.9252 (pt0) cc_final: 0.8996 (tm-30)
REVERT: C  449 MET cc_start: 0.8229 (mtp) cc_final: 0.7872 (mmm)
REVERT: D  123 MET cc_start: 0.1883 (mmm) cc_final: 0.1572 (tpt)
REVERT: D  168 MET cc_start: 0.6020 (OUTLIER) cc_final: 0.3352 (mtt)
REVERT: D  259 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8888 (p)
  outliers start: 28
  outliers final: 13
  residues processed: 111
  average time/residue: 0.0942
  time to fit residues: 14.1992
Evaluate side-chains
  92 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   87 ILE
Chi-restraints excluded: chain C residue  155 PHE
Chi-restraints excluded: chain C residue  210 HIS
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  421 ASN
Chi-restraints excluded: chain C residue  433 ASP
Chi-restraints excluded: chain C residue  440 ASN
Chi-restraints excluded: chain D residue   28 HIS
Chi-restraints excluded: chain D residue   47 MET
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  168 MET
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain D residue  400 ASP
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  484 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 90 optimal weight:    4.9990
   chunk 18 optimal weight:    7.9990
   chunk 89 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 85 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 91 optimal weight:    0.8980
   chunk 37 optimal weight:    7.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 256 ASN
C 374 ASN
C 440 ASN
** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 251 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5459 r_free = 0.5459 target = 0.225548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.5254 r_free = 0.5254 target = 0.186126 restraints weight = 23049.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.5230 r_free = 0.5230 target = 0.185798 restraints weight = 23971.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5230 r_free = 0.5230 target = 0.185798 restraints weight = 24673.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5230 r_free = 0.5230 target = 0.185798 restraints weight = 24673.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5230 r_free = 0.5230 target = 0.185798 restraints weight = 24673.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.5099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4737
moved from start:          0.6221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.096   7244  Z= 0.162
  Angle     :  0.683  10.194   9813  Z= 0.349
  Chirality :  0.047   0.212   1116
  Planarity :  0.006   0.079   1274
  Dihedral  :  4.988  20.246    978
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 10.72 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  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: -0.70 (0.26), residues: 923
  helix:  0.68 (0.24), residues: 410
  sheet: -0.63 (0.38), residues: 164
  loop : -1.73 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  38 
 TYR   0.018   0.002   TYR C 428 
 PHE   0.025   0.002   PHE C 174 
 TRP   0.018   0.002   TRP C  61 
 HIS   0.009   0.002   HIS D 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 7244)
  covalent geometry    : angle       0.68261 ( 9813)
  hydrogen bonds       : bond        0.03687 (  350)
  hydrogen bonds       : angle       5.51123 ( 1020)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.298 
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: C   47 MET cc_start: 0.8981 (ptp) cc_final: 0.8718 (ptp)
REVERT: C  252 MET cc_start: 0.6974 (mpp) cc_final: 0.6076 (mpp)
REVERT: C  306 GLU cc_start: 0.9096 (pt0) cc_final: 0.8758 (tm-30)
REVERT: C  449 MET cc_start: 0.8176 (mtp) cc_final: 0.7825 (mmm)
REVERT: D  168 MET cc_start: 0.5836 (OUTLIER) cc_final: 0.4014 (mtt)
REVERT: D  255 LYS cc_start: 0.4929 (mttt) cc_final: 0.4695 (mtpt)
  outliers start: 22
  outliers final: 14
  residues processed: 99
  average time/residue: 0.0870
  time to fit residues: 12.0148
Evaluate side-chains
  90 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  154 ASN
Chi-restraints excluded: chain C residue  210 HIS
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  374 ASN
Chi-restraints excluded: chain C residue  430 HIS
Chi-restraints excluded: chain C residue  433 ASP
Chi-restraints excluded: chain C residue  434 VAL
Chi-restraints excluded: chain C residue  440 ASN
Chi-restraints excluded: chain D residue   28 HIS
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue  168 MET
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain D residue  400 ASP
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  484 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 24 optimal weight:    9.9990
   chunk 40 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 62 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0770
   chunk 48 optimal weight:    8.9990
   chunk 53 optimal weight:    7.9990
   chunk 86 optimal weight:   10.0000
   overall best weight:    4.4146

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

Flipped N/Q/H residues before XYZ refinement:
C 154 ASN
C 421 ASN
** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 204 ASN
D 210 HIS
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 436 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5414 r_free = 0.5414 target = 0.218825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.5274 r_free = 0.5274 target = 0.180823 restraints weight = 20583.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.5241 r_free = 0.5241 target = 0.180752 restraints weight = 20073.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5241 r_free = 0.5241 target = 0.180752 restraints weight = 20264.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5241 r_free = 0.5241 target = 0.180752 restraints weight = 20264.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5241 r_free = 0.5241 target = 0.180752 restraints weight = 20264.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.5134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4879
moved from start:          0.7210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.100   7244  Z= 0.204
  Angle     :  0.714  11.742   9813  Z= 0.374
  Chirality :  0.049   0.275   1116
  Planarity :  0.006   0.086   1274
  Dihedral  :  5.366  22.368    978
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 21.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 12.81 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  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: -0.73 (0.27), residues: 923
  helix:  0.62 (0.25), residues: 411
  sheet: -0.66 (0.39), residues: 169
  loop : -1.69 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 181 
 TYR   0.026   0.002   TYR C 428 
 PHE   0.024   0.003   PHE C 174 
 TRP   0.020   0.002   TRP C  61 
 HIS   0.017   0.003   HIS D 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 7244)
  covalent geometry    : angle       0.71443 ( 9813)
  hydrogen bonds       : bond        0.03802 (  350)
  hydrogen bonds       : angle       5.64938 ( 1020)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  252 MET cc_start: 0.6984 (mpp) cc_final: 0.5866 (mpp)
REVERT: D  123 MET cc_start: 0.1115 (mmm) cc_final: 0.0680 (tpt)
REVERT: D  168 MET cc_start: 0.6177 (mmp) cc_final: 0.4023 (mtt)
REVERT: D  259 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8832 (m)
REVERT: D  261 MET cc_start: 0.4284 (mtp) cc_final: 0.4034 (mtp)
REVERT: D  379 MET cc_start: 0.5521 (ppp) cc_final: 0.5073 (ppp)
REVERT: D  400 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8270 (m-30)
  outliers start: 19
  outliers final: 13
  residues processed: 93
  average time/residue: 0.0892
  time to fit residues: 11.4428
Evaluate side-chains
  87 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   87 ILE
Chi-restraints excluded: chain C residue  154 ASN
Chi-restraints excluded: chain C residue  210 HIS
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  374 ASN
Chi-restraints excluded: chain C residue  433 ASP
Chi-restraints excluded: chain C residue  434 VAL
Chi-restraints excluded: chain C residue  440 ASN
Chi-restraints excluded: chain D residue   28 HIS
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue  147 CYS
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain D residue  400 ASP
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  484 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   chunk 38 optimal weight:    8.9990
   chunk 71 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 59 optimal weight:   40.0000
   chunk 42 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 86 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 33 optimal weight:   20.0000
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
C 374 ASN
** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5424 r_free = 0.5424 target = 0.224651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5280 r_free = 0.5280 target = 0.189923 restraints weight = 21216.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.5244 r_free = 0.5244 target = 0.187092 restraints weight = 23534.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5244 r_free = 0.5244 target = 0.187092 restraints weight = 25932.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5244 r_free = 0.5244 target = 0.187092 restraints weight = 25932.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5244 r_free = 0.5244 target = 0.187092 restraints weight = 25932.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.5124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4794
moved from start:          0.7462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   7244  Z= 0.148
  Angle     :  0.643   9.701   9813  Z= 0.334
  Chirality :  0.047   0.282   1116
  Planarity :  0.006   0.069   1274
  Dihedral  :  5.061  20.509    978
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 16.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 12.81 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.44 (0.28), residues: 923
  helix:  0.81 (0.25), residues: 412
  sheet: -0.40 (0.40), residues: 167
  loop : -1.55 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  38 
 TYR   0.020   0.002   TYR D  76 
 PHE   0.030   0.002   PHE C 153 
 TRP   0.017   0.002   TRP C  61 
 HIS   0.010   0.002   HIS D 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7244)
  covalent geometry    : angle       0.64312 ( 9813)
  hydrogen bonds       : bond        0.03452 (  350)
  hydrogen bonds       : angle       5.40161 ( 1020)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   47 MET cc_start: 0.9009 (ptp) cc_final: 0.8769 (ptp)
REVERT: C  252 MET cc_start: 0.6982 (mpp) cc_final: 0.5962 (mpp)
REVERT: C  430 HIS cc_start: 0.8960 (OUTLIER) cc_final: 0.8354 (m90)
REVERT: C  449 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8110 (tpt)
REVERT: D  115 HIS cc_start: 0.6870 (p90) cc_final: 0.6468 (p90)
REVERT: D  123 MET cc_start: 0.1200 (mmm) cc_final: 0.0682 (tpt)
REVERT: D  168 MET cc_start: 0.5976 (mmp) cc_final: 0.4065 (mtt)
REVERT: D  193 LEU cc_start: 0.8273 (tp) cc_final: 0.7654 (tp)
REVERT: D  247 ARG cc_start: 0.2534 (OUTLIER) cc_final: 0.2228 (mtt90)
REVERT: D  379 MET cc_start: 0.5276 (ppp) cc_final: 0.4680 (ppp)
  outliers start: 18
  outliers final: 8
  residues processed: 87
  average time/residue: 0.0857
  time to fit residues: 10.3226
Evaluate side-chains
  81 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  154 ASN
Chi-restraints excluded: chain C residue  210 HIS
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  430 HIS
Chi-restraints excluded: chain C residue  433 ASP
Chi-restraints excluded: chain C residue  449 MET
Chi-restraints excluded: chain D residue   28 HIS
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue  247 ARG
Chi-restraints excluded: chain D residue  434 VAL
Chi-restraints excluded: chain D residue  484 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 76 optimal weight:   30.0000
   chunk 63 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 39 optimal weight:   10.0000
   chunk 92 optimal weight:    7.9990
   chunk 64 optimal weight:    3.9990
   chunk 12 optimal weight:   30.0000
   chunk 23 optimal weight:   30.0000
   chunk 83 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 283 GLN
** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5367 r_free = 0.5367 target = 0.213602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5229 r_free = 0.5229 target = 0.177464 restraints weight = 21743.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.5209 r_free = 0.5209 target = 0.175935 restraints weight = 23019.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5209 r_free = 0.5209 target = 0.175935 restraints weight = 24406.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5209 r_free = 0.5209 target = 0.175935 restraints weight = 24406.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5209 r_free = 0.5209 target = 0.175935 restraints weight = 24406.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.5052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5001
moved from start:          0.8405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.092   7244  Z= 0.202
  Angle     :  0.723  13.892   9813  Z= 0.377
  Chirality :  0.049   0.241   1116
  Planarity :  0.006   0.068   1274
  Dihedral  :  5.474  22.696    978
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 21.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 14.38 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  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: -0.81 (0.27), residues: 923
  helix:  0.49 (0.25), residues: 410
  sheet: -0.71 (0.40), residues: 164
  loop : -1.62 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 181 
 TYR   0.037   0.003   TYR C 428 
 PHE   0.031   0.003   PHE C 418 
 TRP   0.016   0.002   TRP C  61 
 HIS   0.010   0.002   HIS D 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 7244)
  covalent geometry    : angle       0.72260 ( 9813)
  hydrogen bonds       : bond        0.03864 (  350)
  hydrogen bonds       : angle       5.68094 ( 1020)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 78
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  252 MET cc_start: 0.6954 (mpp) cc_final: 0.5393 (mmm)
REVERT: C  430 HIS cc_start: 0.8893 (OUTLIER) cc_final: 0.8278 (m90)
REVERT: C  449 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8077 (tpt)
REVERT: D  115 HIS cc_start: 0.6971 (p90) cc_final: 0.6454 (p90)
REVERT: D  123 MET cc_start: 0.1232 (mmm) cc_final: 0.0897 (tpt)
REVERT: D  168 MET cc_start: 0.5943 (OUTLIER) cc_final: 0.3967 (mtt)
REVERT: D  247 ARG cc_start: 0.2700 (OUTLIER) cc_final: 0.2106 (mtt90)
REVERT: D  379 MET cc_start: 0.5231 (ppp) cc_final: 0.4685 (ppp)
REVERT: D  443 ILE cc_start: 0.8111 (mm) cc_final: 0.7583 (tt)
  outliers start: 26
  outliers final: 13
  residues processed: 98
  average time/residue: 0.0844
  time to fit residues: 11.5079
Evaluate side-chains
  88 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  430 HIS
Chi-restraints excluded: chain C residue  433 ASP
Chi-restraints excluded: chain C residue  449 MET
Chi-restraints excluded: chain D residue    8 VAL
Chi-restraints excluded: chain D residue   28 HIS
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue  124 MET
Chi-restraints excluded: chain D residue  135 MET
Chi-restraints excluded: chain D residue  168 MET
Chi-restraints excluded: chain D residue  247 ARG
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  417 ILE
Chi-restraints excluded: chain D residue  434 VAL
Chi-restraints excluded: chain D residue  481 THR
Chi-restraints excluded: chain D residue  484 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 65 optimal weight:   10.0000
   chunk 55 optimal weight:   20.0000
   chunk 37 optimal weight:   20.0000
   chunk 56 optimal weight:    0.7980
   chunk 46 optimal weight:   10.0000
   chunk 90 optimal weight:    6.9990
   chunk 10 optimal weight:   20.0000
   chunk 87 optimal weight:   20.0000
   chunk 18 optimal weight:    5.9990
   chunk 11 optimal weight:   20.0000
   chunk 3 optimal weight:   30.0000
   overall best weight:    6.7592

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

Flipped N/Q/H residues before XYZ refinement:
C 154 ASN
C 209 GLN
** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 209 GLN
** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 413 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5187 r_free = 0.5187 target = 0.196108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.5099 r_free = 0.5099 target = 0.164538 restraints weight = 22915.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.5076 r_free = 0.5076 target = 0.163794 restraints weight = 23685.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.5074 r_free = 0.5074 target = 0.163641 restraints weight = 24599.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5074 r_free = 0.5074 target = 0.163641 restraints weight = 24485.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.5074 r_free = 0.5074 target = 0.163640 restraints weight = 24484.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.4990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5215
moved from start:          1.0145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.167   7244  Z= 0.303
  Angle     :  0.903  13.607   9813  Z= 0.485
  Chirality :  0.054   0.313   1116
  Planarity :  0.007   0.061   1274
  Dihedral  :  6.523  25.938    978
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 33.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.82 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  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: -1.73 (0.27), residues: 923
  helix: -0.38 (0.24), residues: 407
  sheet: -1.09 (0.40), residues: 163
  loop : -1.96 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 181 
 TYR   0.027   0.004   TYR C 428 
 PHE   0.041   0.004   PHE D 174 
 TRP   0.023   0.004   TRP D 162 
 HIS   0.011   0.003   HIS D 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00685 ( 7244)
  covalent geometry    : angle       0.90290 ( 9813)
  hydrogen bonds       : bond        0.04984 (  350)
  hydrogen bonds       : angle       6.56180 ( 1020)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  252 MET cc_start: 0.7138 (mpp) cc_final: 0.6218 (mmm)
REVERT: C  299 LYS cc_start: 0.9403 (tmtt) cc_final: 0.9164 (pptt)
REVERT: C  449 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7835 (mmm)
REVERT: D  115 HIS cc_start: 0.7106 (p90) cc_final: 0.6554 (p90)
REVERT: D  123 MET cc_start: 0.1282 (mmm) cc_final: 0.0810 (tpt)
REVERT: D  168 MET cc_start: 0.6284 (OUTLIER) cc_final: 0.4358 (mtt)
REVERT: D  181 ARG cc_start: -0.4611 (OUTLIER) cc_final: -0.7015 (ttm170)
REVERT: D  193 LEU cc_start: 0.8586 (tp) cc_final: 0.8353 (tp)
REVERT: D  247 ARG cc_start: 0.2096 (OUTLIER) cc_final: 0.1286 (mtt180)
REVERT: D  379 MET cc_start: 0.6176 (ppp) cc_final: 0.5625 (ppp)
  outliers start: 24
  outliers final: 17
  residues processed: 98
  average time/residue: 0.0992
  time to fit residues: 13.1806
Evaluate side-chains
  92 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  154 ASN
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  433 ASP
Chi-restraints excluded: chain C residue  434 VAL
Chi-restraints excluded: chain C residue  449 MET
Chi-restraints excluded: chain D residue    8 VAL
Chi-restraints excluded: chain D residue   28 HIS
Chi-restraints excluded: chain D residue  135 MET
Chi-restraints excluded: chain D residue  147 CYS
Chi-restraints excluded: chain D residue  168 MET
Chi-restraints excluded: chain D residue  181 ARG
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  247 ARG
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  417 ILE
Chi-restraints excluded: chain D residue  434 VAL
Chi-restraints excluded: chain D residue  476 GLN
Chi-restraints excluded: chain D residue  481 THR
Chi-restraints excluded: chain D residue  484 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 84 optimal weight:    0.0980
   chunk 86 optimal weight:    2.9990
   chunk 83 optimal weight:    7.9990
   chunk 61 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 72 optimal weight:   20.0000
   chunk 74 optimal weight:    2.9990
   chunk 76 optimal weight:    8.9990
   chunk 35 optimal weight:    8.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
C 172 ASN
** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 204 ASN
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 374 ASN
D 404 GLN
D 408 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5406 r_free = 0.5406 target = 0.220985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.5265 r_free = 0.5265 target = 0.198477 restraints weight = 37434.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.5272 r_free = 0.5272 target = 0.199668 restraints weight = 32839.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.5273 r_free = 0.5273 target = 0.200506 restraints weight = 29642.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.5288 r_free = 0.5288 target = 0.201338 restraints weight = 27640.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.5288 r_free = 0.5288 target = 0.201664 restraints weight = 26013.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.5134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4809
moved from start:          0.9912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.114   7244  Z= 0.164
  Angle     :  0.748  14.936   9813  Z= 0.386
  Chirality :  0.048   0.194   1116
  Planarity :  0.006   0.080   1274
  Dihedral  :  5.780  22.676    978
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 20.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 16.86 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  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: -1.06 (0.27), residues: 923
  helix:  0.25 (0.25), residues: 405
  sheet: -0.85 (0.40), residues: 166
  loop : -1.67 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 181 
 TYR   0.022   0.002   TYR D  76 
 PHE   0.017   0.002   PHE D 174 
 TRP   0.018   0.002   TRP D 484 
 HIS   0.012   0.002   HIS D 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 7244)
  covalent geometry    : angle       0.74783 ( 9813)
  hydrogen bonds       : bond        0.03794 (  350)
  hydrogen bonds       : angle       5.87540 ( 1020)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 73
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  252 MET cc_start: 0.6359 (mpp) cc_final: 0.4318 (mmm)
REVERT: C  397 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7133 (mp0)
REVERT: C  405 ILE cc_start: 0.8112 (mm) cc_final: 0.7871 (tp)
REVERT: C  430 HIS cc_start: 0.8948 (OUTLIER) cc_final: 0.8243 (m90)
REVERT: C  449 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7553 (mmm)
REVERT: C  474 TYR cc_start: 0.3320 (m-80) cc_final: 0.3093 (m-80)
REVERT: D  115 HIS cc_start: 0.7120 (p90) cc_final: 0.6538 (p90)
REVERT: D  123 MET cc_start: 0.0908 (mmm) cc_final: 0.0499 (tpt)
REVERT: D  163 MET cc_start: 0.5577 (ptt) cc_final: 0.5276 (ptt)
REVERT: D  166 MET cc_start: 0.6517 (mmt) cc_final: 0.6075 (mmp)
REVERT: D  168 MET cc_start: 0.5487 (OUTLIER) cc_final: 0.3737 (mtt)
REVERT: D  181 ARG cc_start: -0.5017 (OUTLIER) cc_final: -0.7120 (ttm170)
REVERT: D  193 LEU cc_start: 0.8464 (tp) cc_final: 0.8227 (tp)
REVERT: D  379 MET cc_start: 0.6000 (ppp) cc_final: 0.5233 (ppp)
REVERT: D  443 ILE cc_start: 0.8150 (mm) cc_final: 0.7666 (tt)
  outliers start: 26
  outliers final: 15
  residues processed: 89
  average time/residue: 0.0895
  time to fit residues: 10.9762
Evaluate side-chains
  87 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  154 ASN
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  374 ASN
Chi-restraints excluded: chain C residue  430 HIS
Chi-restraints excluded: chain C residue  433 ASP
Chi-restraints excluded: chain C residue  449 MET
Chi-restraints excluded: chain D residue    8 VAL
Chi-restraints excluded: chain D residue   28 HIS
Chi-restraints excluded: chain D residue  168 MET
Chi-restraints excluded: chain D residue  181 ARG
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  417 ILE
Chi-restraints excluded: chain D residue  434 VAL
Chi-restraints excluded: chain D residue  449 MET
Chi-restraints excluded: chain D residue  476 GLN
Chi-restraints excluded: chain D residue  481 THR
Chi-restraints excluded: chain D residue  484 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 47 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 18 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   chunk 67 optimal weight:    9.9990
   chunk 61 optimal weight:    6.9990
   chunk 68 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 60 optimal weight:   20.0000
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5254 r_free = 0.5254 target = 0.203274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.5221 r_free = 0.5221 target = 0.171852 restraints weight = 21611.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.5137 r_free = 0.5137 target = 0.169534 restraints weight = 23809.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.5138 r_free = 0.5138 target = 0.169377 restraints weight = 26223.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5138 r_free = 0.5138 target = 0.169376 restraints weight = 26538.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5138 r_free = 0.5138 target = 0.169376 restraints weight = 26542.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.5069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5094
moved from start:          1.0300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.112   7244  Z= 0.179
  Angle     :  0.768  12.238   9813  Z= 0.398
  Chirality :  0.048   0.192   1116
  Planarity :  0.006   0.066   1274
  Dihedral  :  5.852  21.966    978
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 22.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 17.78 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.94 (0.27), residues: 923
  helix:  0.41 (0.25), residues: 405
  sheet: -0.79 (0.42), residues: 156
  loop : -1.69 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 312 
 TYR   0.019   0.002   TYR D  76 
 PHE   0.021   0.002   PHE D 174 
 TRP   0.016   0.002   TRP D 484 
 HIS   0.011   0.002   HIS D 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 7244)
  covalent geometry    : angle       0.76824 ( 9813)
  hydrogen bonds       : bond        0.03876 (  350)
  hydrogen bonds       : angle       5.90520 ( 1020)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 0.293 
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: C  252 MET cc_start: 0.6927 (mpp) cc_final: 0.5394 (mmm)
REVERT: C  397 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7448 (mp0)
REVERT: C  449 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7717 (mmm)
REVERT: D  115 HIS cc_start: 0.7138 (p90) cc_final: 0.6595 (p90)
REVERT: D  123 MET cc_start: 0.1346 (mmm) cc_final: 0.0865 (tpt)
REVERT: D  166 MET cc_start: 0.6433 (mmt) cc_final: 0.5995 (mmp)
REVERT: D  168 MET cc_start: 0.5916 (OUTLIER) cc_final: 0.4092 (mtt)
REVERT: D  193 LEU cc_start: 0.8525 (tp) cc_final: 0.8295 (tp)
REVERT: D  247 ARG cc_start: 0.2741 (OUTLIER) cc_final: 0.2295 (mpt-90)
REVERT: D  379 MET cc_start: 0.5630 (ppp) cc_final: 0.4974 (ppp)
REVERT: D  443 ILE cc_start: 0.8230 (mm) cc_final: 0.7841 (tt)
  outliers start: 22
  outliers final: 18
  residues processed: 85
  average time/residue: 0.0866
  time to fit residues: 10.2912
Evaluate side-chains
  88 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  154 ASN
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  374 ASN
Chi-restraints excluded: chain C residue  433 ASP
Chi-restraints excluded: chain C residue  434 VAL
Chi-restraints excluded: chain C residue  449 MET
Chi-restraints excluded: chain D residue    8 VAL
Chi-restraints excluded: chain D residue   28 HIS
Chi-restraints excluded: chain D residue   44 LYS
Chi-restraints excluded: chain D residue  135 MET
Chi-restraints excluded: chain D residue  168 MET
Chi-restraints excluded: chain D residue  181 ARG
Chi-restraints excluded: chain D residue  247 ARG
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  417 ILE
Chi-restraints excluded: chain D residue  434 VAL
Chi-restraints excluded: chain D residue  476 GLN
Chi-restraints excluded: chain D residue  481 THR
Chi-restraints excluded: chain D residue  484 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 33 optimal weight:   30.0000
   chunk 85 optimal weight:    6.9990
   chunk 80 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 21 optimal weight:    8.9990
   chunk 61 optimal weight:    3.9990
   chunk 43 optimal weight:    8.9990
   chunk 78 optimal weight:    0.9980
   chunk 15 optimal weight:    0.4980
   chunk 53 optimal weight:    7.9990
   chunk 77 optimal weight:    4.9990
   overall best weight:    3.4986

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

Flipped N/Q/H residues before XYZ refinement:
** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 257 HIS ** 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 = 0.5356 r_free = 0.5356 target = 0.204506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.5199 r_free = 0.5199 target = 0.170837 restraints weight = 23389.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 17)----------------|
| r_work = 0.5172 r_free = 0.5172 target = 0.170481 restraints weight = 24865.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.5155 r_free = 0.5155 target = 0.169559 restraints weight = 26028.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5155 r_free = 0.5155 target = 0.169559 restraints weight = 26718.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5155 r_free = 0.5155 target = 0.169559 restraints weight = 26718.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.4978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5254
moved from start:          1.0709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.114   7244  Z= 0.182
  Angle     :  0.785  14.518   9813  Z= 0.405
  Chirality :  0.049   0.225   1116
  Planarity :  0.006   0.059   1274
  Dihedral  :  5.991  27.093    978
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 22.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 18.30 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  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: -0.95 (0.28), residues: 923
  helix:  0.44 (0.25), residues: 402
  sheet: -0.86 (0.41), residues: 156
  loop : -1.70 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 240 
 TYR   0.017   0.002   TYR D  76 
 PHE   0.023   0.002   PHE D 174 
 TRP   0.015   0.002   TRP D 162 
 HIS   0.011   0.002   HIS D 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 7244)
  covalent geometry    : angle       0.78465 ( 9813)
  hydrogen bonds       : bond        0.03980 (  350)
  hydrogen bonds       : angle       5.91189 ( 1020)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.286 
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: C  252 MET cc_start: 0.7191 (mpp) cc_final: 0.5721 (mmm)
REVERT: C  379 MET cc_start: 0.6426 (ptt) cc_final: 0.6159 (ptt)
REVERT: C  400 ASP cc_start: 0.8835 (m-30) cc_final: 0.8147 (p0)
REVERT: C  449 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7707 (mmm)
REVERT: D  115 HIS cc_start: 0.7268 (p90) cc_final: 0.6816 (p90)
REVERT: D  166 MET cc_start: 0.6519 (mmt) cc_final: 0.6268 (mmp)
REVERT: D  168 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.4427 (mtt)
REVERT: D  247 ARG cc_start: 0.2633 (OUTLIER) cc_final: 0.2304 (mpt-90)
REVERT: D  261 MET cc_start: 0.3973 (mtt) cc_final: 0.3706 (mtt)
REVERT: D  379 MET cc_start: 0.6328 (ppp) cc_final: 0.5536 (ppp)
REVERT: D  443 ILE cc_start: 0.8093 (mm) cc_final: 0.7768 (tt)
  outliers start: 21
  outliers final: 18
  residues processed: 87
  average time/residue: 0.0811
  time to fit residues: 9.9884
Evaluate side-chains
  89 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  154 ASN
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  433 ASP
Chi-restraints excluded: chain C residue  434 VAL
Chi-restraints excluded: chain C residue  449 MET
Chi-restraints excluded: chain D residue    8 VAL
Chi-restraints excluded: chain D residue   28 HIS
Chi-restraints excluded: chain D residue  135 MET
Chi-restraints excluded: chain D residue  168 MET
Chi-restraints excluded: chain D residue  181 ARG
Chi-restraints excluded: chain D residue  247 ARG
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  417 ILE
Chi-restraints excluded: chain D residue  434 VAL
Chi-restraints excluded: chain D residue  476 GLN
Chi-restraints excluded: chain D residue  481 THR
Chi-restraints excluded: chain D residue  484 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 87 optimal weight:   10.0000
   chunk 90 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 30 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    3.0386

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

Flipped N/Q/H residues before XYZ refinement:
** D 257 HIS ** 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 = 0.5298 r_free = 0.5298 target = 0.187618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4980 r_free = 0.4980 target = 0.160151 restraints weight = 32534.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4998 r_free = 0.4998 target = 0.161583 restraints weight = 29138.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 13)----------------|
| r_work = 0.5004 r_free = 0.5004 target = 0.162200 restraints weight = 26768.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.5011 r_free = 0.5011 target = 0.162809 restraints weight = 25428.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.5023 r_free = 0.5023 target = 0.163763 restraints weight = 24367.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.4978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5143
moved from start:          1.0991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.100   7244  Z= 0.169
  Angle     :  0.763  11.635   9813  Z= 0.391
  Chirality :  0.048   0.169   1116
  Planarity :  0.006   0.054   1274
  Dihedral  :  5.867  24.384    978
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 22.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.04 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  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: -0.83 (0.28), residues: 923
  helix:  0.55 (0.26), residues: 402
  sheet: -0.85 (0.41), residues: 146
  loop : -1.61 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 240 
 TYR   0.025   0.002   TYR D  76 
 PHE   0.027   0.002   PHE D 174 
 TRP   0.015   0.002   TRP D 484 
 HIS   0.011   0.002   HIS D 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 7244)
  covalent geometry    : angle       0.76297 ( 9813)
  hydrogen bonds       : bond        0.03709 (  350)
  hydrogen bonds       : angle       5.87273 ( 1020)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1649.13 seconds
wall clock time: 29 minutes 25.19 seconds (1765.19 seconds total)