Starting phenix.real_space_refine
on Tue Feb 11 05:35:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sp1_25364/02_2025/7sp1_25364.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sp1_25364/02_2025/7sp1_25364.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sp1_25364/02_2025/7sp1_25364.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sp1_25364/02_2025/7sp1_25364.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sp1_25364/02_2025/7sp1_25364.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sp1_25364/02_2025/7sp1_25364.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      18      5.49       5
     S      15      5.16       5
     C    2595      2.51       5
     N     750      2.21       5
     O     965      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4343
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 263
          Classifications: {'peptide': 36}
          Link IDs: {'PTRANS': 3, 'TRANS': 32}
    Chain: "Q"
      Number of atoms: 199
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 199
          Classifications: {'DNA': 1, 'RNA': 9}
          Modifications used: {'5*END': 1, 'rna3p_pur': 9}
          Link IDs: {'rna3p': 9}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'  A%5*END:plan2': 1, '  A%5*END:plan': 1}
          Unresolved non-hydrogen planarities: 13
  Restraints were copied for chains:
    P, C, B, E, D, G, F, I, H, K, J, M, L, O, N
  Time building chain proxies: 1.79, per 1000 atoms: 0.41
  Number of scatterers: 4343
  At special positions: 0
  Unit cell: (81.62, 69.96, 58.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      15     16.00
     P      18     15.00
     O     965      8.00
     N     750      7.00
     C    2595      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Conformation dependent library (CDL) restraints added in 502.2 milliseconds
  

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1020

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 41.7% beta
      0 base pairs and 10 stacking pairs defined.
    Time for finding SS restraints: 1.55
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'I' and resid 392 through 393
      removed outlier: 6.779A  pdb=" N   ILE A 392 " --> pdb=" O   VAL D 393 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ILE D 392 " --> pdb=" O   VAL H 393 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ILE H 392 " --> pdb=" O   VAL K 393 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   ILE K 392 " --> pdb=" O   VAL M 393 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   ILE M 392 " --> pdb=" O   VAL O 393 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'I' and resid 399 through 403
      removed outlier: 5.910A  pdb=" N   SER E 400 " --> pdb=" O   GLY I 401 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   THR I 403 " --> pdb=" O   SER E 400 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ASP E 402 " --> pdb=" O   THR I 403 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   SER A 400 " --> pdb=" O   GLY E 401 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   THR E 403 " --> pdb=" O   SER A 400 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   ASP A 402 " --> pdb=" O   THR E 403 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'I' and resid 407 through 412
      removed outlier: 6.157A  pdb=" N   HIS E 407 " --> pdb=" O   LEU I 408 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   ASN I 410 " --> pdb=" O   HIS E 407 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   SER E 409 " --> pdb=" O   ASN I 410 " (cutoff:3.500A)
      removed outlier: 7.884A  pdb=" N   SER I 412 " --> pdb=" O   SER E 409 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL E 411 " --> pdb=" O   SER I 412 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   HIS A 407 " --> pdb=" O   LEU E 408 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   ASN E 410 " --> pdb=" O   HIS A 407 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   SER A 409 " --> pdb=" O   ASN E 410 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   SER E 412 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   VAL A 411 " --> pdb=" O   SER E 412 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'I' and resid 415 through 420
      removed outlier: 6.215A  pdb=" N   GLY A 415 " --> pdb=" O   SER D 416 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   ASP D 418 " --> pdb=" O   GLY A 415 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ILE A 417 " --> pdb=" O   ASP D 418 " (cutoff:3.500A)
      removed outlier: 8.082A  pdb=" N   VAL D 420 " --> pdb=" O   ILE A 417 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   MET A 419 " --> pdb=" O   VAL D 420 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLY D 415 " --> pdb=" O   SER H 416 " (cutoff:3.500A)
      removed outlier: 7.514A  pdb=" N   ASP H 418 " --> pdb=" O   GLY D 415 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   ILE D 417 " --> pdb=" O   ASP H 418 " (cutoff:3.500A)
      removed outlier: 8.115A  pdb=" N   VAL H 420 " --> pdb=" O   ILE D 417 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   MET D 419 " --> pdb=" O   VAL H 420 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   GLY H 415 " --> pdb=" O   SER K 416 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   ASP K 418 " --> pdb=" O   GLY H 415 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   ILE H 417 " --> pdb=" O   ASP K 418 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   VAL K 420 " --> pdb=" O   ILE H 417 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   MET H 419 " --> pdb=" O   VAL K 420 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   GLY K 415 " --> pdb=" O   SER M 416 " (cutoff:3.500A)
      removed outlier: 7.519A  pdb=" N   ASP M 418 " --> pdb=" O   GLY K 415 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   ILE K 417 " --> pdb=" O   ASP M 418 " (cutoff:3.500A)
      removed outlier: 8.122A  pdb=" N   VAL M 420 " --> pdb=" O   ILE K 417 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   MET K 419 " --> pdb=" O   VAL M 420 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   GLY M 415 " --> pdb=" O   SER O 416 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   ASP O 418 " --> pdb=" O   GLY M 415 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   ILE M 417 " --> pdb=" O   ASP O 418 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   VAL O 420 " --> pdb=" O   ILE M 417 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   MET M 419 " --> pdb=" O   VAL O 420 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'G' and resid 392 through 393
      removed outlier: 6.805A  pdb=" N   ILE B 392 " --> pdb=" O   VAL F 393 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ILE F 392 " --> pdb=" O   VAL J 393 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ILE J 392 " --> pdb=" O   VAL L 393 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ILE L 392 " --> pdb=" O   VAL N 393 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 399 through 403
      removed outlier: 5.913A  pdb=" N   SER C 400 " --> pdb=" O   GLY G 401 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   THR G 403 " --> pdb=" O   SER C 400 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   ASP C 402 " --> pdb=" O   THR G 403 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   SER B 400 " --> pdb=" O   GLY C 401 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   THR C 403 " --> pdb=" O   SER B 400 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   ASP B 402 " --> pdb=" O   THR C 403 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 407 through 412
      removed outlier: 6.158A  pdb=" N   HIS C 407 " --> pdb=" O   LEU G 408 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   ASN G 410 " --> pdb=" O   HIS C 407 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   SER C 409 " --> pdb=" O   ASN G 410 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   SER G 412 " --> pdb=" O   SER C 409 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL C 411 " --> pdb=" O   SER G 412 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   HIS B 407 " --> pdb=" O   LEU C 408 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ASN C 410 " --> pdb=" O   HIS B 407 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   SER B 409 " --> pdb=" O   ASN C 410 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   SER C 412 " --> pdb=" O   SER B 409 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL B 411 " --> pdb=" O   SER C 412 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 415 through 420
      removed outlier: 6.226A  pdb=" N   GLY B 415 " --> pdb=" O   SER F 416 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   ASP F 418 " --> pdb=" O   GLY B 415 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   ILE B 417 " --> pdb=" O   ASP F 418 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   VAL F 420 " --> pdb=" O   ILE B 417 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   MET B 419 " --> pdb=" O   VAL F 420 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   GLY F 415 " --> pdb=" O   SER J 416 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   ASP J 418 " --> pdb=" O   GLY F 415 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   ILE F 417 " --> pdb=" O   ASP J 418 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   VAL J 420 " --> pdb=" O   ILE F 417 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   MET F 419 " --> pdb=" O   VAL J 420 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLY J 415 " --> pdb=" O   SER L 416 " (cutoff:3.500A)
      removed outlier: 7.514A  pdb=" N   ASP L 418 " --> pdb=" O   GLY J 415 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ILE J 417 " --> pdb=" O   ASP L 418 " (cutoff:3.500A)
      removed outlier: 8.116A  pdb=" N   VAL L 420 " --> pdb=" O   ILE J 417 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   MET J 419 " --> pdb=" O   VAL L 420 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   GLY L 415 " --> pdb=" O   SER N 416 " (cutoff:3.500A)
      removed outlier: 7.515A  pdb=" N   ASP N 418 " --> pdb=" O   GLY L 415 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ILE L 417 " --> pdb=" O   ASP N 418 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   VAL N 420 " --> pdb=" O   ILE L 417 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   MET L 419 " --> pdb=" O   VAL N 420 " (cutoff:3.500A)

    105 hydrogen bonds defined for protein.
    315 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      10 stacking parallelities
  Total time for adding SS restraints: 1.19

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1090
        1.33 -     1.45: 830
        1.45 -     1.57: 2469
        1.57 -     1.68: 36
        1.68 -     1.80: 30
  Bond restraints: 4455
  Sorted by residual:
  bond pdb=" N   ARG G 406 "
       pdb=" CA  ARG G 406 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.23e-02 6.61e+03 9.85e+00
  bond pdb=" N   ARG C 406 "
       pdb=" CA  ARG C 406 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.23e-02 6.61e+03 9.85e+00
  bond pdb=" N   ARG N 406 "
       pdb=" CA  ARG N 406 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.038 1.23e-02 6.61e+03 9.76e+00
  bond pdb=" N   ARG I 406 "
       pdb=" CA  ARG I 406 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.23e-02 6.61e+03 9.69e+00
  bond pdb=" N   ARG A 406 "
       pdb=" CA  ARG A 406 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.23e-02 6.61e+03 9.68e+00
  ... (remaining 4450 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 5162
        1.42 -     2.83: 638
        2.83 -     4.25: 240
        4.25 -     5.67: 97
        5.67 -     7.09: 23
  Bond angle restraints: 6160
  Sorted by residual:
  angle pdb=" N   ARG F 406 "
        pdb=" CA  ARG F 406 "
        pdb=" C   ARG F 406 "
      ideal   model   delta    sigma   weight residual
     111.36  117.05   -5.69 1.09e+00 8.42e-01 2.72e+01
  angle pdb=" N   ARG N 406 "
        pdb=" CA  ARG N 406 "
        pdb=" C   ARG N 406 "
      ideal   model   delta    sigma   weight residual
     111.36  117.04   -5.68 1.09e+00 8.42e-01 2.72e+01
  angle pdb=" N   ARG I 406 "
        pdb=" CA  ARG I 406 "
        pdb=" C   ARG I 406 "
      ideal   model   delta    sigma   weight residual
     111.36  117.03   -5.67 1.09e+00 8.42e-01 2.71e+01
  angle pdb=" N   ARG D 406 "
        pdb=" CA  ARG D 406 "
        pdb=" C   ARG D 406 "
      ideal   model   delta    sigma   weight residual
     111.36  117.03   -5.67 1.09e+00 8.42e-01 2.70e+01
  angle pdb=" N   ARG C 406 "
        pdb=" CA  ARG C 406 "
        pdb=" C   ARG C 406 "
      ideal   model   delta    sigma   weight residual
     111.36  117.02   -5.66 1.09e+00 8.42e-01 2.70e+01
  ... (remaining 6155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.35: 2451
       24.35 -    48.71: 218
       48.71 -    73.06: 15
       73.06 -    97.41: 2
       97.41 -   121.76: 16
  Dihedral angle restraints: 2702
    sinusoidal: 1142
      harmonic: 1560
  Sorted by residual:
  dihedral pdb=" CA  SER K 416 "
           pdb=" C   SER K 416 "
           pdb=" N   ILE K 417 "
           pdb=" CA  ILE K 417 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.49   28.51     0      5.00e+00 4.00e-02 3.25e+01
  dihedral pdb=" CA  SER N 416 "
           pdb=" C   SER N 416 "
           pdb=" N   ILE N 417 "
           pdb=" CA  ILE N 417 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.52   28.48     0      5.00e+00 4.00e-02 3.25e+01
  dihedral pdb=" CA  SER A 416 "
           pdb=" C   SER A 416 "
           pdb=" N   ILE A 417 "
           pdb=" CA  ILE A 417 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.55   28.45     0      5.00e+00 4.00e-02 3.24e+01
  ... (remaining 2699 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 364
       0.037 -    0.075: 207
       0.075 -    0.112: 120
       0.112 -    0.149: 46
       0.149 -    0.187: 28
  Chirality restraints: 765
  Sorted by residual:
  chirality pdb=" C4'   A Q  13 "
            pdb=" C5'   A Q  13 "
            pdb=" O4'   A Q  13 "
            pdb=" C3'   A Q  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.31   -0.19 2.00e-01 2.50e+01 8.70e-01
  chirality pdb=" C4'   A P  14 "
            pdb=" C5'   A P  14 "
            pdb=" O4'   A P  14 "
            pdb=" C3'   A P  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.31   -0.19 2.00e-01 2.50e+01 8.63e-01
  chirality pdb=" C4'   A Q  14 "
            pdb=" C5'   A Q  14 "
            pdb=" O4'   A Q  14 "
            pdb=" C3'   A Q  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.32   -0.18 2.00e-01 2.50e+01 7.80e-01
  ... (remaining 762 not shown)

  Planarity restraints: 723
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER G 404 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.06e+00
        pdb=" C   SER G 404 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   SER G 404 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PRO G 405 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER E 404 "   -0.009 2.00e-02 2.50e+03   1.74e-02 3.04e+00
        pdb=" C   SER E 404 "    0.030 2.00e-02 2.50e+03
        pdb=" O   SER E 404 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   PRO E 405 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER H 404 "   -0.009 2.00e-02 2.50e+03   1.74e-02 3.03e+00
        pdb=" C   SER H 404 "    0.030 2.00e-02 2.50e+03
        pdb=" O   SER H 404 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   PRO H 405 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 720 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 958
        2.81 -     3.33: 3845
        3.33 -     3.86: 8097
        3.86 -     4.38: 7893
        4.38 -     4.90: 17425
  Nonbonded interactions: 38218
  Sorted by model distance:
  nonbonded pdb=" OP1   A P  11 "
            pdb=" NH2 ARG N 406 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" O2'   A P  11 "
            pdb=" NE2 HIS L 407 "
     model   vdw
     2.342 3.120
  nonbonded pdb=" OP1   A P  11 "
            pdb=" CZ  ARG N 406 "
     model   vdw
     2.441 3.270
  nonbonded pdb=" O   SER H 422 "
            pdb=" OG  SER H 422 "
     model   vdw
     2.483 3.040
  nonbonded pdb=" O   SER G 422 "
            pdb=" OG  SER G 422 "
     model   vdw
     2.483 3.040
  ... (remaining 38213 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'Q'
  selection = chain 'P'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'L'
  selection = chain 'O'
  selection = chain 'N'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.250
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
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      :  0.006   0.039   4455  Z= 0.399
  Angle     :  1.288   7.086   6160  Z= 0.781
  Chirality :  0.065   0.187    765
  Planarity :  0.008   0.033    723
  Dihedral  : 19.389 121.762   1682
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.12 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.42 (0.33), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.84 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS B 407 
 TYR   0.008   0.002   TYR C 394 
 ARG   0.001   0.000   ARG I 406 

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.480 
Fit side-chains
REVERT: D  419 MET cc_start: 0.8199 (mtp) cc_final: 0.7993 (mtm)
REVERT: G  406 ARG cc_start: 0.7065 (mtp85) cc_final: 0.6281 (mtm-85)
REVERT: I  406 ARG cc_start: 0.6718 (mtp85) cc_final: 0.6404 (mtm180)
REVERT: K  419 MET cc_start: 0.8060 (mtp) cc_final: 0.7753 (mtm)
REVERT: N  406 ARG cc_start: 0.6509 (mtp85) cc_final: 0.5637 (mmt180)
REVERT: O  406 ARG cc_start: 0.7051 (mtp85) cc_final: 0.5905 (mmt180)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1660
  time to fit residues: 30.3892
Evaluate side-chains
  108 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 35 optimal weight:   20.0000
   chunk 19 optimal weight:   20.0000
   chunk 12 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   chunk 27 optimal weight:    7.9990
   chunk 42 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5211 r_free = 0.5211 target = 0.236009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4845 r_free = 0.4845 target = 0.186846 restraints weight = 4192.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.4799 rms_B_bonded: 2.76
r_work: 0.4651 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.4651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.3906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032   4455  Z= 0.418
  Angle     :  0.887   6.749   6160  Z= 0.466
  Chirality :  0.056   0.179    765
  Planarity :  0.008   0.041    723
  Dihedral  : 21.675 123.870    767
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 15.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.61 %
    Favored  : 90.39 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 13.54 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.35), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS G 407 
 TYR   0.015   0.003   TYR G 394 
 ARG   0.005   0.001   ARG F 406 

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.479 
Fit side-chains
REVERT: C  406 ARG cc_start: 0.7991 (mtt180) cc_final: 0.7728 (mtt90)
REVERT: D  419 MET cc_start: 0.8849 (mtp) cc_final: 0.8393 (mtm)
REVERT: G  406 ARG cc_start: 0.7550 (mtp85) cc_final: 0.6090 (mtm-85)
REVERT: I  406 ARG cc_start: 0.6991 (mtp85) cc_final: 0.5798 (mtm180)
REVERT: K  419 MET cc_start: 0.8538 (mtp) cc_final: 0.7981 (mtm)
REVERT: L  418 ASP cc_start: 0.8389 (p0) cc_final: 0.8152 (p0)
  outliers start: 19
  outliers final: 13
  residues processed: 127
  average time/residue: 0.1722
  time to fit residues: 27.1912
Evaluate side-chains
  108 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  409 SER
Chi-restraints excluded: chain E residue  409 SER
Chi-restraints excluded: chain F residue  404 SER
Chi-restraints excluded: chain G residue  399 VAL
Chi-restraints excluded: chain G residue  409 SER
Chi-restraints excluded: chain H residue  404 SER
Chi-restraints excluded: chain J residue  408 LEU
Chi-restraints excluded: chain J residue  409 SER
Chi-restraints excluded: chain K residue  409 SER
Chi-restraints excluded: chain L residue  419 MET
Chi-restraints excluded: chain M residue  404 SER
Chi-restraints excluded: chain N residue  404 SER
Chi-restraints excluded: chain N residue  409 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 21 optimal weight:   20.0000
   chunk 23 optimal weight:    9.9990
   chunk 12 optimal weight:   20.0000
   chunk 17 optimal weight:    8.9990
   chunk 20 optimal weight:    0.5980
   chunk 22 optimal weight:    6.9990
   chunk 39 optimal weight:   30.0000
   chunk 29 optimal weight:    9.9990
   chunk 40 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   chunk 33 optimal weight:    8.9990
   overall best weight:    6.1188

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

Flipped N/Q/H residues before XYZ refinement:
** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5252 r_free = 0.5252 target = 0.235026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4904 r_free = 0.4904 target = 0.187903 restraints weight = 4036.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.4854 rms_B_bonded: 2.49
r_work: 0.4712 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.4712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.4473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4455  Z= 0.350
  Angle     :  0.804   5.852   6160  Z= 0.420
  Chirality :  0.052   0.180    765
  Planarity :  0.007   0.041    723
  Dihedral  : 21.305 122.927    767
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.16 %
    Favored  : 87.84 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 16.57 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.82 (0.35), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 407 
 TYR   0.016   0.002   TYR O 394 
 ARG   0.007   0.001   ARG D 406 

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.478 
Fit side-chains
REVERT: G  406 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.5969 (mtm-85)
REVERT: H  406 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7436 (mtm-85)
REVERT: I  406 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.5763 (mtm180)
REVERT: K  419 MET cc_start: 0.8465 (mtp) cc_final: 0.8015 (mtm)
REVERT: N  406 ARG cc_start: 0.6891 (mtt-85) cc_final: 0.5127 (mmt180)
REVERT: O  421 ASP cc_start: 0.8891 (t0) cc_final: 0.8593 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 111
  average time/residue: 0.1790
  time to fit residues: 24.6667
Evaluate side-chains
  111 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain E residue  422 SER
Chi-restraints excluded: chain F residue  404 SER
Chi-restraints excluded: chain G residue  406 ARG
Chi-restraints excluded: chain G residue  409 SER
Chi-restraints excluded: chain H residue  404 SER
Chi-restraints excluded: chain H residue  406 ARG
Chi-restraints excluded: chain H residue  419 MET
Chi-restraints excluded: chain I residue  403 THR
Chi-restraints excluded: chain I residue  406 ARG
Chi-restraints excluded: chain J residue  409 SER
Chi-restraints excluded: chain L residue  419 MET
Chi-restraints excluded: chain M residue  404 SER
Chi-restraints excluded: chain M residue  419 MET
Chi-restraints excluded: chain N residue  404 SER
Chi-restraints excluded: chain N residue  416 SER
Chi-restraints excluded: chain O residue  416 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 37 optimal weight:    9.9990
   chunk 17 optimal weight:    8.9990
   chunk 23 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 13 optimal weight:    9.9990
   chunk 34 optimal weight:   10.0000
   chunk 35 optimal weight:   20.0000
   chunk 38 optimal weight:    6.9990
   overall best weight:    8.1990

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

Flipped N/Q/H residues before XYZ refinement:
** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5187 r_free = 0.5187 target = 0.220829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4754 r_free = 0.4754 target = 0.173764 restraints weight = 4172.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.4776 rms_B_bonded: 2.67
r_work: 0.4628 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.4628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.5105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.034   4455  Z= 0.448
  Angle     :  0.875   6.812   6160  Z= 0.457
  Chirality :  0.055   0.184    765
  Planarity :  0.008   0.038    723
  Dihedral  : 21.399 122.260    767
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 16.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.90 %
    Favored  : 85.10 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 15.15 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.20 (0.34), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.43 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 407 
 TYR   0.018   0.003   TYR N 394 
 ARG   0.008   0.001   ARG D 406 

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.503 
Fit side-chains
REVERT: G  406 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.5687 (mtm180)
REVERT: I  406 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.5828 (mtm180)
REVERT: K  419 MET cc_start: 0.8592 (mtp) cc_final: 0.8379 (mtm)
REVERT: N  406 ARG cc_start: 0.7181 (mtt-85) cc_final: 0.5411 (mmt180)
REVERT: O  421 ASP cc_start: 0.8942 (t0) cc_final: 0.8658 (t0)
  outliers start: 27
  outliers final: 17
  residues processed: 122
  average time/residue: 0.1615
  time to fit residues: 24.7904
Evaluate side-chains
  125 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain B residue  409 SER
Chi-restraints excluded: chain E residue  422 SER
Chi-restraints excluded: chain F residue  404 SER
Chi-restraints excluded: chain G residue  406 ARG
Chi-restraints excluded: chain G residue  409 SER
Chi-restraints excluded: chain H residue  404 SER
Chi-restraints excluded: chain H residue  419 MET
Chi-restraints excluded: chain I residue  403 THR
Chi-restraints excluded: chain I residue  406 ARG
Chi-restraints excluded: chain J residue  404 SER
Chi-restraints excluded: chain J residue  409 SER
Chi-restraints excluded: chain L residue  419 MET
Chi-restraints excluded: chain M residue  404 SER
Chi-restraints excluded: chain M residue  419 MET
Chi-restraints excluded: chain N residue  404 SER
Chi-restraints excluded: chain N residue  416 SER
Chi-restraints excluded: chain O residue  414 THR
Chi-restraints excluded: chain O residue  416 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 40 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 26 optimal weight:    0.6980
   chunk 30 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   chunk 13 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   overall best weight:    5.5388

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

Flipped N/Q/H residues before XYZ refinement:
** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5275 r_free = 0.5275 target = 0.234858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4921 r_free = 0.4921 target = 0.187878 restraints weight = 4117.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.4863 rms_B_bonded: 2.48
r_work: 0.4720 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.4720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.5150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   4455  Z= 0.318
  Angle     :  0.797   6.238   6160  Z= 0.411
  Chirality :  0.051   0.182    765
  Planarity :  0.007   0.033    723
  Dihedral  : 21.079 122.027    767
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 15.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.71 %
    Favored  : 85.29 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 17.78 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.20 (0.34), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.43 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 407 
 TYR   0.013   0.002   TYR N 394 
 ARG   0.006   0.001   ARG D 406 

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.504 
Fit side-chains
REVERT: D  406 ARG cc_start: 0.7586 (mtt-85) cc_final: 0.7375 (ttm-80)
REVERT: G  406 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.5720 (mtm180)
REVERT: I  406 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.5664 (mtm180)
REVERT: L  406 ARG cc_start: 0.7534 (mtt-85) cc_final: 0.7320 (mtt-85)
REVERT: N  406 ARG cc_start: 0.7013 (mtt-85) cc_final: 0.5171 (mmt180)
REVERT: N  421 ASP cc_start: 0.8803 (t0) cc_final: 0.8393 (t0)
REVERT: O  421 ASP cc_start: 0.8913 (t0) cc_final: 0.8650 (t0)
  outliers start: 24
  outliers final: 17
  residues processed: 112
  average time/residue: 0.1742
  time to fit residues: 24.1806
Evaluate side-chains
  116 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain B residue  409 SER
Chi-restraints excluded: chain D residue  419 MET
Chi-restraints excluded: chain F residue  404 SER
Chi-restraints excluded: chain F residue  419 MET
Chi-restraints excluded: chain G residue  406 ARG
Chi-restraints excluded: chain G residue  409 SER
Chi-restraints excluded: chain G residue  411 VAL
Chi-restraints excluded: chain H residue  404 SER
Chi-restraints excluded: chain I residue  406 ARG
Chi-restraints excluded: chain J residue  404 SER
Chi-restraints excluded: chain J residue  419 MET
Chi-restraints excluded: chain L residue  419 MET
Chi-restraints excluded: chain M residue  404 SER
Chi-restraints excluded: chain M residue  419 MET
Chi-restraints excluded: chain N residue  404 SER
Chi-restraints excluded: chain N residue  416 SER
Chi-restraints excluded: chain O residue  414 THR
Chi-restraints excluded: chain O residue  416 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 41 optimal weight:   20.0000
   chunk 38 optimal weight:    6.9990
   chunk 44 optimal weight:    9.9990
   chunk 21 optimal weight:    5.9990
   chunk 7 optimal weight:   20.0000
   chunk 34 optimal weight:    9.9990
   chunk 4 optimal weight:   50.0000
   chunk 9 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5318 r_free = 0.5318 target = 0.240992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4984 r_free = 0.4984 target = 0.194524 restraints weight = 4094.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.4954 rms_B_bonded: 2.45
r_work: 0.4783 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.4783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.5429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   4455  Z= 0.372
  Angle     :  0.817   6.402   6160  Z= 0.423
  Chirality :  0.053   0.187    765
  Planarity :  0.007   0.036    723
  Dihedral  : 21.033 122.258    767
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.29 %
    Favored  : 84.71 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 17.98 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.43 (0.34), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.61 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 407 
 TYR   0.015   0.002   TYR N 394 
 ARG   0.005   0.001   ARG H 406 

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 106
  time to evaluate  : 0.494 
Fit side-chains
REVERT: D  406 ARG cc_start: 0.7713 (mtt-85) cc_final: 0.7425 (tpp-160)
REVERT: G  406 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6104 (mtm-85)
REVERT: H  404 SER cc_start: 0.8278 (OUTLIER) cc_final: 0.7804 (t)
REVERT: H  408 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7406 (mt)
REVERT: I  406 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.5929 (mtm180)
REVERT: L  406 ARG cc_start: 0.7676 (mtt-85) cc_final: 0.7448 (mtt-85)
REVERT: N  406 ARG cc_start: 0.7213 (mtt-85) cc_final: 0.5381 (mmt180)
REVERT: N  421 ASP cc_start: 0.8838 (t0) cc_final: 0.8438 (t0)
REVERT: O  421 ASP cc_start: 0.8885 (t0) cc_final: 0.8663 (t0)
  outliers start: 30
  outliers final: 21
  residues processed: 121
  average time/residue: 0.1627
  time to fit residues: 24.5626
Evaluate side-chains
  128 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain B residue  409 SER
Chi-restraints excluded: chain D residue  419 MET
Chi-restraints excluded: chain F residue  404 SER
Chi-restraints excluded: chain F residue  419 MET
Chi-restraints excluded: chain G residue  406 ARG
Chi-restraints excluded: chain G residue  409 SER
Chi-restraints excluded: chain G residue  411 VAL
Chi-restraints excluded: chain H residue  404 SER
Chi-restraints excluded: chain H residue  408 LEU
Chi-restraints excluded: chain H residue  419 MET
Chi-restraints excluded: chain I residue  406 ARG
Chi-restraints excluded: chain I residue  422 SER
Chi-restraints excluded: chain J residue  404 SER
Chi-restraints excluded: chain J residue  419 MET
Chi-restraints excluded: chain L residue  419 MET
Chi-restraints excluded: chain M residue  404 SER
Chi-restraints excluded: chain M residue  413 SER
Chi-restraints excluded: chain M residue  419 MET
Chi-restraints excluded: chain N residue  404 SER
Chi-restraints excluded: chain N residue  416 SER
Chi-restraints excluded: chain N residue  419 MET
Chi-restraints excluded: chain O residue  414 THR
Chi-restraints excluded: chain O residue  416 SER
Chi-restraints excluded: chain O residue  419 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 19 optimal weight:   20.0000
   chunk 42 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 36 optimal weight:    9.9990
   chunk 41 optimal weight:   20.0000
   chunk 32 optimal weight:    7.9990
   chunk 25 optimal weight:    8.9990
   chunk 23 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    6.7988

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

Flipped N/Q/H residues before XYZ refinement:
** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5342 r_free = 0.5342 target = 0.241456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4996 r_free = 0.4996 target = 0.195107 restraints weight = 4076.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.4977 rms_B_bonded: 2.45
r_work: 0.4818 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.4818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.5617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062   4455  Z= 0.393
  Angle     :  0.826   6.632   6160  Z= 0.428
  Chirality :  0.055   0.263    765
  Planarity :  0.006   0.034    723
  Dihedral  : 20.969 122.208    767
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 18.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.10 %
    Favored  : 84.90 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 18.59 %
    Favored  : 75.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.62 (0.33), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.75 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 407 
 TYR   0.017   0.002   TYR N 394 
 ARG   0.006   0.001   ARG H 406 

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 0.463 
Fit side-chains
REVERT: D  406 ARG cc_start: 0.7747 (mtt-85) cc_final: 0.7480 (ttm-80)
REVERT: F  400 SER cc_start: 0.9343 (t) cc_final: 0.9096 (p)
REVERT: G  406 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.5942 (mtm180)
REVERT: H  408 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7454 (mt)
REVERT: I  406 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6050 (mtm180)
REVERT: L  406 ARG cc_start: 0.7698 (mtt-85) cc_final: 0.7439 (ttm-80)
REVERT: N  406 ARG cc_start: 0.7151 (mtt-85) cc_final: 0.5339 (mmt180)
REVERT: N  421 ASP cc_start: 0.8795 (t0) cc_final: 0.8353 (t0)
  outliers start: 29
  outliers final: 21
  residues processed: 120
  average time/residue: 0.1688
  time to fit residues: 25.2326
Evaluate side-chains
  127 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain B residue  409 SER
Chi-restraints excluded: chain D residue  419 MET
Chi-restraints excluded: chain F residue  404 SER
Chi-restraints excluded: chain G residue  406 ARG
Chi-restraints excluded: chain G residue  409 SER
Chi-restraints excluded: chain G residue  411 VAL
Chi-restraints excluded: chain H residue  404 SER
Chi-restraints excluded: chain H residue  408 LEU
Chi-restraints excluded: chain H residue  419 MET
Chi-restraints excluded: chain I residue  403 THR
Chi-restraints excluded: chain I residue  406 ARG
Chi-restraints excluded: chain I residue  422 SER
Chi-restraints excluded: chain J residue  404 SER
Chi-restraints excluded: chain J residue  419 MET
Chi-restraints excluded: chain L residue  419 MET
Chi-restraints excluded: chain M residue  404 SER
Chi-restraints excluded: chain M residue  413 SER
Chi-restraints excluded: chain M residue  419 MET
Chi-restraints excluded: chain N residue  404 SER
Chi-restraints excluded: chain N residue  416 SER
Chi-restraints excluded: chain O residue  414 THR
Chi-restraints excluded: chain O residue  416 SER
Chi-restraints excluded: chain O residue  419 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 20 optimal weight:    0.0980
   chunk 34 optimal weight:    6.9990
   chunk 6 optimal weight:   20.0000
   chunk 12 optimal weight:    9.9990
   chunk 37 optimal weight:   20.0000
   chunk 39 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 27 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    4.8188

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

Flipped N/Q/H residues before XYZ refinement:
** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5414 r_free = 0.5414 target = 0.232118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.5027 r_free = 0.5027 target = 0.191903 restraints weight = 4239.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.5028 rms_B_bonded: 2.50
r_work: 0.4877 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.4877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.5671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   4455  Z= 0.303
  Angle     :  0.771   6.188   6160  Z= 0.398
  Chirality :  0.051   0.254    765
  Planarity :  0.006   0.034    723
  Dihedral  : 20.726 121.642    767
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 16.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.51 %
    Favored  : 85.49 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 18.59 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.67 (0.33), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.79 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 407 
 TYR   0.014   0.002   TYR N 394 
 ARG   0.009   0.001   ARG H 406 

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.427 
Fit side-chains
REVERT: F  400 SER cc_start: 0.9326 (t) cc_final: 0.9088 (p)
REVERT: G  406 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.5894 (mtm180)
REVERT: H  408 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7249 (mt)
REVERT: I  406 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.5847 (mtm180)
REVERT: L  406 ARG cc_start: 0.7596 (mtt-85) cc_final: 0.7386 (ttm-80)
REVERT: N  406 ARG cc_start: 0.7002 (mtt-85) cc_final: 0.5234 (mmt180)
REVERT: N  413 SER cc_start: 0.8133 (m) cc_final: 0.7818 (p)
REVERT: N  421 ASP cc_start: 0.8774 (t0) cc_final: 0.8299 (t0)
REVERT: O  421 ASP cc_start: 0.8935 (t0) cc_final: 0.8724 (t0)
  outliers start: 28
  outliers final: 22
  residues processed: 120
  average time/residue: 0.1539
  time to fit residues: 23.2955
Evaluate side-chains
  131 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain B residue  409 SER
Chi-restraints excluded: chain D residue  419 MET
Chi-restraints excluded: chain F residue  404 SER
Chi-restraints excluded: chain F residue  419 MET
Chi-restraints excluded: chain G residue  406 ARG
Chi-restraints excluded: chain G residue  411 VAL
Chi-restraints excluded: chain H residue  404 SER
Chi-restraints excluded: chain H residue  408 LEU
Chi-restraints excluded: chain H residue  419 MET
Chi-restraints excluded: chain I residue  403 THR
Chi-restraints excluded: chain I residue  406 ARG
Chi-restraints excluded: chain I residue  422 SER
Chi-restraints excluded: chain J residue  404 SER
Chi-restraints excluded: chain J residue  408 LEU
Chi-restraints excluded: chain J residue  419 MET
Chi-restraints excluded: chain L residue  419 MET
Chi-restraints excluded: chain M residue  404 SER
Chi-restraints excluded: chain M residue  413 SER
Chi-restraints excluded: chain M residue  419 MET
Chi-restraints excluded: chain N residue  393 VAL
Chi-restraints excluded: chain N residue  416 SER
Chi-restraints excluded: chain O residue  414 THR
Chi-restraints excluded: chain O residue  416 SER
Chi-restraints excluded: chain O residue  419 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 30 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   chunk 7 optimal weight:   20.0000
   chunk 34 optimal weight:    7.9990
   chunk 14 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 43 optimal weight:    9.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5368 r_free = 0.5368 target = 0.225619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4960 r_free = 0.4960 target = 0.184869 restraints weight = 4400.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.4970 rms_B_bonded: 2.53
r_work: 0.4816 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.4816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.5879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   4455  Z= 0.403
  Angle     :  0.833   6.642   6160  Z= 0.434
  Chirality :  0.055   0.231    765
  Planarity :  0.007   0.039    723
  Dihedral  : 20.818 122.009    767
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 19.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.47 %
    Favored  : 83.53 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 18.59 %
    Favored  : 75.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.90 (0.32), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.97 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 407 
 TYR   0.015   0.002   TYR N 394 
 ARG   0.006   0.001   ARG F 406 

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 0.454 
Fit side-chains
REVERT: D  406 ARG cc_start: 0.7601 (mmt90) cc_final: 0.7260 (tpp-160)
REVERT: F  400 SER cc_start: 0.9296 (t) cc_final: 0.9030 (p)
REVERT: G  406 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6056 (mtm-85)
REVERT: H  408 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7529 (mt)
REVERT: I  406 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.5900 (mtm180)
REVERT: L  406 ARG cc_start: 0.7595 (mtt-85) cc_final: 0.7351 (ttm-80)
REVERT: N  406 ARG cc_start: 0.7175 (mtt-85) cc_final: 0.5393 (mmt180)
REVERT: N  421 ASP cc_start: 0.8791 (t0) cc_final: 0.8290 (t0)
REVERT: O  421 ASP cc_start: 0.8995 (t0) cc_final: 0.8787 (t0)
  outliers start: 29
  outliers final: 24
  residues processed: 123
  average time/residue: 0.1646
  time to fit residues: 25.2359
Evaluate side-chains
  137 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain B residue  409 SER
Chi-restraints excluded: chain D residue  419 MET
Chi-restraints excluded: chain F residue  404 SER
Chi-restraints excluded: chain G residue  406 ARG
Chi-restraints excluded: chain G residue  409 SER
Chi-restraints excluded: chain G residue  411 VAL
Chi-restraints excluded: chain G residue  422 SER
Chi-restraints excluded: chain H residue  393 VAL
Chi-restraints excluded: chain H residue  404 SER
Chi-restraints excluded: chain H residue  408 LEU
Chi-restraints excluded: chain H residue  419 MET
Chi-restraints excluded: chain I residue  403 THR
Chi-restraints excluded: chain I residue  406 ARG
Chi-restraints excluded: chain I residue  422 SER
Chi-restraints excluded: chain J residue  404 SER
Chi-restraints excluded: chain J residue  408 LEU
Chi-restraints excluded: chain J residue  419 MET
Chi-restraints excluded: chain L residue  419 MET
Chi-restraints excluded: chain M residue  404 SER
Chi-restraints excluded: chain M residue  413 SER
Chi-restraints excluded: chain M residue  419 MET
Chi-restraints excluded: chain N residue  404 SER
Chi-restraints excluded: chain N residue  416 SER
Chi-restraints excluded: chain O residue  414 THR
Chi-restraints excluded: chain O residue  416 SER
Chi-restraints excluded: chain O residue  419 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 44 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   chunk 33 optimal weight:   20.0000
   chunk 46 optimal weight:   10.0000
   chunk 3 optimal weight:   50.0000
   chunk 36 optimal weight:   10.0000
   chunk 1 optimal weight:    0.8980
   overall best weight:    6.7788

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

Flipped N/Q/H residues before XYZ refinement:
** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5395 r_free = 0.5395 target = 0.227106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.5001 r_free = 0.5001 target = 0.187251 restraints weight = 4272.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.5000 rms_B_bonded: 2.44
r_work: 0.4849 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.4849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.5955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   4455  Z= 0.388
  Angle     :  0.824   6.556   6160  Z= 0.428
  Chirality :  0.054   0.251    765
  Planarity :  0.006   0.041    723
  Dihedral  : 20.761 121.799    767
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 18.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.86 %
    Favored  : 83.14 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 19.19 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.95 (0.31), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.00 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 407 
 TYR   0.014   0.002   TYR N 394 
 ARG   0.007   0.001   ARG F 406 

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.535 
Fit side-chains
REVERT: F  400 SER cc_start: 0.9305 (t) cc_final: 0.9054 (p)
REVERT: G  406 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.5865 (mtm180)
REVERT: H  408 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7432 (mt)
REVERT: H  421 ASP cc_start: 0.8726 (t0) cc_final: 0.8400 (t0)
REVERT: I  406 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.5890 (mtm180)
REVERT: L  406 ARG cc_start: 0.7617 (mtt-85) cc_final: 0.7370 (ttm-80)
REVERT: N  406 ARG cc_start: 0.7143 (mtt-85) cc_final: 0.5349 (mmt180)
REVERT: N  421 ASP cc_start: 0.8770 (t0) cc_final: 0.8249 (t0)
REVERT: O  421 ASP cc_start: 0.9003 (t0) cc_final: 0.8792 (t0)
  outliers start: 27
  outliers final: 23
  residues processed: 126
  average time/residue: 0.1744
  time to fit residues: 27.8147
Evaluate side-chains
  136 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain B residue  409 SER
Chi-restraints excluded: chain D residue  419 MET
Chi-restraints excluded: chain F residue  404 SER
Chi-restraints excluded: chain G residue  406 ARG
Chi-restraints excluded: chain G residue  411 VAL
Chi-restraints excluded: chain G residue  422 SER
Chi-restraints excluded: chain H residue  393 VAL
Chi-restraints excluded: chain H residue  404 SER
Chi-restraints excluded: chain H residue  408 LEU
Chi-restraints excluded: chain H residue  419 MET
Chi-restraints excluded: chain I residue  403 THR
Chi-restraints excluded: chain I residue  406 ARG
Chi-restraints excluded: chain I residue  422 SER
Chi-restraints excluded: chain J residue  404 SER
Chi-restraints excluded: chain J residue  408 LEU
Chi-restraints excluded: chain J residue  419 MET
Chi-restraints excluded: chain L residue  419 MET
Chi-restraints excluded: chain M residue  404 SER
Chi-restraints excluded: chain M residue  413 SER
Chi-restraints excluded: chain M residue  419 MET
Chi-restraints excluded: chain N residue  404 SER
Chi-restraints excluded: chain N residue  416 SER
Chi-restraints excluded: chain O residue  414 THR
Chi-restraints excluded: chain O residue  416 SER
Chi-restraints excluded: chain O residue  419 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 52.7684 > 50:
  distance: 20 - 117:   3.428
  distance: 28 - 120:  20.854
  distance: 31 - 127:  17.835
  distance: 40 - 130:  20.809
  distance: 80 - 169:   8.520
  distance: 83 - 184:  10.303
  distance: 94 - 187:  16.465
  distance: 117 - 118:  18.974
  distance: 118 - 119:   5.997
  distance: 118 - 121:  23.271
  distance: 119 - 120:  16.485
  distance: 119 - 123:   4.348
  distance: 121 - 122:   9.577
  distance: 123 - 124:   6.520
  distance: 123 - 212:  20.470
  distance: 124 - 125:  10.513
  distance: 125 - 126:  21.378
  distance: 125 - 127:  25.006
  distance: 126 - 217:  22.369
  distance: 127 - 128:  13.625
  distance: 128 - 129:  23.182
  distance: 128 - 131:   9.086
  distance: 129 - 130:  11.446
  distance: 129 - 135:  16.722
  distance: 131 - 132:   9.635
  distance: 132 - 133:   7.464
  distance: 135 - 136:  14.071
  distance: 135 - 220:   5.929
  distance: 136 - 137:  25.235
  distance: 136 - 139:  20.498
  distance: 137 - 138:  17.225
  distance: 137 - 142:  37.391
  distance: 139 - 140:   9.538
  distance: 139 - 141:  12.631
  distance: 142 - 143:  13.436
  distance: 143 - 144:  28.445
  distance: 143 - 146:  18.561
  distance: 144 - 145:  17.692
  distance: 144 - 148:   6.541
  distance: 146 - 147:  37.862
  distance: 148 - 149:  17.641
  distance: 148 - 154:  15.875
  distance: 149 - 150:   9.195
  distance: 149 - 152:  22.312
  distance: 150 - 155:   7.858
  distance: 152 - 153:   8.393
  distance: 153 - 154:  25.208
  distance: 155 - 156:   9.307
  distance: 156 - 157:   8.514
  distance: 156 - 159:   4.479
  distance: 157 - 158:   4.809
  distance: 157 - 166:   5.544
  distance: 159 - 160:   5.145
  distance: 160 - 161:  10.447
  distance: 161 - 162:   5.402
  distance: 162 - 163:   5.137
  distance: 163 - 164:   7.364
  distance: 163 - 165:   4.702
  distance: 166 - 167:   7.509
  distance: 167 - 168:   9.022
  distance: 167 - 170:  11.033
  distance: 168 - 169:   7.132
  distance: 168 - 176:   8.338
  distance: 170 - 171:   5.850
  distance: 171 - 172:   4.773
  distance: 171 - 173:  12.579
  distance: 172 - 174:   6.830
  distance: 173 - 175:   9.814
  distance: 174 - 175:   7.302
  distance: 176 - 177:   4.313
  distance: 176 - 258:  13.742
  distance: 177 - 178:   3.393
  distance: 177 - 180:   3.763
  distance: 178 - 179:  16.127
  distance: 178 - 184:   6.226
  distance: 179 - 273:   4.526
  distance: 180 - 181:   3.396
  distance: 181 - 182:   5.427
  distance: 181 - 183:  19.722
  distance: 184 - 185:   6.486
  distance: 185 - 186:   8.981
  distance: 185 - 188:  17.608
  distance: 186 - 187:   6.452
  distance: 186 - 190:  11.606
  distance: 188 - 189:  12.683