Starting phenix.real_space_refine
on Sun May 11 16:02:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9em9_19814/05_2025/9em9_19814.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9em9_19814/05_2025/9em9_19814.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9em9_19814/05_2025/9em9_19814.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9em9_19814/05_2025/9em9_19814.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9em9_19814/05_2025/9em9_19814.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9em9_19814/05_2025/9em9_19814.cif"
  }
  resolution = 3.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.066
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      24      5.16       5
     C    5110      2.51       5
     N    1430      2.21       5
     O    1610      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8182
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 4058
          Classifications: {'peptide': 512}
          Link IDs: {'PTRANS': 14, 'TRANS': 497}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GNP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.30, per 1000 atoms: 1.01
  Number of scatterers: 8182
  At special positions: 0
  Unit cell: (128.112, 99.552, 102.816, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      24     16.00
     P       6     15.00
     Mg      2     11.99
     O    1610      8.00
     N    1430      7.00
     C    5110      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   8 " - pdb=" SG  CYS A 763 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   8 " - pdb=" SG  CYS B 763 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.00
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1936

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 5 sheets defined
      65.4% alpha, 7.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 24
      removed outlier: 4.298A  pdb=" N   ARG A  12 " --> pdb=" O   CYS A   8 " (cutoff:3.500A)
      removed outlier: 5.250A  pdb=" N   GLU A  13 " --> pdb=" O   GLN A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 32
    Processing helix  chain 'A' and resid 33 through 46
      removed outlier: 4.003A  pdb=" N   VAL A  37 " --> pdb=" O   ASP A  33 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER A  46 " --> pdb=" O   GLY A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 70
    Processing helix  chain 'A' and resid 92 through 95
    Processing helix  chain 'A' and resid 104 through 120
    Processing helix  chain 'A' and resid 130 through 149
    Processing helix  chain 'A' and resid 154 through 174
    Processing helix  chain 'A' and resid 195 through 203
      removed outlier: 3.544A  pdb=" N   ARG A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 225
      removed outlier: 3.801A  pdb=" N   LYS A 224 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ASP A 225 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 220 through 225'
    Processing helix  chain 'A' and resid 239 through 252
    Processing helix  chain 'A' and resid 263 through 268
    Processing helix  chain 'A' and resid 271 through 284
      removed outlier: 3.614A  pdb=" N   ASN A 284 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 290
      removed outlier: 3.847A  pdb=" N   ASP A 289 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 304
      removed outlier: 3.883A  pdb=" N   TRP A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   TYR A 303 " --> pdb=" O   ASP A 299 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASN A 304 " --> pdb=" O   ASP A 300 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 298 through 304'
    Processing helix  chain 'A' and resid 304 through 319
    Processing helix  chain 'A' and resid 329 through 342
      removed outlier: 3.812A  pdb=" N   TYR A 335 " --> pdb=" O   LEU A 331 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN A 341 " --> pdb=" O   SER A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 359
      removed outlier: 4.112A  pdb=" N   LYS A 359 " --> pdb=" O   ALA A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 379
      removed outlier: 4.284A  pdb=" N   TYR A 377 " --> pdb=" O   GLU A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 387
    Processing helix  chain 'A' and resid 400 through 423
      removed outlier: 3.719A  pdb=" N   ILE A 406 " --> pdb=" O   ASN A 402 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLU A 409 " --> pdb=" O   ARG A 405 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   ILE A 412 " --> pdb=" O   SER A 408 " (cutoff:3.500A)
      Proline residue:  A 413  - end of helix
      removed outlier: 3.746A  pdb=" N   ASP A 416 " --> pdb=" O   ILE A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 437
      removed outlier: 3.562A  pdb=" N   SER A 429 " --> pdb=" O   GLU A 425 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA A 436 " --> pdb=" O   GLY A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 472
      Proline residue:  A 453  - end of helix
    Processing helix  chain 'A' and resid 736 through 767
    Processing helix  chain 'B' and resid 5 through 24
      removed outlier: 4.299A  pdb=" N   ARG B  12 " --> pdb=" O   CYS B   8 " (cutoff:3.500A)
      removed outlier: 5.250A  pdb=" N   GLU B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 32
    Processing helix  chain 'B' and resid 33 through 46
      removed outlier: 4.002A  pdb=" N   VAL B  37 " --> pdb=" O   ASP B  33 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER B  46 " --> pdb=" O   GLY B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 70
    Processing helix  chain 'B' and resid 92 through 95
    Processing helix  chain 'B' and resid 104 through 120
    Processing helix  chain 'B' and resid 130 through 149
    Processing helix  chain 'B' and resid 154 through 174
    Processing helix  chain 'B' and resid 195 through 203
      removed outlier: 3.544A  pdb=" N   ARG B 203 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 225
      removed outlier: 3.801A  pdb=" N   LYS B 224 " --> pdb=" O   HIS B 220 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ASP B 225 " --> pdb=" O   SER B 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 220 through 225'
    Processing helix  chain 'B' and resid 239 through 252
    Processing helix  chain 'B' and resid 263 through 268
    Processing helix  chain 'B' and resid 271 through 284
      removed outlier: 3.614A  pdb=" N   ASN B 284 " --> pdb=" O   ARG B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 290
      removed outlier: 3.847A  pdb=" N   ASP B 289 " --> pdb=" O   GLY B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 304
      removed outlier: 3.884A  pdb=" N   TRP B 302 " --> pdb=" O   ILE B 298 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   TYR B 303 " --> pdb=" O   ASP B 299 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASN B 304 " --> pdb=" O   ASP B 300 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 298 through 304'
    Processing helix  chain 'B' and resid 304 through 319
    Processing helix  chain 'B' and resid 329 through 342
      removed outlier: 3.813A  pdb=" N   TYR B 335 " --> pdb=" O   LEU B 331 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN B 341 " --> pdb=" O   SER B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 359
      removed outlier: 4.113A  pdb=" N   LYS B 359 " --> pdb=" O   ALA B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 379
      removed outlier: 4.285A  pdb=" N   TYR B 377 " --> pdb=" O   GLU B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 387
    Processing helix  chain 'B' and resid 400 through 423
      removed outlier: 3.719A  pdb=" N   ILE B 406 " --> pdb=" O   ASN B 402 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLU B 409 " --> pdb=" O   ARG B 405 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   ILE B 412 " --> pdb=" O   SER B 408 " (cutoff:3.500A)
      Proline residue:  B 413  - end of helix
      removed outlier: 3.746A  pdb=" N   ASP B 416 " --> pdb=" O   ILE B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 437
      removed outlier: 3.562A  pdb=" N   SER B 429 " --> pdb=" O   GLU B 425 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA B 436 " --> pdb=" O   GLY B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 472
      Proline residue:  B 453  - end of helix
    Processing helix  chain 'B' and resid 736 through 767
    Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52
      removed outlier: 6.083A  pdb=" N   PHE A  49 " --> pdb=" O   VAL A 228 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   VAL A 230 " --> pdb=" O   PHE A  49 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   ILE A  51 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 8.418A  pdb=" N   ASN A 227 " --> pdb=" O   TYR A  90 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   TYR A  90 " --> pdb=" O   ASN A 227 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ARG A 213 " --> pdb=" O   THR A 101 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ARG A  97 " --> pdb=" O   PHE A 217 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   TYR A 185 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 262
      removed outlier: 6.121A  pdb=" N   CYS A 260 " --> pdb=" O   VAL A 294 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 394
    Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 52
      removed outlier: 6.084A  pdb=" N   PHE B  49 " --> pdb=" O   VAL B 228 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   VAL B 230 " --> pdb=" O   PHE B  49 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   ILE B  51 " --> pdb=" O   VAL B 230 " (cutoff:3.500A)
      removed outlier: 8.417A  pdb=" N   ASN B 227 " --> pdb=" O   TYR B  90 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   TYR B  90 " --> pdb=" O   ASN B 227 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ARG B 213 " --> pdb=" O   THR B 101 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ARG B  97 " --> pdb=" O   PHE B 217 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   TYR B 185 " --> pdb=" O   LEU B 100 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 259 through 262
      removed outlier: 6.121A  pdb=" N   CYS B 260 " --> pdb=" O   VAL B 294 " (cutoff:3.500A)

    464 hydrogen bonds defined for protein.
    1362 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.34

  Time building geometry restraints manager: 2.28 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2782
        1.34 -     1.46: 1387
        1.46 -     1.58: 4101
        1.58 -     1.70: 6
        1.70 -     1.82: 34
  Bond restraints: 8310
  Sorted by residual:
  bond pdb=" N3B GNP A 801 "
       pdb=" PG  GNP A 801 "
    ideal  model  delta    sigma   weight residual
    1.801  1.705  0.096 2.00e-02 2.50e+03 2.31e+01
  bond pdb=" N3B GNP B 801 "
       pdb=" PG  GNP B 801 "
    ideal  model  delta    sigma   weight residual
    1.801  1.705  0.096 2.00e-02 2.50e+03 2.31e+01
  bond pdb=" O5' GNP A 801 "
       pdb=" PA  GNP A 801 "
    ideal  model  delta    sigma   weight residual
    1.660  1.565  0.095 2.00e-02 2.50e+03 2.26e+01
  bond pdb=" O5' GNP B 801 "
       pdb=" PA  GNP B 801 "
    ideal  model  delta    sigma   weight residual
    1.660  1.566  0.094 2.00e-02 2.50e+03 2.23e+01
  bond pdb=" O3A GNP A 801 "
       pdb=" PB  GNP A 801 "
    ideal  model  delta    sigma   weight residual
    1.687  1.635  0.052 2.00e-02 2.50e+03 6.87e+00
  ... (remaining 8305 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 11008
        2.05 -     4.11: 180
        4.11 -     6.16: 40
        6.16 -     8.21: 10
        8.21 -    10.27: 6
  Bond angle restraints: 11244
  Sorted by residual:
  angle pdb=" N   LYS B 263 "
        pdb=" CA  LYS B 263 "
        pdb=" C   LYS B 263 "
      ideal   model   delta    sigma   weight residual
     109.81  120.08  -10.27 2.21e+00 2.05e-01 2.16e+01
  angle pdb=" N   LYS A 263 "
        pdb=" CA  LYS A 263 "
        pdb=" C   LYS A 263 "
      ideal   model   delta    sigma   weight residual
     109.81  120.06  -10.25 2.21e+00 2.05e-01 2.15e+01
  angle pdb=" CA  TYR B 466 "
        pdb=" CB  TYR B 466 "
        pdb=" CG  TYR B 466 "
      ideal   model   delta    sigma   weight residual
     113.90  107.60    6.30 1.80e+00 3.09e-01 1.22e+01
  angle pdb=" CA  TYR A 466 "
        pdb=" CB  TYR A 466 "
        pdb=" CG  TYR A 466 "
      ideal   model   delta    sigma   weight residual
     113.90  107.61    6.29 1.80e+00 3.09e-01 1.22e+01
  angle pdb=" O1B GNP A 801 "
        pdb=" PB  GNP A 801 "
        pdb=" O2B GNP A 801 "
      ideal   model   delta    sigma   weight residual
     119.66  110.05    9.61 3.00e+00 1.11e-01 1.03e+01
  ... (remaining 11239 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.10: 4572
       16.10 -    32.21: 392
       32.21 -    48.31: 76
       48.31 -    64.41: 46
       64.41 -    80.51: 22
  Dihedral angle restraints: 5108
    sinusoidal: 2112
      harmonic: 2996
  Sorted by residual:
  dihedral pdb=" CA  SER B 256 "
           pdb=" C   SER B 256 "
           pdb=" N   ALA B 257 "
           pdb=" CA  ALA B 257 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.18   29.82     0      5.00e+00 4.00e-02 3.56e+01
  dihedral pdb=" CA  SER A 256 "
           pdb=" C   SER A 256 "
           pdb=" N   ALA A 257 "
           pdb=" CA  ALA A 257 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.21   29.79     0      5.00e+00 4.00e-02 3.55e+01
  dihedral pdb=" CA  THR B 255 "
           pdb=" C   THR B 255 "
           pdb=" N   SER B 256 "
           pdb=" CA  SER B 256 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.19   28.81     0      5.00e+00 4.00e-02 3.32e+01
  ... (remaining 5105 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 926
       0.044 -    0.088: 256
       0.088 -    0.132: 59
       0.132 -    0.176: 13
       0.176 -    0.220: 2
  Chirality restraints: 1256
  Sorted by residual:
  chirality pdb=" CA  TYR A 466 "
            pdb=" N   TYR A 466 "
            pdb=" C   TYR A 466 "
            pdb=" CB  TYR A 466 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  TYR B 466 "
            pdb=" N   TYR B 466 "
            pdb=" C   TYR B 466 "
            pdb=" CB  TYR B 466 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  LYS B 263 "
            pdb=" N   LYS B 263 "
            pdb=" C   LYS B 263 "
            pdb=" CB  LYS B 263 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.20e-01
  ... (remaining 1253 not shown)

  Planarity restraints: 1474
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 290 "   -0.409 9.50e-02 1.11e+02   1.85e-01 2.58e+01
        pdb=" NE  ARG A 290 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 290 "   -0.035 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 290 "    0.016 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 290 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 290 "    0.409 9.50e-02 1.11e+02   1.85e-01 2.58e+01
        pdb=" NE  ARG B 290 "   -0.038 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 290 "    0.035 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 290 "   -0.016 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 290 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 372 "    0.017 2.00e-02 2.50e+03   3.44e-02 1.19e+01
        pdb=" C   SER B 372 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   SER B 372 "    0.022 2.00e-02 2.50e+03
        pdb=" N   GLU B 373 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1471 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.46: 28
        2.46 -     3.07: 5636
        3.07 -     3.68: 12218
        3.68 -     4.29: 17778
        4.29 -     4.90: 29257
  Nonbonded interactions: 64917
  Sorted by model distance:
  nonbonded pdb=" O2B GNP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     1.853 2.170
  nonbonded pdb=" O2B GNP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     1.853 2.170
  nonbonded pdb=" OG1 THR B  82 "
            pdb="MG    MG B 802 "
     model   vdw
     1.883 2.170
  nonbonded pdb=" OG1 THR A  82 "
            pdb="MG    MG A 802 "
     model   vdw
     1.885 2.170
  nonbonded pdb=" O1G GNP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     1.937 2.170
  ... (remaining 64912 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             10.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     22.740
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.096   8312  Z= 0.207
  Angle     :  0.754  10.266  11248  Z= 0.419
  Chirality :  0.044   0.220   1256
  Planarity :  0.011   0.185   1474
  Dihedral  : 14.920  80.515   3166
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.24), residues: 1016
  helix: -0.27 (0.19), residues: 600
  sheet: -0.10 (0.41), residues: 118
  loop : -0.68 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 302 
 HIS   0.004   0.001   HIS B 164 
 PHE   0.019   0.002   PHE B 348 
 TYR   0.028   0.005   TYR B 466 
 ARG   0.040   0.004   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13341 (  464)
  hydrogen bonds       : angle       6.65202 ( 1362)
  SS BOND              : bond        0.00171 (    2)
  SS BOND              : angle       1.01650 (    4)
  covalent geometry    : bond        0.00421 ( 8310)
  covalent geometry    : angle       0.75395 (11244)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.934 
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: A  187 MET cc_start: 0.4999 (mmt) cc_final: 0.4727 (mtt)
REVERT: A  444 PHE cc_start: 0.7811 (m-80) cc_final: 0.7586 (m-10)
REVERT: A  447 LEU cc_start: 0.8910 (tp) cc_final: 0.8672 (tt)
REVERT: B  187 MET cc_start: 0.4964 (mmt) cc_final: 0.4708 (mtt)
REVERT: B  444 PHE cc_start: 0.7943 (m-80) cc_final: 0.7713 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2405
  time to fit residues: 46.0015
Evaluate side-chains
  76 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 77 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
A  10 ASN
A  92 ASN
A 276 GLN
A 309 GLN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 417 GLN
B   9 GLN
B  10 ASN
B 276 GLN
B 309 GLN
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 417 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.121191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.097356 restraints weight = 24303.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.096689 restraints weight = 20579.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.097574 restraints weight = 21858.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8312  Z= 0.172
  Angle     :  0.675   9.429  11248  Z= 0.349
  Chirality :  0.043   0.277   1256
  Planarity :  0.005   0.061   1474
  Dihedral  : 10.776  62.326   1186
  Min Nonbonded Distance : 1.791

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.07 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  :  8.94 %
    Favored  : 88.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.26), residues: 1016
  helix:  0.94 (0.20), residues: 604
  sheet:  0.04 (0.44), residues: 122
  loop : -0.02 (0.40), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 302 
 HIS   0.006   0.001   HIS B 164 
 PHE   0.013   0.002   PHE A 319 
 TYR   0.037   0.003   TYR B 201 
 ARG   0.006   0.001   ARG B 738 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04607 (  464)
  hydrogen bonds       : angle       5.05785 ( 1362)
  SS BOND              : bond        0.00601 (    2)
  SS BOND              : angle       0.72767 (    4)
  covalent geometry    : bond        0.00383 ( 8310)
  covalent geometry    : angle       0.67466 (11244)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 80
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   38 GLU cc_start: 0.9043 (tt0) cc_final: 0.8715 (tm-30)
  outliers start: 26
  outliers final: 19
  residues processed: 94
  average time/residue: 0.2059
  time to fit residues: 26.7034
Evaluate side-chains
  72 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 53
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLN
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain B residue  451 LEU
Chi-restraints excluded: chain B residue  461 PHE
Chi-restraints excluded: chain B residue  753 TYR
Chi-restraints excluded: chain B residue  759 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   chunk 49 optimal weight:    3.9990
   chunk 59 optimal weight:    0.1980
   chunk 95 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 94 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  16 ASN
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 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 = 0.4164 r_free = 0.4164 target = 0.120658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.091842 restraints weight = 25184.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.093799 restraints weight = 16000.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.095293 restraints weight = 12075.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.3477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8312  Z= 0.168
  Angle     :  0.685  11.531  11248  Z= 0.347
  Chirality :  0.042   0.225   1256
  Planarity :  0.004   0.048   1474
  Dihedral  :  9.325  51.055   1186
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  :  9.73 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.26), residues: 1016
  helix:  0.75 (0.20), residues: 608
  sheet: -0.31 (0.44), residues: 124
  loop : -0.21 (0.40), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 410 
 HIS   0.007   0.001   HIS B 164 
 PHE   0.015   0.001   PHE A 319 
 TYR   0.044   0.002   TYR B 201 
 ARG   0.004   0.000   ARG B 204 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04341 (  464)
  hydrogen bonds       : angle       4.92972 ( 1362)
  SS BOND              : bond        0.00396 (    2)
  SS BOND              : angle       4.54486 (    4)
  covalent geometry    : bond        0.00373 ( 8310)
  covalent geometry    : angle       0.67938 (11244)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 GLU cc_start: 0.9507 (tt0) cc_final: 0.9281 (tp30)
REVERT: A  454 LEU cc_start: 0.9493 (tp) cc_final: 0.9265 (pp)
REVERT: B   38 GLU cc_start: 0.9506 (tt0) cc_final: 0.8943 (tm-30)
  outliers start: 27
  outliers final: 15
  residues processed: 86
  average time/residue: 0.1699
  time to fit residues: 21.3771
Evaluate side-chains
  76 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  255 THR
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  753 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 93 optimal weight:    0.6980
   chunk 50 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   chunk 73 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
A  10 ASN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   9 GLN
B  10 ASN
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.120447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.097099 restraints weight = 26235.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.096841 restraints weight = 21115.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.097419 restraints weight = 20336.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.4080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8312  Z= 0.178
  Angle     :  0.684  10.942  11248  Z= 0.340
  Chirality :  0.043   0.276   1256
  Planarity :  0.005   0.057   1474
  Dihedral  :  7.334  43.519   1186
  Min Nonbonded Distance : 1.804

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 11.20 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.26), residues: 1016
  helix:  0.89 (0.21), residues: 590
  sheet: -0.64 (0.44), residues: 122
  loop : -0.24 (0.38), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 410 
 HIS   0.001   0.000   HIS B 164 
 PHE   0.015   0.002   PHE B 319 
 TYR   0.039   0.002   TYR A 201 
 ARG   0.003   0.000   ARG B 738 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04302 (  464)
  hydrogen bonds       : angle       4.95374 ( 1362)
  SS BOND              : bond        0.00599 (    2)
  SS BOND              : angle       2.08477 (    4)
  covalent geometry    : bond        0.00404 ( 8310)
  covalent geometry    : angle       0.68321 (11244)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 69
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7779 (tm-30)
REVERT: A  270 MET cc_start: 0.8526 (mmm) cc_final: 0.8306 (mtt)
REVERT: B   38 GLU cc_start: 0.9068 (tt0) cc_final: 0.8625 (tm-30)
REVERT: B  115 LEU cc_start: 0.8930 (mm) cc_final: 0.8674 (mm)
REVERT: B  197 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7520 (tm-30)
  outliers start: 26
  outliers final: 20
  residues processed: 90
  average time/residue: 0.1705
  time to fit residues: 22.4040
Evaluate side-chains
  81 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLN
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  753 TYR
Chi-restraints excluded: chain B residue  759 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0970
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.120595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.097253 restraints weight = 25539.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.096310 restraints weight = 22456.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.096825 restraints weight = 23056.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.4307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8312  Z= 0.151
  Angle     :  0.693  14.637  11248  Z= 0.331
  Chirality :  0.044   0.354   1256
  Planarity :  0.004   0.046   1474
  Dihedral  :  6.227  43.057   1186
  Min Nonbonded Distance : 1.813

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 12.10 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.26), residues: 1016
  helix:  0.93 (0.21), residues: 598
  sheet: -0.55 (0.45), residues: 122
  loop : -0.31 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 410 
 HIS   0.003   0.000   HIS B 164 
 PHE   0.015   0.001   PHE B 319 
 TYR   0.035   0.002   TYR B 201 
 ARG   0.002   0.000   ARG B  12 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04066 (  464)
  hydrogen bonds       : angle       4.94354 ( 1362)
  SS BOND              : bond        0.00498 (    2)
  SS BOND              : angle       1.84872 (    4)
  covalent geometry    : bond        0.00335 ( 8310)
  covalent geometry    : angle       0.69186 (11244)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 MET cc_start: 0.4587 (mtt) cc_final: 0.4383 (mtm)
REVERT: A  197 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7982 (tm-30)
REVERT: B   38 GLU cc_start: 0.9081 (tt0) cc_final: 0.8641 (tm-30)
REVERT: B  115 LEU cc_start: 0.9000 (mm) cc_final: 0.8727 (mm)
REVERT: B  197 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7793 (tm-30)
  outliers start: 23
  outliers final: 18
  residues processed: 85
  average time/residue: 0.1876
  time to fit residues: 22.7552
Evaluate side-chains
  82 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  753 TYR
Chi-restraints excluded: chain B residue  759 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 35 optimal weight:    0.0050
   chunk 59 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 62 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 51 optimal weight:    9.9990
   chunk 88 optimal weight:    0.0980
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  16 ASN
B  80 HIS
B  92 ASN
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.120604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.097161 restraints weight = 24694.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.096584 restraints weight = 21408.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.097295 restraints weight = 20775.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.4575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8312  Z= 0.121
  Angle     :  0.659  12.815  11248  Z= 0.316
  Chirality :  0.044   0.326   1256
  Planarity :  0.004   0.043   1474
  Dihedral  :  5.641  35.723   1186
  Min Nonbonded Distance : 1.850

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.91 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.26), residues: 1016
  helix:  1.05 (0.21), residues: 602
  sheet: -0.58 (0.45), residues: 122
  loop : -0.27 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 410 
 HIS   0.001   0.000   HIS B 164 
 PHE   0.011   0.001   PHE A 319 
 TYR   0.034   0.002   TYR B 462 
 ARG   0.004   0.000   ARG B 204 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03740 (  464)
  hydrogen bonds       : angle       4.76585 ( 1362)
  SS BOND              : bond        0.00407 (    2)
  SS BOND              : angle       2.28799 (    4)
  covalent geometry    : bond        0.00259 ( 8310)
  covalent geometry    : angle       0.65801 (11244)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7856 (tm-30)
REVERT: A  201 TYR cc_start: 0.6119 (p90) cc_final: 0.5822 (p90)
REVERT: B   38 GLU cc_start: 0.8991 (tt0) cc_final: 0.8774 (tp30)
REVERT: B  115 LEU cc_start: 0.8914 (mm) cc_final: 0.8652 (mm)
REVERT: B  197 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7674 (tm-30)
REVERT: B  749 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8249 (tttt)
  outliers start: 15
  outliers final: 11
  residues processed: 77
  average time/residue: 0.1973
  time to fit residues: 21.5729
Evaluate side-chains
  75 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  749 LYS
Chi-restraints excluded: chain B residue  753 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 99 optimal weight:    0.2980
   chunk 30 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0070
   chunk 63 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0670
   chunk 27 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0980
   chunk 54 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9990
   overall best weight:    0.2736

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

Flipped N/Q/H residues before XYZ refinement:
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 452 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.122459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.099746 restraints weight = 25818.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.098463 restraints weight = 23280.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.099262 restraints weight = 22570.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.4770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8312  Z= 0.110
  Angle     :  0.672  14.156  11248  Z= 0.314
  Chirality :  0.044   0.354   1256
  Planarity :  0.003   0.037   1474
  Dihedral  :  5.400  36.738   1186
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.46 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.26), residues: 1016
  helix:  1.06 (0.21), residues: 602
  sheet: -0.56 (0.46), residues: 122
  loop : -0.26 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 410 
 HIS   0.002   0.000   HIS B 164 
 PHE   0.008   0.001   PHE A 292 
 TYR   0.033   0.001   TYR B 201 
 ARG   0.003   0.000   ARG B 204 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03706 (  464)
  hydrogen bonds       : angle       4.71448 ( 1362)
  SS BOND              : bond        0.00118 (    2)
  SS BOND              : angle       2.10525 (    4)
  covalent geometry    : bond        0.00227 ( 8310)
  covalent geometry    : angle       0.67065 (11244)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7546 (tm-30)
REVERT: A  201 TYR cc_start: 0.6138 (p90) cc_final: 0.5840 (p90)
REVERT: A  462 TYR cc_start: 0.8093 (t80) cc_final: 0.7852 (t80)
REVERT: B   38 GLU cc_start: 0.9040 (tt0) cc_final: 0.8788 (tp30)
REVERT: B  115 LEU cc_start: 0.8943 (mm) cc_final: 0.8681 (mm)
REVERT: B  197 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7767 (tm-30)
REVERT: B  749 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8230 (tttt)
  outliers start: 18
  outliers final: 15
  residues processed: 80
  average time/residue: 0.2004
  time to fit residues: 22.9091
Evaluate side-chains
  82 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  749 LYS
Chi-restraints excluded: chain B residue  753 TYR
Chi-restraints excluded: chain B residue  759 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 28 optimal weight:    0.4980
   chunk 40 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 88 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0980
   chunk 63 optimal weight:    0.0470
   overall best weight:    0.3878

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

Flipped N/Q/H residues before XYZ refinement:
A  80 HIS
A 111 GLN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 452 GLN
B 220 HIS
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 772 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.120640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.096847 restraints weight = 24726.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.096528 restraints weight = 20154.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.097204 restraints weight = 20827.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.4945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8312  Z= 0.117
  Angle     :  0.651  12.709  11248  Z= 0.315
  Chirality :  0.045   0.346   1256
  Planarity :  0.003   0.033   1474
  Dihedral  :  5.333  38.879   1186
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 14.14 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.26), residues: 1016
  helix:  1.06 (0.21), residues: 602
  sheet: -0.46 (0.47), residues: 122
  loop : -0.27 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 410 
 HIS   0.003   0.000   HIS B 164 
 PHE   0.009   0.001   PHE A 319 
 TYR   0.035   0.002   TYR B 462 
 ARG   0.004   0.000   ARG A 390 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03751 (  464)
  hydrogen bonds       : angle       4.72268 ( 1362)
  SS BOND              : bond        0.00389 (    2)
  SS BOND              : angle       1.82799 (    4)
  covalent geometry    : bond        0.00248 ( 8310)
  covalent geometry    : angle       0.65066 (11244)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7408 (tm-30)
REVERT: A  201 TYR cc_start: 0.6139 (p90) cc_final: 0.5886 (p90)
REVERT: A  462 TYR cc_start: 0.8116 (t80) cc_final: 0.7862 (t80)
REVERT: A  742 LEU cc_start: 0.7911 (mt) cc_final: 0.7639 (tp)
REVERT: B   38 GLU cc_start: 0.9046 (tt0) cc_final: 0.8811 (tp30)
REVERT: B  749 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8182 (tttt)
  outliers start: 19
  outliers final: 16
  residues processed: 80
  average time/residue: 0.1850
  time to fit residues: 21.8101
Evaluate side-chains
  87 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  461 PHE
Chi-restraints excluded: chain B residue  749 LYS
Chi-restraints excluded: chain B residue  753 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0980
   chunk 85 optimal weight:    1.9990
   chunk 7 optimal weight:    0.4980
   chunk 70 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 92 optimal weight:    0.3980
   chunk 14 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 452 GLN
** B 380 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 = 0.4144 r_free = 0.4144 target = 0.119893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.096053 restraints weight = 24866.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.095480 restraints weight = 20226.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.096069 restraints weight = 20440.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.5101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8312  Z= 0.133
  Angle     :  0.682  13.273  11248  Z= 0.326
  Chirality :  0.045   0.357   1256
  Planarity :  0.004   0.038   1474
  Dihedral  :  5.377  40.795   1186
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 14.59 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.26), residues: 1016
  helix:  0.95 (0.21), residues: 606
  sheet: -0.50 (0.47), residues: 122
  loop : -0.19 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 410 
 HIS   0.003   0.000   HIS B 164 
 PHE   0.011   0.001   PHE B 319 
 TYR   0.040   0.002   TYR B 201 
 ARG   0.007   0.000   ARG A 204 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03828 (  464)
  hydrogen bonds       : angle       4.79015 ( 1362)
  SS BOND              : bond        0.00230 (    2)
  SS BOND              : angle       1.56732 (    4)
  covalent geometry    : bond        0.00292 ( 8310)
  covalent geometry    : angle       0.68159 (11244)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7459 (tm-30)
REVERT: A  742 LEU cc_start: 0.7888 (mt) cc_final: 0.7632 (tp)
REVERT: B   38 GLU cc_start: 0.9018 (tt0) cc_final: 0.8791 (tp30)
REVERT: B  452 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8176 (mm-40)
  outliers start: 18
  outliers final: 15
  residues processed: 75
  average time/residue: 0.1873
  time to fit residues: 20.4314
Evaluate side-chains
  75 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  753 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 28 optimal weight:    0.4980
   chunk 57 optimal weight:    0.1980
   chunk 59 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0570
   chunk 101 optimal weight:    4.9990
   chunk 88 optimal weight:    0.0980
   chunk 85 optimal weight:    0.3980
   chunk 97 optimal weight:    0.8980
   chunk 17 optimal weight:    0.4980
   overall best weight:    0.2498

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

Flipped N/Q/H residues before XYZ refinement:
A 120 ASN
A 276 GLN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 452 GLN
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.120456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.096799 restraints weight = 24803.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.096898 restraints weight = 19302.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.097313 restraints weight = 18713.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.5272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8312  Z= 0.116
  Angle     :  0.692  13.630  11248  Z= 0.335
  Chirality :  0.045   0.361   1256
  Planarity :  0.003   0.036   1474
  Dihedral  :  5.227  41.478   1186
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 14.93 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.26), residues: 1016
  helix:  1.04 (0.21), residues: 604
  sheet: -0.49 (0.48), residues: 122
  loop : -0.22 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B 410 
 HIS   0.002   0.000   HIS B 164 
 PHE   0.012   0.001   PHE B 444 
 TYR   0.039   0.002   TYR B 201 
 ARG   0.005   0.000   ARG A 204 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03664 (  464)
  hydrogen bonds       : angle       4.80592 ( 1362)
  SS BOND              : bond        0.00282 (    2)
  SS BOND              : angle       1.73282 (    4)
  covalent geometry    : bond        0.00241 ( 8310)
  covalent geometry    : angle       0.69165 (11244)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  452 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8025 (mm-40)
  outliers start: 17
  outliers final: 14
  residues processed: 70
  average time/residue: 0.1737
  time to fit residues: 18.1820
Evaluate side-chains
  71 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  461 PHE
Chi-restraints excluded: chain B residue  753 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 77 optimal weight:    0.0170
   chunk 56 optimal weight:    2.9990
   chunk 55 optimal weight:    0.2980
   chunk 78 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 82 optimal weight:    0.2980
   chunk 49 optimal weight:    1.9990
   chunk 91 optimal weight:    0.3980
   chunk 2 optimal weight:    0.4980
   chunk 92 optimal weight:    0.6980
   overall best weight:    0.3018

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

Flipped N/Q/H residues before XYZ refinement:
A 120 ASN
A 276 GLN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 GLN
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.121440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.097810 restraints weight = 24976.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.097466 restraints weight = 19814.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.098004 restraints weight = 19157.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.5405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8312  Z= 0.116
  Angle     :  0.702  13.620  11248  Z= 0.340
  Chirality :  0.045   0.366   1256
  Planarity :  0.003   0.033   1474
  Dihedral  :  5.201  42.933   1186
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 15.05 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.26), residues: 1016
  helix:  1.05 (0.21), residues: 604
  sheet: -0.51 (0.48), residues: 122
  loop : -0.24 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B 410 
 HIS   0.002   0.000   HIS B 164 
 PHE   0.012   0.001   PHE B 444 
 TYR   0.042   0.002   TYR A 201 
 ARG   0.006   0.000   ARG A 204 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03641 (  464)
  hydrogen bonds       : angle       4.82872 ( 1362)
  SS BOND              : bond        0.00361 (    2)
  SS BOND              : angle       1.41329 (    4)
  covalent geometry    : bond        0.00243 ( 8310)
  covalent geometry    : angle       0.70188 (11244)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2717.08 seconds
wall clock time: 48 minutes 53.22 seconds (2933.22 seconds total)