Starting phenix.real_space_refine
on Fri Jul  3 05:37:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v25_42898/07_2026/8v25_42898_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v25_42898/07_2026/8v25_42898.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v25_42898/07_2026/8v25_42898.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v25_42898/07_2026/8v25_42898.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v25_42898/07_2026/8v25_42898_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v25_42898/07_2026/8v25_42898_neut.cif"
  }
  resolution = 3.32
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.019
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     288      5.49       5
     S      16      5.16       5
     C    7063      2.51       5
     N    2387      2.21       5
     O    2935      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12689
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 859
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 859
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 5, 'TRANS': 105}
    Chain: "D"
      Number of atoms: 764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 764
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 94}
    Chain: "E"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 817
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 841
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 754
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "I"
      Number of atoms: 2952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2952
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 604
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   ARG K  74 " occ=0.95
      ... (9 atoms not shown)
      pdb=" NH2 ARG K  74 " occ=0.95
    residue:
      pdb=" N   GLY K  75 " occ=0.65
      ... (2 atoms not shown)
      pdb=" O   GLY K  75 " occ=0.65
  Time building chain proxies: 2.56, per 1000 atoms: 0.20
  Number of scatterers: 12689
  At special positions: 0
  Unit cell: (101.85, 122.22, 119.31, 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      16     16.00
     P     288     15.00
     O    2935      8.00
     N    2387      7.00
     C    7063      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: 0.98
  Conformation dependent library (CDL) restraints added in 379.4 milliseconds
  

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1592

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 9 sheets defined
      66.9% alpha, 4.2% beta
      138 base pairs and 255 stacking pairs defined.
    Time for finding SS restraints: 1.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.520A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.803A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.860A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.622A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLY A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.099A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.656A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.649A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
      removed outlier: 3.588A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 121
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.558A  pdb=" N   SER E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.599A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.607A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.533A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 77
      removed outlier: 4.190A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 93
      removed outlier: 3.543A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.506A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
      removed outlier: 3.520A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 3.611A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
    Processing helix  chain 'K' and resid 22 through 34
    Processing helix  chain 'K' and resid 37 through 39
      No H-bonds generated for 'chain 'K' and resid 37 through 39'
    Processing helix  chain 'K' and resid 55 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.109A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.324A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.895A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.346A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'K' and resid 12 through 16

    421 hydrogen bonds defined for protein.
    1245 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      354 hydrogen bonds
      708 hydrogen bond angles
      0 basepair planarities
      138 basepair parallelities
      255 stacking parallelities
  Total time for adding SS restraints: 2.15

  Time building geometry restraints manager: 1.37 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2639
        1.33 -     1.45: 4191
        1.45 -     1.57: 6065
        1.57 -     1.69: 576
        1.69 -     1.81: 27
  Bond restraints: 13498
  Sorted by residual:
  bond pdb=" C1'  DT I -72 "
       pdb=" N1   DT I -72 "
    ideal  model  delta    sigma   weight residual
    1.468  1.549 -0.081 1.40e-02 5.10e+03 3.31e+01
  bond pdb=" C1'  DT J -72 "
       pdb=" N1   DT J -72 "
    ideal  model  delta    sigma   weight residual
    1.468  1.547 -0.079 1.40e-02 5.10e+03 3.22e+01
  bond pdb=" C1'  DG J -70 "
       pdb=" N9   DG J -70 "
    ideal  model  delta    sigma   weight residual
    1.468  1.389  0.079 1.40e-02 5.10e+03 3.18e+01
  bond pdb=" C1'  DC J  70 "
       pdb=" N1   DC J  70 "
    ideal  model  delta    sigma   weight residual
    1.468  1.545 -0.077 1.40e-02 5.10e+03 3.06e+01
  bond pdb=" C1'  DG I -70 "
       pdb=" N9   DG I -70 "
    ideal  model  delta    sigma   weight residual
    1.468  1.391  0.077 1.40e-02 5.10e+03 3.04e+01
  ... (remaining 13493 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 19026
        2.27 -     4.53: 407
        4.53 -     6.80: 29
        6.80 -     9.06: 3
        9.06 -    11.33: 1
  Bond angle restraints: 19466
  Sorted by residual:
  angle pdb=" C3'  DG J  71 "
        pdb=" O3'  DG J  71 "
        pdb=" P    DA J  72 "
      ideal   model   delta    sigma   weight residual
     120.20  108.87   11.33 1.50e+00 4.44e-01 5.71e+01
  angle pdb=" C3'  DG I  71 "
        pdb=" O3'  DG I  71 "
        pdb=" P    DA I  72 "
      ideal   model   delta    sigma   weight residual
     120.20  112.34    7.86 1.50e+00 4.44e-01 2.74e+01
  angle pdb=" C3'  DC J  70 "
        pdb=" O3'  DC J  70 "
        pdb=" P    DG J  71 "
      ideal   model   delta    sigma   weight residual
     120.20  113.10    7.10 1.50e+00 4.44e-01 2.24e+01
  angle pdb=" O4'  DA I -67 "
        pdb=" C4'  DA I -67 "
        pdb=" C3'  DA I -67 "
      ideal   model   delta    sigma   weight residual
     106.00  103.20    2.80 6.00e-01 2.78e+00 2.17e+01
  angle pdb=" N3   DT J   9 "
        pdb=" C4   DT J   9 "
        pdb=" O4   DT J   9 "
      ideal   model   delta    sigma   weight residual
     119.90  122.64   -2.74 6.00e-01 2.78e+00 2.08e+01
  ... (remaining 19461 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.81: 6017
       35.81 -    71.62: 1378
       71.62 -   107.44: 8
      107.44 -   143.25: 4
      143.25 -   179.06: 1
  Dihedral angle restraints: 7408
    sinusoidal: 4945
      harmonic: 2463
  Sorted by residual:
  dihedral pdb=" CA  MET K   1 "
           pdb=" C   MET K   1 "
           pdb=" N   GLN K   2 "
           pdb=" CA  GLN K   2 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.83  -28.17     0      5.00e+00 4.00e-02 3.17e+01
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.06 -179.06     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DT J  54 "
           pdb=" C3'  DT J  54 "
           pdb=" O3'  DT J  54 "
           pdb=" P    DC J  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   94.61  125.39     1      3.50e+01 8.16e-04 1.24e+01
  ... (remaining 7405 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 2148
       0.100 -    0.200: 65
       0.200 -    0.300: 0
       0.300 -    0.400: 0
       0.400 -    0.500: 6
  Chirality restraints: 2219
  Sorted by residual:
  chirality pdb=" P    DG J  71 "
            pdb=" OP1  DG J  71 "
            pdb=" OP2  DG J  71 "
            pdb=" O5'  DG J  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.84   -0.50 2.00e-01 2.50e+01 6.25e+00
  chirality pdb=" P    DT J  69 "
            pdb=" OP1  DT J  69 "
            pdb=" OP2  DT J  69 "
            pdb=" O5'  DT J  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.80   -0.47 2.00e-01 2.50e+01 5.50e+00
  chirality pdb=" P    DG I  71 "
            pdb=" OP1  DG I  71 "
            pdb=" OP2  DG I  71 "
            pdb=" O5'  DG I  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.79   -0.46 2.00e-01 2.50e+01 5.28e+00
  ... (remaining 2216 not shown)

  Planarity restraints: 1463
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP F  24 "    0.013 2.00e-02 2.50e+03   2.52e-02 6.33e+00
        pdb=" C   ASP F  24 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   ASP F  24 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ASN F  25 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "    0.025 2.00e-02 2.50e+03   1.03e-02 3.15e+00
        pdb=" N9   DG I  47 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "    0.008 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DG I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DG I  47 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  37 "    0.026 5.00e-02 4.00e+02   3.85e-02 2.37e+00
        pdb=" N   PRO A  38 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A  38 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A  38 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1460 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2675
        2.81 -     3.33: 10636
        3.33 -     3.85: 22521
        3.85 -     4.38: 26626
        4.38 -     4.90: 38325
  Nonbonded interactions: 100783
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU K  51 "
            pdb=" OH  TYR K  59 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OH  TYR B  98 "
            pdb=" OD2 ASP H  65 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" O   ASP F  24 "
            pdb=" OD1 ASP F  24 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" OE1 GLU A  73 "
            pdb=" ND2 ASN B  25 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" O   THR E  58 "
            pdb=" OG1 THR E  58 "
     model   vdw
     2.315 3.040
  ... (remaining 100778 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and resid 37 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 23 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 10 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 26 through 121)
  selection = chain 'H'
}

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=0.62 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:             1.570
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.240
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8873
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   0.081  13498  Z= 0.526
  Angle     :  0.750  11.331  19466  Z= 0.648
  Chirality :  0.050   0.500   2219
  Planarity :  0.004   0.038   1463
  Dihedral  : 27.354 179.059   5816
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 20.34 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.59 (0.30), residues: 831
  helix:  3.13 (0.22), residues: 523
  sheet:  1.31 (0.88), residues: 26
  loop : -1.14 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  83 
 TYR   0.008   0.001   TYR H  37 
 PHE   0.008   0.001   PHE F  61 
 HIS   0.003   0.001   HIS K  68 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00592 /  0.53 (13498)
  covalent geometry    : angle       0.74997 /  0.65 (19466)
  hydrogen bonds       : bond        0.12257 /  8.59 (  775)
  hydrogen bonds       : angle       3.86195 /  2.62 ( 1953)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 131
  time to evaluate  : 0.344 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 133
  average time/residue: 0.1596
  time to fit residues: 27.6465
Evaluate side-chains
  129 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 127
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain F residue   85 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0020
   chunk 100 optimal weight:   20.0000
   chunk 106 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.3192

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.092476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.062436 restraints weight = 28864.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 1.97
r_work: 0.2655 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2657
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2657 r_free = 0.2657    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (12 function evaluations)
r_final: 0.2656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8937
moved from start:          0.0636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13498  Z= 0.161
  Angle     :  0.598   7.165  19466  Z= 0.364
  Chirality :  0.045   0.223   2219
  Planarity :  0.004   0.037   1463
  Dihedral  : 29.751 176.754   4118
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 19.50 %
    Favored  : 78.54 %
  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:  2.73 (0.30), residues: 831
  helix:  3.08 (0.22), residues: 547
  sheet:  1.55 (0.89), residues: 26
  loop : -1.14 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  83 
 TYR   0.008   0.001   TYR K  59 
 PHE   0.008   0.001   PHE F  61 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.16 (13498)
  covalent geometry    : angle       0.59821 /  0.36 (19466)
  hydrogen bonds       : bond        0.06566 /  4.39 (  775)
  hydrogen bonds       : angle       3.09898 /  2.19 ( 1953)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.349 
Fit side-chains
REVERT: B   24 ASP cc_start: 0.7876 (t0) cc_final: 0.7644 (t0)
REVERT: B   27 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8564 (mp10)
REVERT: F   24 ASP cc_start: 0.7554 (p0) cc_final: 0.7288 (p0)
REVERT: K    1 MET cc_start: 0.7057 (ppp) cc_final: 0.6807 (ppp)
  outliers start: 14
  outliers final: 12
  residues processed: 135
  average time/residue: 0.1622
  time to fit residues: 28.6352
Evaluate side-chains
  137 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain K residue   70 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 99 optimal weight:   20.0000
   chunk 48 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 73 optimal weight:   30.0000
   chunk 78 optimal weight:   20.0000
   chunk 74 optimal weight:   20.0000
   chunk 36 optimal weight:    0.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  75 HIS
** K  31 GLN ** 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 = 0.3414 r_free = 0.3414 target = 0.092067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.061862 restraints weight = 28868.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.2815 rms_B_bonded: 1.98
r_work: 0.2643 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2643
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2641
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2641 r_free = 0.2641    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2641 r_free = 0.2641    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2641
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8943
moved from start:          0.0847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13498  Z= 0.164
  Angle     :  0.572   7.311  19466  Z= 0.350
  Chirality :  0.043   0.213   2219
  Planarity :  0.004   0.051   1463
  Dihedral  : 29.823 177.081   4114
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 19.21 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.79 (0.30), residues: 831
  helix:  3.15 (0.22), residues: 550
  sheet:  1.33 (0.87), residues: 26
  loop : -1.22 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  83 
 TYR   0.008   0.001   TYR K  59 
 PHE   0.008   0.001   PHE F  61 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.16 (13498)
  covalent geometry    : angle       0.57226 /  0.35 (19466)
  hydrogen bonds       : bond        0.06526 /  4.37 (  775)
  hydrogen bonds       : angle       3.02215 /  2.13 ( 1953)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 ASP cc_start: 0.7969 (t0) cc_final: 0.7707 (t0)
REVERT: B   27 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8560 (mp10)
REVERT: F   24 ASP cc_start: 0.7589 (p0) cc_final: 0.7336 (p0)
REVERT: F   92 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8455 (mtp85)
REVERT: H   31 LYS cc_start: 0.8682 (mmmt) cc_final: 0.8373 (mmmt)
REVERT: K    1 MET cc_start: 0.7131 (ppp) cc_final: 0.6499 (ppp)
  outliers start: 19
  outliers final: 14
  residues processed: 141
  average time/residue: 0.1582
  time to fit residues: 29.0284
Evaluate side-chains
  139 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LYS
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
Chi-restraints excluded: chain K residue   70 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 75 optimal weight:   10.0000
   chunk 88 optimal weight:   20.0000
   chunk 54 optimal weight:   10.0000
   chunk 57 optimal weight:    0.5980
   chunk 29 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    1.3984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.092233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.062109 restraints weight = 28568.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.2824 rms_B_bonded: 1.89
r_work: 0.2657 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2658
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2658
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8933
moved from start:          0.0952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13498  Z= 0.157
  Angle     :  0.568   7.745  19466  Z= 0.347
  Chirality :  0.042   0.212   2219
  Planarity :  0.004   0.050   1463
  Dihedral  : 29.829 176.823   4114
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 19.78 %
    Favored  : 76.86 %
  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:  2.82 (0.30), residues: 831
  helix:  3.23 (0.22), residues: 547
  sheet:  1.23 (0.88), residues: 26
  loop : -1.29 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  83 
 TYR   0.008   0.001   TYR K  59 
 PHE   0.008   0.001   PHE F  61 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.16 (13498)
  covalent geometry    : angle       0.56849 /  0.35 (19466)
  hydrogen bonds       : bond        0.06221 /  4.16 (  775)
  hydrogen bonds       : angle       2.94754 /  2.07 ( 1953)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 ASP cc_start: 0.7991 (t0) cc_final: 0.7688 (t0)
REVERT: B   25 ASN cc_start: 0.8851 (m-40) cc_final: 0.8351 (m110)
REVERT: B   27 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8576 (mp10)
REVERT: F   92 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8449 (mtp85)
REVERT: H   65 ASP cc_start: 0.9126 (t0) cc_final: 0.8807 (t0)
REVERT: K    1 MET cc_start: 0.7216 (ppp) cc_final: 0.6626 (ppp)
  outliers start: 24
  outliers final: 14
  residues processed: 148
  average time/residue: 0.1488
  time to fit residues: 29.0950
Evaluate side-chains
  144 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
Chi-restraints excluded: chain H residue   88 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 94 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9990
   chunk 78 optimal weight:   20.0000
   chunk 9 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0670
   chunk 49 optimal weight:    0.9980
   chunk 105 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.7318

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.093928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.064091 restraints weight = 28882.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 1.89
r_work: 0.2705 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8879
moved from start:          0.1130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13498  Z= 0.139
  Angle     :  0.538   7.219  19466  Z= 0.333
  Chirality :  0.041   0.211   2219
  Planarity :  0.004   0.047   1463
  Dihedral  : 29.825 176.440   4114
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 20.62 %
    Favored  : 76.58 %
  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:  2.92 (0.30), residues: 831
  helix:  3.28 (0.22), residues: 553
  sheet:  1.04 (0.84), residues: 26
  loop : -1.24 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  83 
 TYR   0.006   0.001   TYR D  37 
 PHE   0.008   0.001   PHE F  61 
 HIS   0.002   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00214 /  0.14 (13498)
  covalent geometry    : angle       0.53850 /  0.33 (19466)
  hydrogen bonds       : bond        0.05419 /  3.61 (  775)
  hydrogen bonds       : angle       2.80254 /  1.95 ( 1953)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 ASP cc_start: 0.7941 (t0) cc_final: 0.7649 (t0)
REVERT: B   25 ASN cc_start: 0.8809 (m-40) cc_final: 0.8276 (m110)
REVERT: B   27 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8597 (mp10)
REVERT: F   24 ASP cc_start: 0.7800 (p0) cc_final: 0.7599 (p0)
REVERT: F   92 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8417 (mtp85)
REVERT: H   65 ASP cc_start: 0.9108 (t0) cc_final: 0.8773 (t0)
REVERT: K    1 MET cc_start: 0.6973 (ppp) cc_final: 0.6213 (ppp)
  outliers start: 20
  outliers final: 12
  residues processed: 149
  average time/residue: 0.1399
  time to fit residues: 27.5739
Evaluate side-chains
  147 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain D residue   32 GLU
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 105 optimal weight:   20.0000
   chunk 26 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 34 optimal weight:    0.3980
   chunk 22 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.2384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.093196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.063214 restraints weight = 28658.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 1.88
r_work: 0.2686 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2688
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8895
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  13498  Z= 0.149
  Angle     :  0.548   7.302  19466  Z= 0.334
  Chirality :  0.041   0.208   2219
  Planarity :  0.004   0.044   1463
  Dihedral  : 29.870 176.566   4114
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 20.90 %
    Favored  : 76.58 %
  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:  2.98 (0.30), residues: 831
  helix:  3.31 (0.22), residues: 555
  sheet:  1.06 (0.85), residues: 26
  loop : -1.23 (0.38), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  83 
 TYR   0.007   0.001   TYR H  37 
 PHE   0.008   0.001   PHE F  61 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.15 (13498)
  covalent geometry    : angle       0.54796 /  0.33 (19466)
  hydrogen bonds       : bond        0.05796 /  3.87 (  775)
  hydrogen bonds       : angle       2.84366 /  1.99 ( 1953)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 ASP cc_start: 0.7984 (t0) cc_final: 0.7695 (t0)
REVERT: B   25 ASN cc_start: 0.8884 (m-40) cc_final: 0.8292 (m110)
REVERT: B   27 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8598 (mp10)
REVERT: F   92 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8437 (mtp85)
REVERT: G   42 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7966 (mtm180)
REVERT: H   65 ASP cc_start: 0.9121 (t0) cc_final: 0.8757 (t0)
REVERT: K    1 MET cc_start: 0.7362 (ppp) cc_final: 0.6588 (ppp)
  outliers start: 18
  outliers final: 12
  residues processed: 145
  average time/residue: 0.1628
  time to fit residues: 30.8635
Evaluate side-chains
  143 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
Chi-restraints excluded: chain H residue   88 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 101 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 73 optimal weight:   20.0000
   chunk 13 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 82 optimal weight:   20.0000
   chunk 6 optimal weight:    0.7980
   chunk 28 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    1.5586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.092714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.062702 restraints weight = 28643.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 1.88
r_work: 0.2674 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2676
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2676
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8906
moved from start:          0.1238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13498  Z= 0.157
  Angle     :  0.556   7.371  19466  Z= 0.337
  Chirality :  0.041   0.209   2219
  Planarity :  0.004   0.039   1463
  Dihedral  : 29.878 176.682   4114
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 20.48 %
    Favored  : 76.58 %
  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:  2.91 (0.30), residues: 831
  helix:  3.32 (0.22), residues: 550
  sheet:  0.64 (0.80), residues: 26
  loop : -1.29 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  83 
 TYR   0.008   0.001   TYR H  37 
 PHE   0.008   0.001   PHE F  61 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.16 (13498)
  covalent geometry    : angle       0.55584 /  0.34 (19466)
  hydrogen bonds       : bond        0.06004 /  4.00 (  775)
  hydrogen bonds       : angle       2.85696 /  2.00 ( 1953)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7537 (pm20)
REVERT: B   27 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8579 (mp10)
REVERT: F   92 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8407 (mtp85)
REVERT: G   42 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7983 (mtm180)
REVERT: H   65 ASP cc_start: 0.9126 (t0) cc_final: 0.8752 (t0)
REVERT: K    1 MET cc_start: 0.7284 (ppp) cc_final: 0.6363 (ppp)
  outliers start: 21
  outliers final: 14
  residues processed: 147
  average time/residue: 0.1654
  time to fit residues: 31.8091
Evaluate side-chains
  144 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LYS
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain D residue   32 GLU
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
Chi-restraints excluded: chain H residue   88 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    0.6980
   chunk 26 optimal weight:    6.9990
   chunk 67 optimal weight:    0.6980
   chunk 73 optimal weight:   20.0000
   chunk 102 optimal weight:   10.0000
   overall best weight:    2.2786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.091165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.060659 restraints weight = 28394.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.2795 rms_B_bonded: 1.96
r_work: 0.2620 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2623
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2623 r_free = 0.2623    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2623 r_free = 0.2623    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2623
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8964
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13498  Z= 0.190
  Angle     :  0.602   7.559  19466  Z= 0.355
  Chirality :  0.044   0.209   2219
  Planarity :  0.004   0.038   1463
  Dihedral  : 29.910 176.953   4114
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 21.74 %
    Favored  : 75.88 %
  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:  2.78 (0.30), residues: 831
  helix:  3.17 (0.22), residues: 552
  sheet:  1.10 (0.96), residues: 20
  loop : -1.24 (0.37), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  83 
 TYR   0.008   0.001   TYR K  59 
 PHE   0.011   0.001   PHE H  67 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00386 /  0.19 (13498)
  covalent geometry    : angle       0.60150 /  0.36 (19466)
  hydrogen bonds       : bond        0.06931 /  4.63 (  775)
  hydrogen bonds       : angle       3.02063 /  2.13 ( 1953)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7696 (pm20)
REVERT: B   27 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8567 (mp10)
REVERT: F   92 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8447 (mtp85)
REVERT: G   42 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8076 (mtm180)
REVERT: K    1 MET cc_start: 0.7501 (ppp) cc_final: 0.6531 (ppp)
  outliers start: 17
  outliers final: 13
  residues processed: 136
  average time/residue: 0.1523
  time to fit residues: 27.0028
Evaluate side-chains
  140 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LYS
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
Chi-restraints excluded: chain H residue   88 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 84 optimal weight:   20.0000
   chunk 45 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 103 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   overall best weight:    1.1582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.091894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.061653 restraints weight = 28565.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 1.90
r_work: 0.2646 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2649 r_free = 0.2649    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2649 r_free = 0.2649    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2649
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8946
moved from start:          0.1274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  13498  Z= 0.149
  Angle     :  0.575   7.448  19466  Z= 0.346
  Chirality :  0.043   0.212   2219
  Planarity :  0.004   0.038   1463
  Dihedral  : 29.897 177.016   4114
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.18 %
    Favored  : 75.74 %
  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:  2.81 (0.30), residues: 831
  helix:  3.18 (0.22), residues: 553
  sheet:  1.24 (1.01), residues: 20
  loop : -1.24 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  83 
 TYR   0.008   0.001   TYR H  37 
 PHE   0.008   0.001   PHE F  61 
 HIS   0.002   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.15 (13498)
  covalent geometry    : angle       0.57545 /  0.35 (19466)
  hydrogen bonds       : bond        0.06486 /  4.32 (  775)
  hydrogen bonds       : angle       2.93371 /  2.06 ( 1953)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7642 (pm20)
REVERT: B   27 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8548 (mp10)
REVERT: F   92 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8419 (mtp85)
REVERT: G   42 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8061 (mtm180)
REVERT: H   65 ASP cc_start: 0.9148 (t0) cc_final: 0.8769 (t0)
REVERT: K    1 MET cc_start: 0.7470 (ppp) cc_final: 0.6638 (ppp)
  outliers start: 22
  outliers final: 16
  residues processed: 142
  average time/residue: 0.1730
  time to fit residues: 32.1119
Evaluate side-chains
  144 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LYS
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  116 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 97 optimal weight:   20.0000
   chunk 75 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 28 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9980
   chunk 85 optimal weight:   20.0000
   chunk 35 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   overall best weight:    2.1184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.091073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.060689 restraints weight = 28739.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.2792 rms_B_bonded: 1.97
r_work: 0.2618 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2619
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2619 r_free = 0.2619    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2619 r_free = 0.2619    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2619
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8963
moved from start:          0.1315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13498  Z= 0.184
  Angle     :  0.601   7.582  19466  Z= 0.356
  Chirality :  0.043   0.211   2219
  Planarity :  0.004   0.039   1463
  Dihedral  : 29.910 176.987   4114
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 21.18 %
    Favored  : 75.60 %
  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:  2.68 (0.30), residues: 831
  helix:  3.15 (0.22), residues: 549
  sheet:  0.95 (1.02), residues: 20
  loop : -1.35 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  83 
 TYR   0.010   0.001   TYR K  59 
 PHE   0.010   0.001   PHE H  67 
 HIS   0.002   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.18 (13498)
  covalent geometry    : angle       0.60131 /  0.36 (19466)
  hydrogen bonds       : bond        0.06840 /  4.57 (  775)
  hydrogen bonds       : angle       3.01769 /  2.12 ( 1953)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.427 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7687 (pm20)
REVERT: B   27 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8562 (mp10)
REVERT: F   92 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8387 (mtp85)
REVERT: G   42 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8079 (mtm180)
REVERT: H   31 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8337 (mmtm)
REVERT: K    1 MET cc_start: 0.7716 (ppp) cc_final: 0.6774 (ppp)
  outliers start: 23
  outliers final: 17
  residues processed: 135
  average time/residue: 0.1709
  time to fit residues: 30.0459
Evaluate side-chains
  140 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LYS
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   42 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   83 ARG
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  116 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 97 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9990
   chunk 102 optimal weight:    6.9990
   chunk 42 optimal weight:    0.7980
   chunk 60 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9990
   chunk 89 optimal weight:   20.0000
   chunk 91 optimal weight:   20.0000
   chunk 107 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   overall best weight:    3.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  44 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.089084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.058437 restraints weight = 28559.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.2745 rms_B_bonded: 1.96
r_work: 0.2566 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2567
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2567 r_free = 0.2567    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2567 r_free = 0.2567    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2567
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9008
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13498  Z= 0.234
  Angle     :  0.663   7.861  19466  Z= 0.383
  Chirality :  0.047   0.214   2219
  Planarity :  0.005   0.040   1463
  Dihedral  : 29.981 177.596   4114
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 21.60 %
    Favored  : 75.46 %
  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:  2.34 (0.30), residues: 831
  helix:  2.91 (0.22), residues: 544
  sheet:  1.36 (1.11), residues: 20
  loop : -1.50 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  83 
 TYR   0.008   0.001   TYR H  37 
 PHE   0.016   0.002   PHE H  67 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00512 /  0.23 (13498)
  covalent geometry    : angle       0.66250 /  0.38 (19466)
  hydrogen bonds       : bond        0.08178 /  5.47 (  775)
  hydrogen bonds       : angle       3.25415 /  2.31 ( 1953)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2357.65 seconds
wall clock time: 41 minutes 7.97 seconds (2467.97 seconds total)