Starting phenix.real_space_refine
on Fri Aug 22 22:00:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9em9_19814/08_2025/9em9_19814.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9em9_19814/08_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_19814/08_2025/9em9_19814.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9em9_19814/08_2025/9em9_19814.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9em9_19814/08_2025/9em9_19814.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9em9_19814/08_2025/9em9_19814.cif"
  }
  resolution = 3.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.93, per 1000 atoms: 0.36
  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: 0.46
  Conformation dependent library (CDL) restraints added in 413.6 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.33
  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: 1.44

  Time building geometry restraints manager: 0.67 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: 0.02
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:             9.200
  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:             0.020
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.590
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.650
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (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
 ARG   0.040   0.004   ARG A 290 
 TYR   0.028   0.005   TYR B 466 
 PHE   0.019   0.002   PHE B 348 
 TRP   0.012   0.002   TRP A 302 
 HIS   0.004   0.001   HIS B 164 

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

*********************** 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  : 0.308 
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: 0.1047
  time to fit residues: 20.1271
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  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 276 GLN
A 309 GLN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 417 GLN
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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.120770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.096792 restraints weight = 24463.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.096407 restraints weight = 20470.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.097151 restraints weight = 21609.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.097372 restraints weight = 13862.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.097831 restraints weight = 13010.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8312  Z= 0.185
  Angle     :  0.689   9.417  11248  Z= 0.356
  Chirality :  0.043   0.266   1256
  Planarity :  0.005   0.062   1474
  Dihedral  : 10.886  63.102   1186
  Min Nonbonded Distance : 1.783

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  :  9.39 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.26), residues: 1016
  helix:  0.91 (0.20), residues: 604
  sheet:  0.00 (0.44), residues: 122
  loop : -0.03 (0.40), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 738 
 TYR   0.038   0.003   TYR B 201 
 PHE   0.013   0.002   PHE A 319 
 TRP   0.008   0.002   TRP A 302 
 HIS   0.006   0.001   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 8310)
  covalent geometry    : angle       0.68905 (11244)
  SS BOND              : bond        0.00381 (    2)
  SS BOND              : angle       0.34594 (    4)
  hydrogen bonds       : bond        0.04639 (  464)
  hydrogen bonds       : angle       5.09753 ( 1362)

*********************** 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
  104 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 80
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   38 GLU cc_start: 0.9049 (tt0) cc_final: 0.8716 (tm-30)
  outliers start: 24
  outliers final: 17
  residues processed: 94
  average time/residue: 0.0913
  time to fit residues: 11.8548
Evaluate side-chains
  71 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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 34 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 74 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 69 optimal weight:    4.9990
   chunk 92 optimal weight:    0.2980
   overall best weight:    1.0386

-------------------------------------------------------------------------------
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 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 = 0.4142 r_free = 0.4142 target = 0.119221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.090173 restraints weight = 24686.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.092167 restraints weight = 15923.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.093524 restraints weight = 12076.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.094186 restraints weight = 10135.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.094666 restraints weight = 9191.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.3624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8312  Z= 0.201
  Angle     :  0.711  10.675  11248  Z= 0.358
  Chirality :  0.043   0.196   1256
  Planarity :  0.005   0.058   1474
  Dihedral  :  9.394  51.932   1186
  Min Nonbonded Distance : 1.783

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 10.41 %
    Favored  : 86.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.26), residues: 1016
  helix:  0.81 (0.20), residues: 598
  sheet: -0.43 (0.44), residues: 124
  loop : -0.17 (0.40), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 741 
 TYR   0.047   0.002   TYR B 201 
 PHE   0.017   0.002   PHE A 319 
 TRP   0.007   0.001   TRP A 410 
 HIS   0.001   0.000   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 8310)
  covalent geometry    : angle       0.70680 (11244)
  SS BOND              : bond        0.00893 (    2)
  SS BOND              : angle       3.98644 (    4)
  hydrogen bonds       : bond        0.04542 (  464)
  hydrogen bonds       : angle       5.04842 ( 1362)

*********************** 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
  98 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 67
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 GLU cc_start: 0.9508 (tt0) cc_final: 0.9273 (tp30)
REVERT: A  197 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7542 (tm-30)
REVERT: A  454 LEU cc_start: 0.9483 (tp) cc_final: 0.9262 (pp)
REVERT: B   38 GLU cc_start: 0.9508 (tt0) cc_final: 0.8935 (tm-30)
  outliers start: 31
  outliers final: 16
  residues processed: 86
  average time/residue: 0.0787
  time to fit residues: 9.8530
Evaluate side-chains
  81 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  197 GLU
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 A residue  759 SER
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  408 SER
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 98 optimal weight:    0.3980
   chunk 51 optimal weight:    9.9990
   chunk 3 optimal weight:    0.0060
   chunk 72 optimal weight:    0.7980
   chunk 65 optimal weight:    8.9990
   chunk 88 optimal weight:    0.4980
   chunk 52 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 85 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.4596

-------------------------------------------------------------------------------
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  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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.121928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.099173 restraints weight = 25804.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.098246 restraints weight = 22353.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.099050 restraints weight = 22232.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.100522 restraints weight = 15578.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.100567 restraints weight = 13216.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.4032

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= 0.129
  Angle     :  0.658  11.300  11248  Z= 0.322
  Chirality :  0.043   0.302   1256
  Planarity :  0.004   0.041   1474
  Dihedral  :  7.400  40.213   1186
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 11.43 %
    Favored  : 86.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.26), residues: 1016
  helix:  0.97 (0.21), residues: 602
  sheet: -0.50 (0.45), residues: 122
  loop : -0.16 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  12 
 TYR   0.035   0.002   TYR B 201 
 PHE   0.012   0.001   PHE A 292 
 TRP   0.009   0.001   TRP A 410 
 HIS   0.001   0.000   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8310)
  covalent geometry    : angle       0.65486 (11244)
  SS BOND              : bond        0.00305 (    2)
  SS BOND              : angle       3.46629 (    4)
  hydrogen bonds       : bond        0.03918 (  464)
  hydrogen bonds       : angle       4.80290 ( 1362)

*********************** 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
  88 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 MET cc_start: 0.8325 (mmm) cc_final: 0.8091 (mtt)
REVERT: B   38 GLU cc_start: 0.8933 (tt0) cc_final: 0.8555 (tm-30)
REVERT: B  115 LEU cc_start: 0.8836 (mm) cc_final: 0.8596 (mm)
REVERT: B  197 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7521 (tm-30)
  outliers start: 20
  outliers final: 16
  residues processed: 80
  average time/residue: 0.0687
  time to fit residues: 8.0534
Evaluate side-chains
  76 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
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  431 ILE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  753 TYR
Chi-restraints excluded: chain B residue  759 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 92 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 51 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 369 GLN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 748 GLN
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.116575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.093068 restraints weight = 24901.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.092818 restraints weight = 22089.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.093256 restraints weight = 21218.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.094567 restraints weight = 14381.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.094550 restraints weight = 11664.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
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      :  0.006   0.057   8312  Z= 0.258
  Angle     :  0.767  11.479  11248  Z= 0.375
  Chirality :  0.045   0.282   1256
  Planarity :  0.005   0.066   1474
  Dihedral  :  6.349  48.068   1186
  Min Nonbonded Distance : 1.750

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 12.44 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.26), residues: 1016
  helix:  0.52 (0.20), residues: 616
  sheet: -0.81 (0.44), residues: 126
  loop : -0.50 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 738 
 TYR   0.041   0.003   TYR B 201 
 PHE   0.023   0.002   PHE B 319 
 TRP   0.009   0.002   TRP A 410 
 HIS   0.004   0.001   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00589 ( 8310)
  covalent geometry    : angle       0.76552 (11244)
  SS BOND              : bond        0.00205 (    2)
  SS BOND              : angle       2.95523 (    4)
  hydrogen bonds       : bond        0.04618 (  464)
  hydrogen bonds       : angle       5.18332 ( 1362)

*********************** 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
  93 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 66
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   38 GLU cc_start: 0.9038 (tt0) cc_final: 0.8607 (tm-30)
REVERT: B  115 LEU cc_start: 0.9001 (mm) cc_final: 0.8759 (mm)
  outliers start: 27
  outliers final: 19
  residues processed: 89
  average time/residue: 0.0785
  time to fit residues: 10.0226
Evaluate side-chains
  81 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  346 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  391 VAL
Chi-restraints excluded: chain A residue  404 VAL
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  271 SER
Chi-restraints excluded: chain B residue  346 THR
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  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 16 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 84 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9990
   chunk 14 optimal weight:    0.2980
   chunk 77 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0980
   chunk 47 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.5380

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.119229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.095238 restraints weight = 24392.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.095453 restraints weight = 19425.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.095914 restraints weight = 20085.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.096312 restraints weight = 12838.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.096902 restraints weight = 11688.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.4757

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= 0.136
  Angle     :  0.688  12.802  11248  Z= 0.338
  Chirality :  0.045   0.329   1256
  Planarity :  0.004   0.039   1474
  Dihedral  :  5.724  36.274   1186
  Min Nonbonded Distance : 1.851

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.46 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.26), residues: 1016
  helix:  0.82 (0.20), residues: 612
  sheet: -0.87 (0.45), residues: 122
  loop : -0.52 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  12 
 TYR   0.033   0.002   TYR B 201 
 PHE   0.011   0.001   PHE A 461 
 TRP   0.007   0.001   TRP A 410 
 HIS   0.003   0.000   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8310)
  covalent geometry    : angle       0.68617 (11244)
  SS BOND              : bond        0.00411 (    2)
  SS BOND              : angle       2.62248 (    4)
  hydrogen bonds       : bond        0.03979 (  464)
  hydrogen bonds       : angle       4.91593 ( 1362)

*********************** 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: 19
    poor density    : 70
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 TYR cc_start: 0.6139 (p90) cc_final: 0.5888 (p90)
REVERT: B   38 GLU cc_start: 0.9099 (tt0) cc_final: 0.8626 (tm-30)
REVERT: B  115 LEU cc_start: 0.9017 (mm) cc_final: 0.8753 (mm)
REVERT: B  749 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8309 (tttt)
  outliers start: 19
  outliers final: 14
  residues processed: 82
  average time/residue: 0.0840
  time to fit residues: 9.7333
Evaluate side-chains
  77 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  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  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 18 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 100 optimal weight:    0.8980
   chunk 90 optimal weight:    0.5980
   chunk 31 optimal weight:    0.4980
   chunk 55 optimal weight:    3.9990
   chunk 23 optimal weight:    8.9990
   chunk 78 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 50 optimal weight:    5.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 452 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.117892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.088149 restraints weight = 24941.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.090273 restraints weight = 15380.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.091695 restraints weight = 11384.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.092597 restraints weight = 9462.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.093055 restraints weight = 8461.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.4940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8312  Z= 0.147
  Angle     :  0.702  13.802  11248  Z= 0.334
  Chirality :  0.045   0.321   1256
  Planarity :  0.004   0.038   1474
  Dihedral  :  5.613  39.598   1186
  Min Nonbonded Distance : 1.805

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 14.48 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.26), residues: 1016
  helix:  0.87 (0.21), residues: 610
  sheet: -0.80 (0.46), residues: 122
  loop : -0.57 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 204 
 TYR   0.042   0.002   TYR B 201 
 PHE   0.013   0.001   PHE B 319 
 TRP   0.007   0.001   TRP A 410 
 HIS   0.004   0.000   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 8310)
  covalent geometry    : angle       0.70047 (11244)
  SS BOND              : bond        0.00415 (    2)
  SS BOND              : angle       2.42210 (    4)
  hydrogen bonds       : bond        0.04042 (  464)
  hydrogen bonds       : angle       4.91689 ( 1362)

*********************** 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: 22
    poor density    : 64
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   38 GLU cc_start: 0.9401 (tt0) cc_final: 0.8974 (tp30)
REVERT: B  115 LEU cc_start: 0.9108 (mm) cc_final: 0.8847 (mm)
REVERT: B  749 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8523 (tttt)
  outliers start: 22
  outliers final: 18
  residues processed: 81
  average time/residue: 0.0916
  time to fit residues: 10.4360
Evaluate side-chains
  78 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 59
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 THR
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  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   65 ILE
Chi-restraints excluded: chain B residue   84 THR
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 101 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 82 optimal weight:    0.6980
   chunk 87 optimal weight:    0.0770
   chunk 50 optimal weight:    0.2980
   chunk 70 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
A 120 ASN
A 276 GLN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 452 GLN
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 452 GLN ** 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 = 0.4133 r_free = 0.4133 target = 0.118149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.094614 restraints weight = 24482.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.094363 restraints weight = 20696.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.094966 restraints weight = 21825.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.095317 restraints weight = 14004.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.095767 restraints weight = 12848.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.5106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8312  Z= 0.139
  Angle     :  0.689  12.467  11248  Z= 0.336
  Chirality :  0.045   0.344   1256
  Planarity :  0.003   0.035   1474
  Dihedral  :  5.501  40.446   1186
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.16 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.26), residues: 1016
  helix:  0.87 (0.21), residues: 612
  sheet: -0.76 (0.47), residues: 122
  loop : -0.52 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 204 
 TYR   0.046   0.002   TYR B 462 
 PHE   0.012   0.001   PHE B 319 
 TRP   0.005   0.001   TRP A 410 
 HIS   0.004   0.000   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8310)
  covalent geometry    : angle       0.68756 (11244)
  SS BOND              : bond        0.00329 (    2)
  SS BOND              : angle       2.36707 (    4)
  hydrogen bonds       : bond        0.03946 (  464)
  hydrogen bonds       : angle       4.90260 ( 1362)

*********************** 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
  84 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 63
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   38 GLU cc_start: 0.8984 (tt0) cc_final: 0.8760 (tp30)
REVERT: B  115 LEU cc_start: 0.8951 (mm) cc_final: 0.8699 (mm)
REVERT: B  749 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8255 (tttt)
  outliers start: 21
  outliers final: 18
  residues processed: 81
  average time/residue: 0.0904
  time to fit residues: 10.4745
Evaluate side-chains
  80 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 THR
Chi-restraints excluded: chain A residue  141 CYS
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  391 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  271 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  749 LYS
Chi-restraints excluded: chain B residue  753 TYR
Chi-restraints excluded: chain B residue  759 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 72 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 70 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 68 optimal weight:    0.5980
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.5780

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.118684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.095275 restraints weight = 24987.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.094944 restraints weight = 22279.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.095424 restraints weight = 21505.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.097121 restraints weight = 14989.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.097029 restraints weight = 11471.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.5268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   8312  Z= 0.140
  Angle     :  0.704  12.998  11248  Z= 0.342
  Chirality :  0.046   0.358   1256
  Planarity :  0.003   0.035   1474
  Dihedral  :  5.432  41.368   1186
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.38 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.26), residues: 1016
  helix:  0.76 (0.21), residues: 616
  sheet: -0.75 (0.48), residues: 122
  loop : -0.42 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 204 
 TYR   0.035   0.002   TYR A 201 
 PHE   0.014   0.001   PHE B 444 
 TRP   0.004   0.001   TRP B 410 
 HIS   0.005   0.000   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8310)
  covalent geometry    : angle       0.70272 (11244)
  SS BOND              : bond        0.00297 (    2)
  SS BOND              : angle       2.23223 (    4)
  hydrogen bonds       : bond        0.04035 (  464)
  hydrogen bonds       : angle       4.95863 ( 1362)

*********************** 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
  80 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 59
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   38 GLU cc_start: 0.8991 (tt0) cc_final: 0.8768 (tp30)
REVERT: B  452 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8150 (mm-40)
  outliers start: 21
  outliers final: 19
  residues processed: 77
  average time/residue: 0.0910
  time to fit residues: 10.0575
Evaluate side-chains
  76 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 57
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 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  391 VAL
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  759 SER
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  271 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 65 optimal weight:    0.0030
   chunk 51 optimal weight:   10.0000
   chunk 28 optimal weight:    0.3980
   chunk 76 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0170
   chunk 10 optimal weight:    0.7980
   chunk 77 optimal weight:    0.0670
   chunk 70 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.2166

-------------------------------------------------------------------------------
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**
A 452 GLN
** 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 = 0.4162 r_free = 0.4162 target = 0.121013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.097550 restraints weight = 24456.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.096877 restraints weight = 20592.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.097508 restraints weight = 20087.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.099065 restraints weight = 13525.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.099033 restraints weight = 11075.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.5399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.080   8312  Z= 0.115
  Angle     :  0.686  13.524  11248  Z= 0.332
  Chirality :  0.046   0.363   1256
  Planarity :  0.003   0.033   1474
  Dihedral  :  5.250  41.882   1186
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.27 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.27), residues: 1016
  helix:  0.99 (0.21), residues: 606
  sheet: -0.68 (0.48), residues: 122
  loop : -0.16 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 204 
 TYR   0.053   0.002   TYR B 462 
 PHE   0.008   0.001   PHE B 354 
 TRP   0.002   0.000   TRP A 302 
 HIS   0.004   0.000   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 8310)
  covalent geometry    : angle       0.68453 (11244)
  SS BOND              : bond        0.00209 (    2)
  SS BOND              : angle       2.14702 (    4)
  hydrogen bonds       : bond        0.03732 (  464)
  hydrogen bonds       : angle       4.86961 ( 1362)

********************** 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
  81 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   38 GLU cc_start: 0.9035 (tt0) cc_final: 0.8801 (tp30)
  outliers start: 18
  outliers final: 17
  residues processed: 74
  average time/residue: 0.0855
  time to fit residues: 9.1163
Evaluate side-chains
  79 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 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  391 VAL
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  271 SER
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  461 PHE
Chi-restraints excluded: chain B residue  753 TYR
Chi-restraints excluded: chain B residue  759 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 70.4755 > 50:
  distance: 64 - 88:  17.620
  distance: 67 - 85:  27.521
  distance: 80 - 85:  29.230
  distance: 85 - 86:  36.789
  distance: 86 - 87:  41.391
  distance: 86 - 89:  48.173
  distance: 87 - 88:  44.688
  distance: 87 - 93:  47.669
  distance: 89 - 90:  33.120
  distance: 90 - 91:  55.306
  distance: 90 - 92:  25.532
  distance: 93 - 94:   3.480
  distance: 94 - 95:  46.492
  distance: 94 - 97:  26.402
  distance: 95 - 96:  47.945
  distance: 95 - 101:  60.955
  distance: 97 - 98:  50.782
  distance: 98 - 99:  30.924
  distance: 98 - 100:   9.827
  distance: 101 - 102:  24.903
  distance: 101 - 107:  26.939
  distance: 102 - 103:  33.609
  distance: 102 - 105:  43.886
  distance: 103 - 104:  18.979
  distance: 103 - 108:  55.549
  distance: 105 - 106:  30.513
  distance: 106 - 107:  36.794
  distance: 108 - 109:   4.411
  distance: 109 - 110:  41.146
  distance: 110 - 111:  42.691
  distance: 110 - 112:  42.254
  distance: 112 - 113:  34.930
  distance: 113 - 114:  35.082
  distance: 113 - 116:  51.567
  distance: 114 - 115:  41.044
  distance: 114 - 120:  48.834
  distance: 116 - 117:  39.010
  distance: 116 - 118:  54.679
  distance: 117 - 119:  16.648
  distance: 120 - 121:  24.423
  distance: 121 - 122:  17.644
  distance: 121 - 124:  51.778
  distance: 122 - 123:  48.076
  distance: 122 - 128:  24.439
  distance: 124 - 125:  17.681
  distance: 125 - 126:  37.525
  distance: 125 - 127:  28.081
  distance: 128 - 129:  22.440
  distance: 129 - 130:  28.960
  distance: 129 - 132:  51.488
  distance: 130 - 131:  25.830
  distance: 130 - 133:  50.165
  distance: 133 - 134:  25.492
  distance: 133 - 139:  41.411
  distance: 134 - 135:  46.482
  distance: 134 - 137:  13.538
  distance: 135 - 136:  19.083
  distance: 135 - 140:  25.741
  distance: 137 - 138:  13.126
  distance: 138 - 139:  58.027
  distance: 140 - 141:  24.578
  distance: 141 - 142:  24.478
  distance: 141 - 144:  11.145
  distance: 142 - 143:   7.687
  distance: 142 - 147:  22.820
  distance: 143 - 169:  17.047
  distance: 144 - 145:  25.848
  distance: 144 - 146:  28.635
  distance: 147 - 148:  15.849
  distance: 148 - 149:  38.595
  distance: 148 - 151:  14.563
  distance: 149 - 150:  27.422
  distance: 149 - 156:  17.512
  distance: 150 - 174:  16.424
  distance: 151 - 152:  19.851
  distance: 152 - 153:  11.954
  distance: 153 - 154:  18.989
  distance: 154 - 155:  17.481