Starting phenix.real_space_refine
on Tue Apr 29 00:26:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9em9_19814/04_2025/9em9_19814.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9em9_19814/04_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_19814/04_2025/9em9_19814.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9em9_19814/04_2025/9em9_19814.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9em9_19814/04_2025/9em9_19814.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9em9_19814/04_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 9.00, per 1000 atoms: 1.10
  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: 2.41
  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: 0.88
  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: 2.46

  Time building geometry restraints manager: 2.52 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: 0.04
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:             8.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.200
  Find NCS groups from input model:        0.150
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.800
-------------------------------------------------------------------------------
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  : 0.866 
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: 0.2430
  time to fit residues: 46.5946
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  : 0.981 
-------------------------------------------------------------------------------
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 = 24303.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.096695 restraints weight = 20578.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.097577 restraints weight = 21852.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
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       5.05786 ( 1362)
  SS BOND              : bond        0.00600 (    2)
  SS BOND              : angle       0.72765 (    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  : 1.019 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   38 GLU cc_start: 0.9044 (tt0) cc_final: 0.8715 (tm-30)
  outliers start: 26
  outliers final: 19
  residues processed: 94
  average time/residue: 0.2195
  time to fit residues: 28.5794
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  : 0.972 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 49 optimal weight:    4.9990
   chunk 59 optimal weight:    0.3980
   chunk 95 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 94 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.7584

-------------------------------------------------------------------------------
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 = 0.4166 r_free = 0.4166 target = 0.120703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.091930 restraints weight = 25171.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.093986 restraints weight = 16125.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.095272 restraints weight = 12050.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.3473

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= 0.169
  Angle     :  0.688  11.380  11248  Z= 0.346
  Chirality :  0.042   0.214   1256
  Planarity :  0.004   0.049   1474
  Dihedral  :  9.340  51.213   1186
  Min Nonbonded Distance : 1.820

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 10.18 %
    Favored  : 86.88 %
  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:  0.45 (0.26), residues: 1016
  helix:  0.79 (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   0.007   0.001   TRP A 410 
 HIS   0.006   0.001   HIS B 164 
 PHE   0.015   0.001   PHE A 319 
 TYR   0.043   0.002   TYR B 201 
 ARG   0.004   0.000   ARG B 204 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04346 (  464)
  hydrogen bonds       : angle       4.93904 ( 1362)
  SS BOND              : bond        0.00037 (    2)
  SS BOND              : angle       4.92625 (    4)
  covalent geometry    : bond        0.00381 ( 8310)
  covalent geometry    : angle       0.68161 (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
  94 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 68
  time to evaluate  : 1.061 
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: 0.9519 (tt0) cc_final: 0.9290 (tp30)
REVERT: B   38 GLU cc_start: 0.9519 (tt0) cc_final: 0.8952 (tm-30)
  outliers start: 26
  outliers final: 15
  residues processed: 83
  average time/residue: 0.3136
  time to fit residues: 38.1058
Evaluate side-chains
  74 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 0 optimal weight:    9.9990
   chunk 93 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   chunk 73 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 8 optimal weight:    0.3980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
A  10 ASN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   9 GLN
B  10 ASN
B  80 HIS
** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.120821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.092085 restraints weight = 26306.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.094373 restraints weight = 15915.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.095942 restraints weight = 11631.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.4059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8312  Z= 0.170
  Angle     :  0.671  11.620  11248  Z= 0.335
  Chirality :  0.043   0.298   1256
  Planarity :  0.004   0.053   1474
  Dihedral  :  7.369  43.014   1186
  Min Nonbonded Distance : 1.813

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 11.09 %
    Favored  : 86.20 %
  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: 590
  sheet: -0.61 (0.45), residues: 122
  loop : -0.25 (0.38), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 410 
 HIS   0.002   0.000   HIS B 164 
 PHE   0.014   0.001   PHE B 319 
 TYR   0.038   0.002   TYR A 201 
 ARG   0.003   0.000   ARG B 738 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04226 (  464)
  hydrogen bonds       : angle       4.87147 ( 1362)
  SS BOND              : bond        0.00404 (    2)
  SS BOND              : angle       2.73310 (    4)
  covalent geometry    : bond        0.00380 ( 8310)
  covalent geometry    : angle       0.66877 (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
  92 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 68
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 GLU cc_start: 0.9571 (tt0) cc_final: 0.9320 (tp30)
REVERT: A  197 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7845 (tm-30)
REVERT: A  270 MET cc_start: 0.8395 (mmm) cc_final: 0.8187 (mtt)
REVERT: A  444 PHE cc_start: 0.6909 (m-10) cc_final: 0.6331 (m-10)
REVERT: A  454 LEU cc_start: 0.9538 (tp) cc_final: 0.9303 (pp)
REVERT: B   38 GLU cc_start: 0.9566 (tt0) cc_final: 0.8901 (tm-30)
REVERT: B  115 LEU cc_start: 0.9104 (mm) cc_final: 0.8842 (mm)
REVERT: B  197 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7520 (tm-30)
  outliers start: 24
  outliers final: 18
  residues processed: 86
  average time/residue: 0.1883
  time to fit residues: 23.2993
Evaluate side-chains
  81 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    0.4980
   chunk 33 optimal weight:    0.6980
   chunk 82 optimal weight:    0.0370
   chunk 78 optimal weight:    0.8980
   chunk 101 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 57 optimal weight:    0.2980
   chunk 46 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.4258

-------------------------------------------------------------------------------
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 = 0.4194 r_free = 0.4194 target = 0.121856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.099418 restraints weight = 25252.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.098560 restraints weight = 22609.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.099112 restraints weight = 23203.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.4260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8312  Z= 0.128
  Angle     :  0.665  12.084  11248  Z= 0.325
  Chirality :  0.042   0.366   1256
  Planarity :  0.004   0.041   1474
  Dihedral  :  6.205  37.128   1186
  Min Nonbonded Distance : 1.832

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.99 %
    Favored  : 85.97 %
  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:  0.60 (0.26), residues: 1016
  helix:  0.99 (0.20), residues: 602
  sheet: -0.46 (0.45), residues: 122
  loop : -0.24 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 410 
 HIS   0.002   0.000   HIS B 164 
 PHE   0.012   0.001   PHE B 319 
 TYR   0.033   0.002   TYR B 201 
 ARG   0.003   0.000   ARG A 204 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03914 (  464)
  hydrogen bonds       : angle       4.83778 ( 1362)
  SS BOND              : bond        0.00394 (    2)
  SS BOND              : angle       6.25927 (    4)
  covalent geometry    : bond        0.00277 ( 8310)
  covalent geometry    : angle       0.65466 (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
  89 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.950 
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: 0.8214 (tm-30) cc_final: 0.7769 (tm-30)
REVERT: B   38 GLU cc_start: 0.8905 (tt0) cc_final: 0.8544 (tm-30)
REVERT: B  115 LEU cc_start: 0.8860 (mm) cc_final: 0.8614 (mm)
REVERT: B  197 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7645 (tm-30)
  outliers start: 18
  outliers final: 15
  residues processed: 82
  average time/residue: 0.1977
  time to fit residues: 23.1068
Evaluate side-chains
  74 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  431 ILE
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain A residue  759 SER
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
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:    0.0980
   chunk 59 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 62 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 42 optimal weight:    0.4980
   chunk 40 optimal weight:    0.6980
   chunk 51 optimal weight:   10.0000
   chunk 88 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  16 ASN
B  92 ASN
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.121067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.097207 restraints weight = 24769.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.096416 restraints weight = 20448.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.097195 restraints weight = 21816.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.4542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8312  Z= 0.137
  Angle     :  0.691  15.470  11248  Z= 0.325
  Chirality :  0.044   0.322   1256
  Planarity :  0.004   0.043   1474
  Dihedral  :  5.714  36.687   1186
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.01 %
    Favored  : 84.62 %
  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:  0.60 (0.26), residues: 1016
  helix:  1.01 (0.21), residues: 602
  sheet: -0.59 (0.47), residues: 118
  loop : -0.22 (0.38), residues: 296

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   0.013   0.001   PHE A 319 
 TYR   0.037   0.002   TYR B 201 
 ARG   0.004   0.000   ARG B 204 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03875 (  464)
  hydrogen bonds       : angle       4.77777 ( 1362)
  SS BOND              : bond        0.00822 (    2)
  SS BOND              : angle       2.75613 (    4)
  covalent geometry    : bond        0.00301 ( 8310)
  covalent geometry    : angle       0.68873 (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
  89 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7843 (tm-30)
REVERT: A  201 TYR cc_start: 0.6104 (p90) cc_final: 0.5869 (p90)
REVERT: A  742 LEU cc_start: 0.7900 (mt) cc_final: 0.7574 (tp)
REVERT: B   38 GLU cc_start: 0.9029 (tt0) cc_final: 0.8778 (tp30)
REVERT: B  115 LEU cc_start: 0.8950 (mm) cc_final: 0.8691 (mm)
REVERT: B  749 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8230 (tttt)
  outliers start: 21
  outliers final: 18
  residues processed: 81
  average time/residue: 0.2135
  time to fit residues: 25.6960
Evaluate side-chains
  84 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 65
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
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  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  749 LYS
Chi-restraints excluded: chain B residue  753 TYR
Chi-restraints excluded: chain B residue  759 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 99 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0010
   chunk 33 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 54 optimal weight:    9.9990
   chunk 13 optimal weight:    0.8980
   chunk 87 optimal weight:    0.3980
   chunk 96 optimal weight:    0.9990
   overall best weight:    0.5386

-------------------------------------------------------------------------------
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 = 0.4165 r_free = 0.4165 target = 0.121155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.097526 restraints weight = 24755.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.096442 restraints weight = 20999.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.097291 restraints weight = 20532.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.4762

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= 0.131
  Angle     :  0.678  12.518  11248  Z= 0.324
  Chirality :  0.045   0.347   1256
  Planarity :  0.004   0.042   1474
  Dihedral  :  5.533  36.635   1186
  Min Nonbonded Distance : 1.884

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 12.90 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.56 (0.26), residues: 1016
  helix:  0.96 (0.21), residues: 602
  sheet: -0.62 (0.48), residues: 118
  loop : -0.21 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 410 
 HIS   0.002   0.000   HIS B 164 
 PHE   0.012   0.001   PHE B 319 
 TYR   0.036   0.002   TYR B 201 
 ARG   0.004   0.000   ARG A 390 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03772 (  464)
  hydrogen bonds       : angle       4.75759 ( 1362)
  SS BOND              : bond        0.00229 (    2)
  SS BOND              : angle       3.55366 (    4)
  covalent geometry    : bond        0.00287 ( 8310)
  covalent geometry    : angle       0.67430 (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
  86 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7658 (tm-30)
REVERT: A  201 TYR cc_start: 0.6131 (p90) cc_final: 0.5879 (p90)
REVERT: A  462 TYR cc_start: 0.8072 (t80) cc_final: 0.7783 (t80)
REVERT: A  742 LEU cc_start: 0.7897 (mt) cc_final: 0.7614 (tp)
REVERT: B   38 GLU cc_start: 0.9027 (tt0) cc_final: 0.8785 (tp30)
REVERT: B  115 LEU cc_start: 0.8939 (mm) cc_final: 0.8683 (mm)
REVERT: B  749 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8212 (tttt)
  outliers start: 20
  outliers final: 16
  residues processed: 79
  average time/residue: 0.2002
  time to fit residues: 24.4533
Evaluate side-chains
  76 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
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  461 PHE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain B residue  141 CYS
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
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:    0.0980
   chunk 34 optimal weight:    0.4980
   chunk 28 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 63 optimal weight:    0.2980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 HIS
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.119918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.096052 restraints weight = 24595.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.096285 restraints weight = 19870.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.096686 restraints weight = 18883.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.4904

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= 0.128
  Angle     :  0.687  12.958  11248  Z= 0.326
  Chirality :  0.045   0.371   1256
  Planarity :  0.004   0.035   1474
  Dihedral  :  5.433  38.811   1186
  Min Nonbonded Distance : 1.886

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 14.37 %
    Favored  : 83.48 %
  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:  0.53 (0.26), residues: 1016
  helix:  0.94 (0.20), residues: 602
  sheet: -0.56 (0.47), residues: 122
  loop : -0.24 (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   0.010   0.001   PHE B 319 
 TYR   0.044   0.002   TYR B 201 
 ARG   0.003   0.000   ARG A 390 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03760 (  464)
  hydrogen bonds       : angle       4.76420 ( 1362)
  SS BOND              : bond        0.00269 (    2)
  SS BOND              : angle       2.53933 (    4)
  covalent geometry    : bond        0.00279 ( 8310)
  covalent geometry    : angle       0.68496 (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
  85 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.905 
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: 0.8370 (tm-30) cc_final: 0.7518 (tm-30)
REVERT: A  201 TYR cc_start: 0.6142 (p90) cc_final: 0.5900 (p90)
REVERT: A  462 TYR cc_start: 0.8058 (t80) cc_final: 0.7789 (t80)
REVERT: A  742 LEU cc_start: 0.7904 (mt) cc_final: 0.7621 (tp)
REVERT: B   38 GLU cc_start: 0.9050 (tt0) cc_final: 0.8796 (tp30)
REVERT: B  749 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7941 (tttt)
  outliers start: 19
  outliers final: 16
  residues processed: 77
  average time/residue: 0.1842
  time to fit residues: 21.0313
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  : 0.963 
-------------------------------------------------------------------------------
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 A residue  759 SER
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  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:    0.9980
   chunk 26 optimal weight:    0.4980
   chunk 85 optimal weight:    1.9990
   chunk 7 optimal weight:    0.3980
   chunk 70 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   chunk 92 optimal weight:    0.0000
   chunk 14 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   chunk 41 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
** A 380 ASN ** 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 = 0.4146 r_free = 0.4146 target = 0.119123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.095302 restraints weight = 24847.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.095420 restraints weight = 19761.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.095855 restraints weight = 19177.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.5082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8312  Z= 0.126
  Angle     :  0.686  13.730  11248  Z= 0.326
  Chirality :  0.045   0.378   1256
  Planarity :  0.004   0.033   1474
  Dihedral  :  5.368  40.972   1186
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 14.25 %
    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:  0.54 (0.26), residues: 1016
  helix:  0.94 (0.21), residues: 604
  sheet: -0.56 (0.48), residues: 122
  loop : -0.22 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 410 
 HIS   0.002   0.000   HIS B 164 
 PHE   0.010   0.001   PHE A 319 
 TYR   0.035   0.002   TYR B 201 
 ARG   0.003   0.000   ARG B 204 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03746 (  464)
  hydrogen bonds       : angle       4.74578 ( 1362)
  SS BOND              : bond        0.00603 (    2)
  SS BOND              : angle       5.16050 (    4)
  covalent geometry    : bond        0.00273 ( 8310)
  covalent geometry    : angle       0.67947 (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
  82 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.977 
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: 0.8360 (tm-30) cc_final: 0.7478 (tm-30)
REVERT: A  462 TYR cc_start: 0.7984 (t80) cc_final: 0.7772 (t80)
REVERT: A  742 LEU cc_start: 0.7826 (mt) cc_final: 0.7544 (tp)
REVERT: B   38 GLU cc_start: 0.9022 (tt0) cc_final: 0.8788 (tp30)
REVERT: B  452 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8184 (mm-40)
  outliers start: 18
  outliers final: 17
  residues processed: 75
  average time/residue: 0.1771
  time to fit residues: 19.8614
Evaluate side-chains
  77 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 LEU
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 A residue  759 SER
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 82 optimal weight:    0.0870
   chunk 28 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0970
   chunk 59 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 1 optimal weight:    7.9990
   chunk 101 optimal weight:    0.9990
   chunk 88 optimal weight:    0.2980
   chunk 85 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.4156

-------------------------------------------------------------------------------
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 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 772 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.120407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.096641 restraints weight = 24527.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.096251 restraints weight = 20004.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.096820 restraints weight = 19293.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.5256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080   8312  Z= 0.128
  Angle     :  0.732  13.826  11248  Z= 0.352
  Chirality :  0.046   0.377   1256
  Planarity :  0.004   0.035   1474
  Dihedral  :  5.384  42.077   1186
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 14.71 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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:  0.50 (0.26), residues: 1016
  helix:  0.91 (0.21), residues: 604
  sheet: -0.58 (0.47), residues: 122
  loop : -0.25 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 410 
 HIS   0.002   0.000   HIS B 164 
 PHE   0.009   0.001   PHE B 319 
 TYR   0.060   0.002   TYR B 462 
 ARG   0.003   0.000   ARG A 390 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03789 (  464)
  hydrogen bonds       : angle       4.83854 ( 1362)
  SS BOND              : bond        0.00587 (    2)
  SS BOND              : angle       4.79146 (    4)
  covalent geometry    : bond        0.00283 ( 8310)
  covalent geometry    : angle       0.72664 (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
  78 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8244 (tm-30)
REVERT: A  452 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7905 (mm-40)
REVERT: A  742 LEU cc_start: 0.7757 (mt) cc_final: 0.7512 (tp)
REVERT: B  452 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8126 (mm-40)
  outliers start: 17
  outliers final: 16
  residues processed: 70
  average time/residue: 0.1505
  time to fit residues: 16.3888
Evaluate side-chains
  71 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 LEU
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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 77 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 82 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 91 optimal weight:    0.3980
   chunk 2 optimal weight:    0.4980
   chunk 92 optimal weight:    0.2980
   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 120 ASN
A 220 HIS
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.120046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.096181 restraints weight = 24725.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.097442 restraints weight = 19715.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.097650 restraints weight = 17650.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.5364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8312  Z= 0.138
  Angle     :  0.726  13.764  11248  Z= 0.347
  Chirality :  0.046   0.369   1256
  Planarity :  0.004   0.038   1474
  Dihedral  :  5.412  43.118   1186
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.16 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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:  0.50 (0.26), residues: 1016
  helix:  0.98 (0.21), residues: 600
  sheet: -0.65 (0.48), residues: 122
  loop : -0.36 (0.37), residues: 294

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   0.011   0.001   PHE B 319 
 TYR   0.042   0.002   TYR B 462 
 ARG   0.003   0.000   ARG B 204 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03958 (  464)
  hydrogen bonds       : angle       4.88791 ( 1362)
  SS BOND              : bond        0.00839 (    2)
  SS BOND              : angle       5.82983 (    4)
  covalent geometry    : bond        0.00304 ( 8310)
  covalent geometry    : angle       0.71755 (11244)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3224.92 seconds
wall clock time: 58 minutes 5.63 seconds (3485.63 seconds total)