Starting phenix.real_space_refine
on Thu Sep 10 21:59:21 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7sp1_25364/09_2026/7sp1_25364.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sp1_25364/09_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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7sp1_25364/09_2026/7sp1_25364.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7sp1_25364/09_2026/7sp1_25364.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sp1_25364/09_2026/7sp1_25364.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sp1_25364/09_2026/7sp1_25364.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sp1_25364/09_2026/7sp1_25364.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sp1_25364/09_2026/7sp1_25364.map"
  }
  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-2.2.1-6174/lib/python3.11/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, 'RNAv2': 9}
          Modifications used: {'5*END': 1, 'rna3p_pur': 9}
          Link IDs: {'rna3p': 9}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 1
          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: 0.75, per 1000 atoms: 0.17
  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: 0.38
  Conformation dependent library (CDL) restraints added in 149.4 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: 0.58
  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: 0.59

  Time building geometry restraints manager: 0.46 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 -     1.62: 5357
        1.62 -     3.25: 511
        3.25 -     4.87: 212
        4.87 -     6.50: 72
        6.50 -     8.12: 2
  Bond angle restraints: 6154
  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 6149 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.86: 2217
        9.86 -    19.72: 224
       19.72 -    29.58: 115
       29.58 -    39.44: 81
       39.44 -    49.30: 63
  Dihedral angle restraints: 2700
    sinusoidal: 1140
      harmonic: 1560
  Sorted by residual:
  dihedral pdb=" O5'   A Q  10 "
           pdb=" C5'   A Q  10 "
           pdb=" C4'   A Q  10 "
           pdb=" C3'   A Q  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -99.96   39.96     3      6.40e+00 2.44e-02 3.90e+01
  dihedral pdb=" O5'   A P  11 "
           pdb=" C5'   A P  11 "
           pdb=" C4'   A P  11 "
           pdb=" C3'   A P  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -99.93   39.93     3      6.40e+00 2.44e-02 3.90e+01
  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
  ... (remaining 2697 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 555
       0.076 -    0.152: 168
       0.152 -    0.228: 26
       0.228 -    0.304: 14
       0.304 -    0.380: 2
  Chirality restraints: 765
  Sorted by residual:
  chirality pdb=" P     A P  11 "
            pdb=" OP1   A P  11 "
            pdb=" OP2   A P  11 "
            pdb=" O5'   A P  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.55   -0.38 2.00e-01 2.50e+01 3.61e+00
  chirality pdb=" P     A Q  10 "
            pdb=" OP1   A Q  10 "
            pdb=" OP2   A Q  10 "
            pdb=" O5'   A Q  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.55   -0.38 2.00e-01 2.50e+01 3.61e+00
  chirality pdb=" P     A P  18 "
            pdb=" OP1   A P  18 "
            pdb=" OP2   A P  18 "
            pdb=" O5'   A P  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.47   -0.30 2.00e-01 2.50e+01 2.22e+00
  ... (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:             0.150
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.830
  Find NCS groups from input model:        0.030
  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:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
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= 0.427
  Angle     :  1.286   8.123   6154  Z= 0.776
  Chirality :  0.078   0.380    765
  Planarity :  0.008   0.033    723
  Dihedral  : 15.152  49.299   1680
  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/Z
  covalent geometry    : bond        0.00606 /  0.43 ( 4455)
  covalent geometry    : angle       1.28557 /  0.78 ( 6154)
  hydrogen bonds       : bond        0.16182 / 10.59 (  105)
  hydrogen bonds       : angle       9.87370 /  6.78 (  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  : 0.130 
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: 0.0679
  time to fit residues: 12.6036
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...
** 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 = 0.5239 r_free = 0.5239 target = 0.241623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4891 r_free = 0.4891 target = 0.194745 restraints weight = 4145.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.4858 rms_B_bonded: 2.65
r_work: 0.4709 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.4709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.3338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4455  Z= 0.228
  Angle     :  0.830   7.389   6154  Z= 0.431
  Chirality :  0.057   0.184    765
  Planarity :  0.007   0.036    723
  Dihedral  : 12.146  50.719    765
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.61 %
    Favored  : 90.39 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 15.56 %
    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: -2.60 (0.35), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.27), residues: 510

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



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00480 /  0.23 ( 4455)
  covalent geometry    : angle       0.82954 /  0.43 ( 6154)
  hydrogen bonds       : bond        0.03557 /  2.47 (  105)
  hydrogen bonds       : angle       6.91902 /  4.88 (  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: 16
    poor density    : 111
  time to evaluate  : 0.129 
Fit side-chains
REVERT: D  419 MET cc_start: 0.8705 (mtp) cc_final: 0.8334 (mtm)
REVERT: G  406 ARG cc_start: 0.7248 (mtp85) cc_final: 0.5793 (mtm-85)
REVERT: I  406 ARG cc_start: 0.7032 (mtp85) cc_final: 0.5884 (mtm180)
REVERT: K  419 MET cc_start: 0.8348 (mtp) cc_final: 0.7956 (mtm)
REVERT: M  422 SER cc_start: 0.8824 (p) cc_final: 0.8576 (p)
  outliers start: 16
  outliers final: 9
  residues processed: 117
  average time/residue: 0.0690
  time to fit residues: 10.0226
Evaluate side-chains
  102 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  409 SER
Chi-restraints excluded: chain E residue  409 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
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:    1.9990
   chunk 18 optimal weight:    8.9990
   chunk 44 optimal weight:    7.9990
   chunk 43 optimal weight:    0.0170
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    7.9990
   chunk 38 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    4.2026

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
J 407 HIS
N 407 HIS
** O 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5284 r_free = 0.5284 target = 0.241574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4918 r_free = 0.4918 target = 0.193114 restraints weight = 4111.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.4885 rms_B_bonded: 2.69
r_work: 0.4735 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.4735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.4071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4455  Z= 0.184
  Angle     :  0.761   4.832   6154  Z= 0.393
  Chirality :  0.053   0.163    765
  Planarity :  0.006   0.035    723
  Dihedral  : 12.161  50.542    765
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.80 %
    Favored  : 90.20 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 15.76 %
    Favored  : 80.81 %
  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: -2.72 (0.35), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 406 
 TYR   0.011   0.002   TYR O 394 
 HIS   0.003   0.001   HIS G 407 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00408 /  0.18 ( 4455)
  covalent geometry    : angle       0.76059 /  0.39 ( 6154)
  hydrogen bonds       : bond        0.03245 /  2.19 (  105)
  hydrogen bonds       : angle       6.10024 /  4.36 (  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
  119 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.158 
Fit side-chains
REVERT: G  406 ARG cc_start: 0.7515 (mtp85) cc_final: 0.5719 (mtm180)
REVERT: I  406 ARG cc_start: 0.6930 (mtp85) cc_final: 0.6035 (mtm180)
REVERT: K  419 MET cc_start: 0.8329 (mtp) cc_final: 0.7919 (mtm)
REVERT: N  406 ARG cc_start: 0.6806 (mtt-85) cc_final: 0.5208 (mmt180)
  outliers start: 17
  outliers final: 13
  residues processed: 109
  average time/residue: 0.0688
  time to fit residues: 9.4654
Evaluate side-chains
  109 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
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  399 VAL
Chi-restraints excluded: chain G residue  409 SER
Chi-restraints excluded: chain H 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  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:    6.9990
   chunk 16 optimal weight:    9.9990
   chunk 18 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 11 optimal weight:   20.0000
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:   20.0000
   chunk 20 optimal weight:    8.9990
   chunk 6 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   overall best weight:    6.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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**
** 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 = 0.5315 r_free = 0.5315 target = 0.245827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4973 r_free = 0.4973 target = 0.197595 restraints weight = 4035.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.4949 rms_B_bonded: 2.57
r_work: 0.4775 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.4775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.4772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   4455  Z= 0.247
  Angle     :  0.821   5.915   6154  Z= 0.422
  Chirality :  0.055   0.183    765
  Planarity :  0.007   0.038    723
  Dihedral  : 12.327  51.290    765
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 17.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.92 %
    Favored  : 86.08 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 15.76 %
    Favored  : 79.19 %
  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 : -2.24 (0.27), residues: 510

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



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00539 /  0.25 ( 4455)
  covalent geometry    : angle       0.82143 /  0.42 ( 6154)
  hydrogen bonds       : bond        0.03140 /  2.11 (  105)
  hydrogen bonds       : angle       5.74366 /  4.13 (  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
  138 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 0.174 
Fit side-chains
REVERT: G  406 ARG cc_start: 0.7804 (mtp85) cc_final: 0.6048 (mtm-85)
REVERT: I  406 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.5913 (mtm180)
REVERT: K  419 MET cc_start: 0.8509 (mtp) cc_final: 0.8056 (mtm)
REVERT: L  406 ARG cc_start: 0.7687 (mtt-85) cc_final: 0.7384 (ttm-80)
REVERT: M  406 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7668 (mtt-85)
REVERT: N  406 ARG cc_start: 0.7211 (mtt-85) cc_final: 0.5533 (mmt180)
REVERT: O  406 ARG cc_start: 0.7324 (mtt-85) cc_final: 0.5391 (mmt180)
REVERT: O  413 SER cc_start: 0.7460 (m) cc_final: 0.7112 (p)
REVERT: O  421 ASP cc_start: 0.8922 (t0) cc_final: 0.8652 (t0)
  outliers start: 25
  outliers final: 19
  residues processed: 126
  average time/residue: 0.0651
  time to fit residues: 10.4219
Evaluate side-chains
  125 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
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  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  393 VAL
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  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  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:    0.7980
   chunk 8 optimal weight:    9.9990
   chunk 39 optimal weight:   30.0000
   chunk 34 optimal weight:    9.9990
   chunk 27 optimal weight:    0.5980
   chunk 29 optimal weight:    5.9990
   chunk 46 optimal weight:   20.0000
   chunk 42 optimal weight:    9.9990
   chunk 5 optimal weight:    0.1980
   chunk 41 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    2.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 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 = 0.5452 r_free = 0.5452 target = 0.243061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5056 r_free = 0.5056 target = 0.198352 restraints weight = 4299.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.5060 rms_B_bonded: 2.89
r_work: 0.4889 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.4889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.4832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4455  Z= 0.146
  Angle     :  0.728   5.390   6154  Z= 0.368
  Chirality :  0.051   0.177    765
  Planarity :  0.006   0.028    723
  Dihedral  : 11.981  51.489    765
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.96 %
    Favored  : 88.04 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 17.58 %
    Favored  : 77.58 %
  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: -2.95 (0.34), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.24 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG J 406 
 TYR   0.009   0.001   TYR N 394 
 HIS   0.002   0.001   HIS J 407 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.15 ( 4455)
  covalent geometry    : angle       0.72840 /  0.37 ( 6154)
  hydrogen bonds       : bond        0.02791 /  1.80 (  105)
  hydrogen bonds       : angle       5.41189 /  3.86 (  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
  122 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.155 
Fit side-chains
REVERT: G  406 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.5703 (mtm180)
REVERT: I  406 ARG cc_start: 0.6931 (OUTLIER) cc_final: 0.5845 (mtm180)
REVERT: K  409 SER cc_start: 0.8949 (m) cc_final: 0.8744 (m)
REVERT: K  419 MET cc_start: 0.8257 (mtp) cc_final: 0.7918 (mtm)
REVERT: N  406 ARG cc_start: 0.7005 (mtt-85) cc_final: 0.5443 (mmt180)
REVERT: O  406 ARG cc_start: 0.7133 (mtt-85) cc_final: 0.5244 (mmt180)
REVERT: O  413 SER cc_start: 0.7435 (m) cc_final: 0.7185 (p)
REVERT: O  421 ASP cc_start: 0.9011 (t0) cc_final: 0.8742 (t0)
  outliers start: 24
  outliers final: 15
  residues processed: 107
  average time/residue: 0.0686
  time to fit residues: 9.2471
Evaluate side-chains
  108 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain B 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  393 VAL
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 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
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:   10.0000
   chunk 36 optimal weight:   20.0000
   chunk 13 optimal weight:   20.0000
   chunk 28 optimal weight:    9.9990
   chunk 33 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:    0.0470
   chunk 35 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   overall best weight:    5.6086

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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**
** 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 = 0.5390 r_free = 0.5390 target = 0.234795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.5003 r_free = 0.5003 target = 0.190384 restraints weight = 4315.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.4983 rms_B_bonded: 2.70
r_work: 0.4817 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.4817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.5148

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= 0.228
  Angle     :  0.794   5.806   6154  Z= 0.405
  Chirality :  0.054   0.184    765
  Planarity :  0.006   0.032    723
  Dihedral  : 12.091  51.766    765
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 18.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.31 %
    Favored  : 85.69 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 16.57 %
    Favored  : 77.98 %
  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: -3.20 (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
 ARG   0.007   0.001   ARG F 406 
 TYR   0.014   0.002   TYR N 394 
 HIS   0.003   0.001   HIS J 407 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00504 /  0.23 ( 4455)
  covalent geometry    : angle       0.79424 /  0.41 ( 6154)
  hydrogen bonds       : bond        0.03134 /  2.06 (  105)
  hydrogen bonds       : angle       5.53363 /  3.96 (  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
  124 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.161 
Fit side-chains
REVERT: G  406 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.5721 (mtm180)
REVERT: H  408 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7170 (mt)
REVERT: I  406 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.5849 (mtm180)
REVERT: I  422 SER cc_start: 0.7844 (p) cc_final: 0.7584 (t)
REVERT: K  419 MET cc_start: 0.8493 (mtp) cc_final: 0.8089 (mtm)
REVERT: N  406 ARG cc_start: 0.7215 (mtt-85) cc_final: 0.5499 (mmt180)
REVERT: N  421 ASP cc_start: 0.8821 (t0) cc_final: 0.8481 (t0)
REVERT: O  406 ARG cc_start: 0.7292 (mtt-85) cc_final: 0.5372 (mmt180)
REVERT: O  413 SER cc_start: 0.7442 (m) cc_final: 0.7216 (p)
REVERT: O  421 ASP cc_start: 0.9004 (t0) cc_final: 0.8728 (t0)
  outliers start: 27
  outliers final: 22
  residues processed: 108
  average time/residue: 0.0577
  time to fit residues: 8.1347
Evaluate side-chains
  119 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain B residue  419 MET
Chi-restraints excluded: chain B residue  422 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 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  393 VAL
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  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  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:   20.0000
   chunk 28 optimal weight:    0.0980
   chunk 32 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 22 optimal weight:    8.9990
   chunk 17 optimal weight:    8.9990
   chunk 24 optimal weight:    0.8980
   chunk 25 optimal weight:    9.9990
   chunk 46 optimal weight:   20.0000
   chunk 7 optimal weight:    5.9990
   chunk 1 optimal weight:    7.9990
   overall best weight:    4.3986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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**
** 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 = 0.5420 r_free = 0.5420 target = 0.236111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5035 r_free = 0.5035 target = 0.193740 restraints weight = 4270.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.5024 rms_B_bonded: 2.60
r_work: 0.4871 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.4871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.5250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4455  Z= 0.184
  Angle     :  0.755   5.486   6154  Z= 0.384
  Chirality :  0.053   0.180    765
  Planarity :  0.006   0.028    723
  Dihedral  : 11.980  52.036    765
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 16.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.73 %
    Favored  : 86.27 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 17.78 %
    Favored  : 77.58 %
  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: -3.29 (0.33), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.50 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 406 
 TYR   0.011   0.002   TYR N 394 
 HIS   0.002   0.001   HIS J 407 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.18 ( 4455)
  covalent geometry    : angle       0.75473 /  0.38 ( 6154)
  hydrogen bonds       : bond        0.02936 /  1.93 (  105)
  hydrogen bonds       : angle       5.36988 /  3.84 (  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
  121 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.172 
Fit side-chains
REVERT: G  406 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.5785 (mtm180)
REVERT: I  406 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.5894 (mtm180)
REVERT: N  406 ARG cc_start: 0.7158 (mtt-85) cc_final: 0.5527 (mmt180)
REVERT: N  421 ASP cc_start: 0.8815 (t0) cc_final: 0.8399 (t0)
REVERT: O  406 ARG cc_start: 0.7369 (mtt-85) cc_final: 0.5409 (mmt180)
REVERT: O  421 ASP cc_start: 0.8986 (t0) cc_final: 0.8734 (t0)
  outliers start: 23
  outliers final: 17
  residues processed: 107
  average time/residue: 0.0641
  time to fit residues: 8.7540
Evaluate side-chains
  113 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain B residue  419 MET
Chi-restraints excluded: chain B residue  422 SER
Chi-restraints excluded: chain D residue  419 MET
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  403 THR
Chi-restraints excluded: chain I residue  406 ARG
Chi-restraints excluded: chain J residue  419 MET
Chi-restraints excluded: chain L residue  419 MET
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:    0.6980
   chunk 16 optimal weight:    9.9990
   chunk 6 optimal weight:   20.0000
   chunk 12 optimal weight:   20.0000
   chunk 24 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 33 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   overall best weight:    3.2586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 407 HIS
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5504 r_free = 0.5504 target = 0.243409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.5118 r_free = 0.5118 target = 0.200120 restraints weight = 4185.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.5072 rms_B_bonded: 2.65
r_work: 0.4924 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.4924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.5374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4455  Z= 0.152
  Angle     :  0.721   5.432   6154  Z= 0.365
  Chirality :  0.052   0.176    765
  Planarity :  0.006   0.030    723
  Dihedral  : 11.820  52.435    765
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.33 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 19.39 %
    Favored  : 76.36 %
  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 (0.33), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 406 
 TYR   0.011   0.001   TYR N 394 
 HIS   0.003   0.001   HIS J 407 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.15 ( 4455)
  covalent geometry    : angle       0.72062 /  0.37 ( 6154)
  hydrogen bonds       : bond        0.02816 /  1.85 (  105)
  hydrogen bonds       : angle       5.28419 /  3.79 (  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
  117 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.109 
Fit side-chains
REVERT: G  406 ARG cc_start: 0.7563 (mtp85) cc_final: 0.5613 (mtm180)
REVERT: H  408 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6972 (mt)
REVERT: I  406 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.5794 (mtm180)
REVERT: N  406 ARG cc_start: 0.7066 (mtt-85) cc_final: 0.5411 (mmt180)
REVERT: N  421 ASP cc_start: 0.8813 (t0) cc_final: 0.8373 (t0)
REVERT: O  406 ARG cc_start: 0.7277 (mtt-85) cc_final: 0.5350 (mmt180)
REVERT: O  421 ASP cc_start: 0.9012 (t0) cc_final: 0.8760 (t0)
  outliers start: 21
  outliers final: 17
  residues processed: 104
  average time/residue: 0.0626
  time to fit residues: 8.2505
Evaluate side-chains
  111 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain B residue  419 MET
Chi-restraints excluded: chain B residue  422 SER
Chi-restraints excluded: chain D residue  419 MET
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  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 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 10 optimal weight:   20.0000
   chunk 42 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 44 optimal weight:    7.9990
   chunk 21 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 4 optimal weight:   50.0000
   chunk 40 optimal weight:    0.0970
   chunk 1 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   overall best weight:    2.6182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 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 = 0.5513 r_free = 0.5513 target = 0.245230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.5130 r_free = 0.5130 target = 0.203564 restraints weight = 4216.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.5120 rms_B_bonded: 2.54
r_work: 0.4969 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.4969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.5480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4455  Z= 0.134
  Angle     :  0.697   5.224   6154  Z= 0.354
  Chirality :  0.051   0.172    765
  Planarity :  0.005   0.028    723
  Dihedral  : 11.707  53.537    765
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.37 %
    Favored  : 88.63 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 19.80 %
    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: -3.50 (0.33), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.66 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG M 406 
 TYR   0.009   0.001   TYR N 394 
 HIS   0.002   0.001   HIS J 407 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.13 ( 4455)
  covalent geometry    : angle       0.69675 /  0.35 ( 6154)
  hydrogen bonds       : bond        0.02706 /  1.76 (  105)
  hydrogen bonds       : angle       5.14498 /  3.68 (  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
  114 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.143 
Fit side-chains
REVERT: F  406 ARG cc_start: 0.7807 (mtt-85) cc_final: 0.7554 (ttm-80)
REVERT: G  406 ARG cc_start: 0.7562 (mtp85) cc_final: 0.5969 (mtm180)
REVERT: H  408 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7003 (mt)
REVERT: I  406 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.5899 (mtm180)
REVERT: K  409 SER cc_start: 0.9026 (m) cc_final: 0.8787 (m)
REVERT: K  419 MET cc_start: 0.8292 (mtp) cc_final: 0.8090 (mtm)
REVERT: N  406 ARG cc_start: 0.7109 (mtt-85) cc_final: 0.5551 (mmt180)
REVERT: N  421 ASP cc_start: 0.8792 (t0) cc_final: 0.8366 (t0)
REVERT: O  406 ARG cc_start: 0.7370 (mtt-85) cc_final: 0.5457 (mmt180)
REVERT: O  421 ASP cc_start: 0.9001 (t0) cc_final: 0.8768 (t0)
  outliers start: 18
  outliers final: 14
  residues processed: 103
  average time/residue: 0.0668
  time to fit residues: 8.7031
Evaluate side-chains
  111 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain B residue  419 MET
Chi-restraints excluded: chain D residue  419 MET
Chi-restraints excluded: chain F residue  419 MET
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 J residue  419 MET
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  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:   30.0000
   chunk 34 optimal weight:    8.9990
   chunk 17 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 9 optimal weight:    9.9990
   chunk 44 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 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 = 0.5504 r_free = 0.5504 target = 0.240887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5109 r_free = 0.5109 target = 0.198601 restraints weight = 4201.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.5085 rms_B_bonded: 2.55
r_work: 0.4939 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.4939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.5621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4455  Z= 0.178
  Angle     :  0.737   5.457   6154  Z= 0.377
  Chirality :  0.053   0.195    765
  Planarity :  0.006   0.030    723
  Dihedral  : 11.810  56.068    765
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 16.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.14 %
    Favored  : 86.86 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 19.80 %
    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: -3.62 (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
 ARG   0.006   0.001   ARG M 406 
 TYR   0.012   0.002   TYR N 394 
 HIS   0.002   0.001   HIS J 407 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00418 /  0.18 ( 4455)
  covalent geometry    : angle       0.73684 /  0.38 ( 6154)
  hydrogen bonds       : bond        0.03048 /  1.92 (  105)
  hydrogen bonds       : angle       5.20180 /  3.74 (  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
  114 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.162 
Fit side-chains
REVERT: G  406 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.5792 (mtm180)
REVERT: H  408 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7017 (mt)
REVERT: I  406 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.5817 (mtm180)
REVERT: N  406 ARG cc_start: 0.7172 (mtt-85) cc_final: 0.5511 (mmt180)
REVERT: N  421 ASP cc_start: 0.8779 (t0) cc_final: 0.8329 (t0)
REVERT: O  406 ARG cc_start: 0.7200 (mtt-85) cc_final: 0.5257 (mmt180)
REVERT: O  421 ASP cc_start: 0.8985 (t0) cc_final: 0.8730 (t0)
  outliers start: 17
  outliers final: 14
  residues processed: 103
  average time/residue: 0.0685
  time to fit residues: 8.8501
Evaluate side-chains
  113 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain B residue  419 MET
Chi-restraints excluded: chain D residue  419 MET
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  406 ARG
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 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:    8.9990
   chunk 11 optimal weight:    0.2980
   chunk 20 optimal weight:   20.0000
   chunk 45 optimal weight:    7.9990
   chunk 0 optimal weight:    0.9990
   chunk 36 optimal weight:    9.9990
   chunk 33 optimal weight:   20.0000
   chunk 29 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 42 optimal weight:    7.9990
   overall best weight:    3.2588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 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 = 0.5523 r_free = 0.5523 target = 0.242743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.5131 r_free = 0.5131 target = 0.200874 restraints weight = 4212.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.5112 rms_B_bonded: 2.51
r_work: 0.4954 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.4954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.5675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4455  Z= 0.156
  Angle     :  0.721   5.290   6154  Z= 0.368
  Chirality :  0.052   0.192    765
  Planarity :  0.006   0.027    723
  Dihedral  : 11.777  56.397    765
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 14.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.16 %
    Favored  : 87.84 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 19.39 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.69 (0.32), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.80 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG M 406 
 TYR   0.010   0.001   TYR N 394 
 HIS   0.002   0.001   HIS D 407 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00376 /  0.16 ( 4455)
  covalent geometry    : angle       0.72139 /  0.37 ( 6154)
  hydrogen bonds       : bond        0.02885 /  1.82 (  105)
  hydrogen bonds       : angle       5.16631 /  3.71 (  315)

===============================================================================
Job complete
usr+sys time: 880.68 seconds
wall clock time: 16 minutes 7.20 seconds (967.20 seconds total)