Starting phenix.real_space_refine
on Tue Mar  3 12:29:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sp1_25364/03_2026/7sp1_25364.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sp1_25364/03_2026/7sp1_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_25364/03_2026/7sp1_25364.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sp1_25364/03_2026/7sp1_25364.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sp1_25364/03_2026/7sp1_25364.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sp1_25364/03_2026/7sp1_25364.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: "P"
      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:plan': 1, '  A%5*END:plan2': 1}
          Unresolved non-hydrogen planarities: 13
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J, K, L, M, N, O, Q
  Time building chain proxies: 0.56, per 1000 atoms: 0.13
  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: 0.32
  Conformation dependent library (CDL) restraints added in 151.9 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: 0.59
  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: 0.66

  Time building geometry restraints manager: 0.45 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
}
ncs_group {
  reference = chain 'P'
  selection = chain 'Q'
}

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:             0.170
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.710
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.330
-------------------------------------------------------------------------------
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= 0.433
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.001   0.000   ARG I 406 
 TYR   0.008   0.002   TYR C 394 
 HIS   0.003   0.002   HIS B 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00607 ( 4455)
  covalent geometry    : angle       1.28787 ( 6160)
  hydrogen bonds       : bond        0.16182 (  105)
  hydrogen bonds       : angle       9.87370 (  315)

*********************** 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  : 0.153 
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: 0.6719 (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: 0.0665
  time to fit residues: 12.2680
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  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:   20.0000
   chunk 19 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.5234 r_free = 0.5234 target = 0.229731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4831 r_free = 0.4831 target = 0.184190 restraints weight = 4470.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.4834 rms_B_bonded: 2.96
r_work: 0.4699 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.4699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   4455  Z= 0.210
  Angle     :  0.800   6.950   6160  Z= 0.418
  Chirality :  0.052   0.171    765
  Planarity :  0.007   0.036    723
  Dihedral  : 21.480 122.784    767
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.80 %
    Favored  : 90.20 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 14.95 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.59 (0.35), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.96 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 406 
 TYR   0.012   0.003   TYR A 394 
 HIS   0.004   0.001   HIS F 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 4455)
  covalent geometry    : angle       0.80043 ( 6160)
  hydrogen bonds       : bond        0.03289 (  105)
  hydrogen bonds       : angle       6.87173 (  315)

*********************** 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
  127 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.152 
Fit side-chains
REVERT: D  419 MET cc_start: 0.8744 (mtp) cc_final: 0.8397 (mtm)
REVERT: G  406 ARG cc_start: 0.7280 (mtp85) cc_final: 0.6003 (mtm-85)
REVERT: I  406 ARG cc_start: 0.7068 (mtp85) cc_final: 0.5920 (mtm180)
REVERT: K  419 MET cc_start: 0.8358 (mtp) cc_final: 0.7975 (mtm)
REVERT: M  422 SER cc_start: 0.8837 (p) cc_final: 0.8572 (p)
  outliers start: 19
  outliers final: 11
  residues processed: 117
  average time/residue: 0.0744
  time to fit residues: 10.8350
Evaluate side-chains
  102 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 4 optimal weight:   50.0000
   chunk 26 optimal weight:    9.9990
   chunk 18 optimal weight:    9.9990
   chunk 44 optimal weight:    4.9990
   chunk 43 optimal weight:   20.0000
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 38 optimal weight:    9.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.5240 r_free = 0.5240 target = 0.235102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4888 r_free = 0.4888 target = 0.187233 restraints weight = 4114.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.4839 rms_B_bonded: 2.53
r_work: 0.4700 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.4700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.4379

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= 0.254
  Angle     :  0.813   5.692   6160  Z= 0.425
  Chirality :  0.052   0.176    765
  Planarity :  0.007   0.037    723
  Dihedral  : 21.303 122.934    767
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.37 %
    Favored  : 88.63 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 14.55 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.88 (0.35), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 406 
 TYR   0.016   0.002   TYR O 394 
 HIS   0.003   0.001   HIS I 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 4455)
  covalent geometry    : angle       0.81307 ( 6160)
  hydrogen bonds       : bond        0.03632 (  105)
  hydrogen bonds       : angle       6.16820 (  315)

*********************** 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
  133 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A  406 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7726 (mtt-85)
REVERT: G  406 ARG cc_start: 0.7475 (mtp85) cc_final: 0.5796 (mtm180)
REVERT: H  406 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7593 (mtm-85)
REVERT: I  406 ARG cc_start: 0.6964 (mtp85) cc_final: 0.5667 (mtm180)
REVERT: K  419 MET cc_start: 0.8557 (mtp) cc_final: 0.8126 (mtm)
REVERT: N  406 ARG cc_start: 0.7164 (mtt-85) cc_final: 0.5301 (mmt180)
REVERT: O  406 ARG cc_start: 0.7254 (mtt-85) cc_final: 0.5294 (mmt180)
REVERT: O  421 ASP cc_start: 0.8782 (t0) cc_final: 0.8483 (t0)
  outliers start: 20
  outliers final: 16
  residues processed: 123
  average time/residue: 0.0775
  time to fit residues: 11.8060
Evaluate side-chains
  120 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain B residue  409 SER
Chi-restraints excluded: chain F residue  404 SER
Chi-restraints excluded: chain F residue  419 MET
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 J residue  408 LEU
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 36 optimal weight:   20.0000
   chunk 28 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 18 optimal weight:   20.0000
   chunk 38 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9990
   chunk 25 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** 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**
** 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 = 0.5300 r_free = 0.5300 target = 0.240731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4952 r_free = 0.4952 target = 0.192844 restraints weight = 3970.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.4898 rms_B_bonded: 2.51
r_work: 0.4750 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.4750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.4672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4455  Z= 0.197
  Angle     :  0.757   5.253   6160  Z= 0.389
  Chirality :  0.050   0.178    765
  Planarity :  0.006   0.040    723
  Dihedral  : 21.046 121.957    767
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.14 %
    Favored  : 86.86 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 15.76 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.94 (0.35), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.23 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 406 
 TYR   0.012   0.002   TYR O 394 
 HIS   0.002   0.001   HIS J 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 4455)
  covalent geometry    : angle       0.75681 ( 6160)
  hydrogen bonds       : bond        0.02881 (  105)
  hydrogen bonds       : angle       5.69059 (  315)

*********************** 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
  130 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.161 
Fit side-chains
REVERT: E  419 MET cc_start: 0.8685 (mtm) cc_final: 0.8484 (mtm)
REVERT: G  406 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.5966 (mtm180)
REVERT: I  406 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.5759 (mtm180)
REVERT: K  406 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7528 (mtm-85)
REVERT: K  419 MET cc_start: 0.8362 (mtp) cc_final: 0.7875 (mtm)
REVERT: L  406 ARG cc_start: 0.7626 (mtt-85) cc_final: 0.7404 (mtt-85)
REVERT: N  406 ARG cc_start: 0.7029 (mtt-85) cc_final: 0.5276 (mmt180)
REVERT: N  413 SER cc_start: 0.7712 (m) cc_final: 0.7508 (m)
REVERT: O  406 ARG cc_start: 0.7113 (mtt-85) cc_final: 0.5140 (mmt180)
REVERT: O  413 SER cc_start: 0.7328 (m) cc_final: 0.6981 (p)
REVERT: O  421 ASP cc_start: 0.8913 (t0) cc_final: 0.8596 (t0)
  outliers start: 27
  outliers final: 17
  residues processed: 115
  average time/residue: 0.0820
  time to fit residues: 11.4819
Evaluate side-chains
  119 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
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 F residue  419 MET
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  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:    8.9990
   chunk 8 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 27 optimal weight:   20.0000
   chunk 29 optimal weight:   20.0000
   chunk 46 optimal weight:    0.0570
   chunk 42 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 41 optimal weight:    9.9990
   chunk 30 optimal weight:   20.0000
   overall best weight:    7.0106

-------------------------------------------------------------------------------
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**
** 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 = 0.5216 r_free = 0.5216 target = 0.225566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4788 r_free = 0.4788 target = 0.177898 restraints weight = 4158.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.4821 rms_B_bonded: 2.72
r_work: 0.4677 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.4677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.5131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   4455  Z= 0.268
  Angle     :  0.823   6.182   6160  Z= 0.428
  Chirality :  0.053   0.187    765
  Planarity :  0.007   0.048    723
  Dihedral  : 21.095 121.977    767
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 17.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.71 %
    Favored  : 85.29 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 15.96 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.23 (0.34), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 406 
 TYR   0.016   0.002   TYR N 394 
 HIS   0.003   0.001   HIS E 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 ( 4455)
  covalent geometry    : angle       0.82324 ( 6160)
  hydrogen bonds       : bond        0.03281 (  105)
  hydrogen bonds       : angle       5.68091 (  315)

*********************** 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
  127 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.162 
Fit side-chains
REVERT: C  406 ARG cc_start: 0.7884 (mtt90) cc_final: 0.7626 (mtt90)
REVERT: G  406 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6092 (mtm180)
REVERT: I  406 ARG cc_start: 0.7315 (mtp85) cc_final: 0.5879 (mtm180)
REVERT: K  406 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7800 (mtt-85)
REVERT: K  419 MET cc_start: 0.8463 (mtp) cc_final: 0.8046 (mtm)
REVERT: L  406 ARG cc_start: 0.7821 (mtt-85) cc_final: 0.7502 (mtt-85)
REVERT: M  406 ARG cc_start: 0.7884 (mtm-85) cc_final: 0.7645 (mtt-85)
REVERT: N  406 ARG cc_start: 0.7116 (mtt-85) cc_final: 0.5351 (mmt180)
REVERT: N  421 ASP cc_start: 0.8781 (t0) cc_final: 0.8406 (t0)
REVERT: O  406 ARG cc_start: 0.7271 (mtt-85) cc_final: 0.5357 (mmt180)
REVERT: O  413 SER cc_start: 0.7423 (m) cc_final: 0.7103 (p)
REVERT: O  421 ASP cc_start: 0.8949 (t0) cc_final: 0.8672 (t0)
  outliers start: 25
  outliers final: 20
  residues processed: 114
  average time/residue: 0.0753
  time to fit residues: 10.7060
Evaluate side-chains
  122 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
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 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  393 VAL
Chi-restraints excluded: chain H residue  404 SER
Chi-restraints excluded: chain H residue  419 MET
Chi-restraints excluded: chain J residue  404 SER
Chi-restraints excluded: chain J residue  408 LEU
Chi-restraints excluded: chain J residue  409 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  419 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 36 optimal weight:   10.0000
   chunk 13 optimal weight:   20.0000
   chunk 28 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   overall best weight:    6.7990

-------------------------------------------------------------------------------
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 = 0.5354 r_free = 0.5354 target = 0.229354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4988 r_free = 0.4988 target = 0.187993 restraints weight = 4418.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.4948 rms_B_bonded: 2.67
r_work: 0.4784 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.4784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.5362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   4455  Z= 0.258
  Angle     :  0.814   6.110   6160  Z= 0.421
  Chirality :  0.052   0.188    765
  Planarity :  0.007   0.048    723
  Dihedral  : 21.019 122.066    767
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 17.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.90 %
    Favored  : 85.10 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 16.36 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.38 (0.34), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 406 
 TYR   0.015   0.002   TYR N 394 
 HIS   0.003   0.001   HIS E 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00571 ( 4455)
  covalent geometry    : angle       0.81389 ( 6160)
  hydrogen bonds       : bond        0.03138 (  105)
  hydrogen bonds       : angle       5.51205 (  315)

*********************** 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
  140 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.118 
Fit side-chains
REVERT: C  400 SER cc_start: 0.9348 (t) cc_final: 0.9122 (p)
REVERT: C  406 ARG cc_start: 0.7849 (mtt90) cc_final: 0.7556 (mtt90)
REVERT: F  418 ASP cc_start: 0.8698 (p0) cc_final: 0.8482 (p0)
REVERT: G  406 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.5941 (mtm180)
REVERT: H  408 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7456 (mt)
REVERT: I  406 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6063 (mtm180)
REVERT: K  406 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7672 (ttm-80)
REVERT: L  406 ARG cc_start: 0.7753 (mtt-85) cc_final: 0.7431 (mtt-85)
REVERT: N  406 ARG cc_start: 0.7077 (mtt-85) cc_final: 0.5344 (mmt180)
REVERT: N  421 ASP cc_start: 0.8765 (t0) cc_final: 0.8333 (t0)
REVERT: O  406 ARG cc_start: 0.7336 (mtt-85) cc_final: 0.5494 (mmt180)
REVERT: O  413 SER cc_start: 0.7494 (m) cc_final: 0.7159 (p)
REVERT: O  421 ASP cc_start: 0.8941 (t0) cc_final: 0.8700 (t0)
  outliers start: 25
  outliers final: 21
  residues processed: 126
  average time/residue: 0.0719
  time to fit residues: 11.1431
Evaluate side-chains
  135 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
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 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  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 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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   chunk 32 optimal weight:   20.0000
   chunk 2 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 17 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 1 optimal weight:    9.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.5267 r_free = 0.5267 target = 0.229806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4871 r_free = 0.4871 target = 0.184741 restraints weight = 4222.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.4938 rms_B_bonded: 2.64
r_work: 0.4782 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.4782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.5530

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= 0.271
  Angle     :  0.828   6.369   6160  Z= 0.430
  Chirality :  0.053   0.190    765
  Planarity :  0.007   0.054    723
  Dihedral  : 20.994 122.580    767
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 17.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.49 %
    Favored  : 84.51 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.58 (0.34), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.72 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 406 
 TYR   0.015   0.002   TYR N 394 
 HIS   0.003   0.001   HIS E 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 ( 4455)
  covalent geometry    : angle       0.82833 ( 6160)
  hydrogen bonds       : bond        0.03293 (  105)
  hydrogen bonds       : angle       5.51787 (  315)

*********************** 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
  138 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 110
  time to evaluate  : 0.165 
Fit side-chains
REVERT: C  400 SER cc_start: 0.9338 (t) cc_final: 0.9129 (p)
REVERT: C  406 ARG cc_start: 0.7881 (mtt90) cc_final: 0.7593 (mtt90)
REVERT: E  421 ASP cc_start: 0.8459 (t0) cc_final: 0.8121 (t70)
REVERT: F  418 ASP cc_start: 0.8665 (p0) cc_final: 0.8465 (p0)
REVERT: G  406 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6201 (mtm-85)
REVERT: H  408 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7480 (mt)
REVERT: I  406 ARG cc_start: 0.7545 (mtp85) cc_final: 0.6070 (mtm180)
REVERT: K  406 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7591 (ttm-80)
REVERT: L  406 ARG cc_start: 0.7813 (mtt-85) cc_final: 0.7302 (ttm-80)
REVERT: N  406 ARG cc_start: 0.7153 (mtt-85) cc_final: 0.5412 (mmt180)
REVERT: N  421 ASP cc_start: 0.8764 (t0) cc_final: 0.8328 (t0)
REVERT: O  406 ARG cc_start: 0.7397 (mtt-85) cc_final: 0.5408 (mmt180)
REVERT: O  413 SER cc_start: 0.7805 (m) cc_final: 0.7423 (p)
REVERT: O  421 ASP cc_start: 0.8927 (t0) cc_final: 0.8710 (t0)
  outliers start: 28
  outliers final: 21
  residues processed: 124
  average time/residue: 0.0682
  time to fit residues: 10.5242
Evaluate side-chains
  133 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
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 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  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  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 21 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   chunk 24 optimal weight:    8.9990
   chunk 9 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0040
   chunk 33 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 29 optimal weight:    9.9990
   overall best weight:    3.7598

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

Flipped N/Q/H residues before XYZ refinement:
** D 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 = 0.5409 r_free = 0.5409 target = 0.234403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5047 r_free = 0.5047 target = 0.194420 restraints weight = 4307.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.5041 rms_B_bonded: 2.53
r_work: 0.4879 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.4879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.5499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4455  Z= 0.169
  Angle     :  0.743   5.622   6160  Z= 0.383
  Chirality :  0.048   0.180    765
  Planarity :  0.006   0.055    723
  Dihedral  : 20.669 121.523    767
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.75 %
    Favored  : 87.25 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 19.60 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.53 (0.34), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.002   ARG E 406 
 TYR   0.012   0.002   TYR N 394 
 HIS   0.001   0.001   HIS E 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 4455)
  covalent geometry    : angle       0.74293 ( 6160)
  hydrogen bonds       : bond        0.02977 (  105)
  hydrogen bonds       : angle       5.33445 (  315)

*********************** 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
  122 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.163 
Fit side-chains
REVERT: G  406 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.5985 (mtm180)
REVERT: H  408 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7315 (mt)
REVERT: I  406 ARG cc_start: 0.7436 (mtp85) cc_final: 0.5719 (mtt90)
REVERT: L  406 ARG cc_start: 0.7619 (mtt-85) cc_final: 0.7255 (ttm-80)
REVERT: N  406 ARG cc_start: 0.7054 (mtt-85) cc_final: 0.5461 (mmt180)
REVERT: N  421 ASP cc_start: 0.8771 (t0) cc_final: 0.8323 (t0)
REVERT: O  406 ARG cc_start: 0.7294 (mtt-85) cc_final: 0.5315 (mmt180)
REVERT: O  421 ASP cc_start: 0.8958 (t0) cc_final: 0.8740 (t0)
  outliers start: 19
  outliers final: 15
  residues processed: 112
  average time/residue: 0.0805
  time to fit residues: 11.0251
Evaluate side-chains
  114 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
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 H residue  404 SER
Chi-restraints excluded: chain H residue  408 LEU
Chi-restraints excluded: chain H residue  419 MET
Chi-restraints excluded: chain J residue  404 SER
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
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 10 optimal weight:   20.0000
   chunk 42 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   chunk 44 optimal weight:   20.0000
   chunk 21 optimal weight:   10.0000
   chunk 36 optimal weight:    9.9990
   chunk 32 optimal weight:    4.9990
   chunk 4 optimal weight:   50.0000
   chunk 40 optimal weight:   20.0000
   chunk 1 optimal weight:    2.9990
   chunk 11 optimal weight:    9.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
** 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**
** 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 = 0.5393 r_free = 0.5393 target = 0.229139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.5017 r_free = 0.5017 target = 0.187877 restraints weight = 4358.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.4968 rms_B_bonded: 2.59
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: 0.7339
moved from start:          0.5734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   4455  Z= 0.273
  Angle     :  0.837   6.488   6160  Z= 0.435
  Chirality :  0.054   0.195    765
  Planarity :  0.007   0.064    723
  Dihedral  : 20.851 124.616    767
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 18.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.08 %
    Favored  : 83.92 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 18.38 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.019   0.002   ARG D 406 
 TYR   0.016   0.002   TYR N 394 
 HIS   0.003   0.001   HIS E 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00610 ( 4455)
  covalent geometry    : angle       0.83653 ( 6160)
  hydrogen bonds       : bond        0.03395 (  105)
  hydrogen bonds       : angle       5.48319 (  315)

*********************** 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
  131 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.097 
Fit side-chains
REVERT: G  406 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6021 (mtm-85)
REVERT: H  408 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7410 (mt)
REVERT: I  406 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.5981 (mtm180)
REVERT: L  406 ARG cc_start: 0.7758 (mtt-85) cc_final: 0.7256 (ttm-80)
REVERT: N  406 ARG cc_start: 0.7083 (mtt-85) cc_final: 0.5373 (mmt180)
REVERT: N  421 ASP cc_start: 0.8739 (t0) cc_final: 0.8208 (t0)
REVERT: O  406 ARG cc_start: 0.7402 (mtt-85) cc_final: 0.5504 (mmt180)
REVERT: O  421 ASP cc_start: 0.8945 (t0) cc_final: 0.8714 (t0)
  outliers start: 24
  outliers final: 19
  residues processed: 117
  average time/residue: 0.0666
  time to fit residues: 9.6445
Evaluate side-chains
  126 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
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 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 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
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 40 optimal weight:   20.0000
   chunk 34 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 9 optimal weight:    8.9990
   chunk 44 optimal weight:   10.0000
   chunk 25 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   chunk 46 optimal weight:    8.9990
   overall best weight:    4.9788

-------------------------------------------------------------------------------
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 = 0.5436 r_free = 0.5436 target = 0.233952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.5064 r_free = 0.5064 target = 0.193027 restraints weight = 4309.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.5030 rms_B_bonded: 2.60
r_work: 0.4871 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.4871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.5728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   4455  Z= 0.203
  Angle     :  0.772   6.183   6160  Z= 0.400
  Chirality :  0.051   0.185    765
  Planarity :  0.006   0.060    723
  Dihedral  : 20.661 124.866    767
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 16.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.10 %
    Favored  : 84.90 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 20.20 %
    Favored  : 75.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.65 (0.33), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.78 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.002   ARG E 406 
 TYR   0.013   0.002   TYR N 394 
 HIS   0.002   0.001   HIS E 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 4455)
  covalent geometry    : angle       0.77235 ( 6160)
  hydrogen bonds       : bond        0.03121 (  105)
  hydrogen bonds       : angle       5.40267 (  315)

********************** 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
  131 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.137 
Fit side-chains
REVERT: G  406 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.5872 (mtm180)
REVERT: H  408 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7322 (mt)
REVERT: I  406 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.5825 (mtt90)
REVERT: L  406 ARG cc_start: 0.7656 (mtt-85) cc_final: 0.7250 (ttm-80)
REVERT: N  406 ARG cc_start: 0.7025 (mtt-85) cc_final: 0.5361 (mmt180)
REVERT: N  421 ASP cc_start: 0.8760 (t0) cc_final: 0.8204 (t0)
REVERT: O  406 ARG cc_start: 0.7355 (mtt-85) cc_final: 0.5402 (mmt180)
REVERT: O  421 ASP cc_start: 0.8932 (t0) cc_final: 0.8721 (t0)
  outliers start: 23
  outliers final: 18
  residues processed: 119
  average time/residue: 0.0794
  time to fit residues: 11.4614
Evaluate side-chains
  127 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 MET
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 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  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 5 optimal weight:    9.9990
   chunk 11 optimal weight:    0.8980
   chunk 20 optimal weight:   20.0000
   chunk 45 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:   20.0000
   chunk 33 optimal weight:   20.0000
   chunk 29 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    4.3586

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.5450 r_free = 0.5450 target = 0.234917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.5076 r_free = 0.5076 target = 0.194757 restraints weight = 4309.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.5068 rms_B_bonded: 2.50
r_work: 0.4912 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.4912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.5782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4455  Z= 0.184
  Angle     :  0.744   6.054   6160  Z= 0.385
  Chirality :  0.049   0.180    765
  Planarity :  0.006   0.033    723
  Dihedral  : 20.478 125.481    767
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 15.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.86 %
    Favored  : 83.14 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 20.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.66 (0.33), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.78 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.002   ARG K 406 
 TYR   0.013   0.002   TYR N 394 
 HIS   0.002   0.001   HIS E 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 4455)
  covalent geometry    : angle       0.74414 ( 6160)
  hydrogen bonds       : bond        0.03042 (  105)
  hydrogen bonds       : angle       5.30351 (  315)

===============================================================================
Job complete
usr+sys time: 903.02 seconds
wall clock time: 16 minutes 27.63 seconds (987.63 seconds total)