Starting phenix.real_space_refine
on Wed Aug  5 22:50:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/10xz_75521/08_2026/10xz_75521.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/10xz_75521/08_2026/10xz_75521.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/10xz_75521/08_2026/10xz_75521.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/10xz_75521/08_2026/10xz_75521.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/10xz_75521/08_2026/10xz_75521.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/10xz_75521/08_2026/10xz_75521.cif"
  }
  resolution = 2.6
  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=   0.000 sd=   0.005
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     294      5.49       5
     S      10      5.16       5
     C    6654      2.51       5
     N    2263      2.21       5
     O    2822      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12043
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 789
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 823
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
      Conformer: "B"
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          bond proxies already assigned to first conformer: 738
    Chain: "E"
      Number of atoms: 808
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
      Conformer: "B"
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
          bond proxies already assigned to first conformer: 803
    Chain: "F"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 641
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 823
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 732
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 727
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  Time building chain proxies: 3.14, per 1000 atoms: 0.26
  Number of scatterers: 12043
  At special positions: 0
  Unit cell: (74.328, 123.228, 116.056, 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      10     16.00
     P     294     15.00
     O    2822      8.00
     N    2263      7.00
     C    6654      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: 0.92
  Conformation dependent library (CDL) restraints added in 488.3 milliseconds
  

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1418

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 9 sheets defined
      73.4% alpha, 2.6% beta
      147 base pairs and 265 stacking pairs defined.
    Time for finding SS restraints: 1.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 50 through 57
      removed outlier: 3.581A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.525A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.690A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.360A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 123
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 4.159A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.701A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 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 45 through 73
      removed outlier: 4.370A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 124
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.070A  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 96 through 98
      removed outlier: 6.716A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.219A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.983A  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: 7.271A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78

    406 hydrogen bonds defined for protein.
    1191 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      376 hydrogen bonds
      752 hydrogen bond angles
      0 basepair planarities
      147 basepair parallelities
      265 stacking parallelities
  Total time for adding SS restraints: 2.30

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2140
        1.33 -     1.45: 4252
        1.45 -     1.57: 5863
        1.57 -     1.69: 586
        1.69 -     1.80: 20
  Bond restraints: 12861
  Sorted by residual:
  bond pdb=" N   MET A 120 "
       pdb=" CA  MET A 120 "
    ideal  model  delta    sigma   weight residual
    1.453  1.483 -0.030 8.30e-03 1.45e+04 1.27e+01
  bond pdb=" C3'  DT J  15 "
       pdb=" C2'  DT J  15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.61e+00
  bond pdb=" C3'  DG J  52 "
       pdb=" C2'  DG J  52 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.23e+00
  bond pdb=" C3'  DT J   7 "
       pdb=" C2'  DT J   7 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.75e+00
  bond pdb=" C3'  DG J  95 "
       pdb=" C2'  DG J  95 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.49e+00
  ... (remaining 12856 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 18055
        2.20 -     4.39: 550
        4.39 -     6.59: 24
        6.59 -     8.78: 3
        8.78 -    10.98: 1
  Bond angle restraints: 18633
  Sorted by residual:
  angle pdb=" N3   DT J  83 "
        pdb=" C4   DT J  83 "
        pdb=" O4   DT J  83 "
      ideal   model   delta    sigma   weight residual
     119.90  122.62   -2.72 6.00e-01 2.78e+00 2.05e+01
  angle pdb=" N3   DT J   7 "
        pdb=" C4   DT J   7 "
        pdb=" O4   DT J   7 "
      ideal   model   delta    sigma   weight residual
     119.90  122.60   -2.70 6.00e-01 2.78e+00 2.03e+01
  angle pdb=" N3   DT J  50 "
        pdb=" C4   DT J  50 "
        pdb=" O4   DT J  50 "
      ideal   model   delta    sigma   weight residual
     119.90  122.60   -2.70 6.00e-01 2.78e+00 2.03e+01
  angle pdb=" N3   DT I 104 "
        pdb=" C4   DT I 104 "
        pdb=" O4   DT I 104 "
      ideal   model   delta    sigma   weight residual
     119.90  122.59   -2.69 6.00e-01 2.78e+00 2.01e+01
  angle pdb=" N3   DT I  32 "
        pdb=" C4   DT I  32 "
        pdb=" O4   DT I  32 "
      ideal   model   delta    sigma   weight residual
     119.90  122.58   -2.68 6.00e-01 2.78e+00 2.00e+01
  ... (remaining 18628 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.91: 5092
       28.91 -    57.82: 1769
       57.82 -    86.72: 119
       86.72 -   115.63: 1
      115.63 -   144.54: 3
  Dihedral angle restraints: 6984
    sinusoidal: 4782
      harmonic: 2202
  Sorted by residual:
  dihedral pdb=" CA  LEU A  48 "
           pdb=" C   LEU A  48 "
           pdb=" N   ARG A  49 "
           pdb=" CA  ARG A  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.17   24.83     0      5.00e+00 4.00e-02 2.47e+01
  dihedral pdb=" C4'  DG J  82 "
           pdb=" C3'  DG J  82 "
           pdb=" O3'  DG J  82 "
           pdb=" P    DT J  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   75.46  144.54     1      3.50e+01 8.16e-04 1.42e+01
  dihedral pdb=" C4'  DT J  15 "
           pdb=" C3'  DT J  15 "
           pdb=" O3'  DT J  15 "
           pdb=" P    DC J  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   77.53  142.47     1      3.50e+01 8.16e-04 1.41e+01
  ... (remaining 6981 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1700
       0.056 -    0.113: 377
       0.113 -    0.169: 39
       0.169 -    0.225: 3
       0.225 -    0.282: 1
  Chirality restraints: 2120
  Sorted by residual:
  chirality pdb=" CG  LEU D 101 "
            pdb=" CB  LEU D 101 "
            pdb=" CD1 LEU D 101 "
            pdb=" CD2 LEU D 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.31   -0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" CA  MET A 120 "
            pdb=" N   MET A 120 "
            pdb=" C   MET A 120 "
            pdb=" CB  MET A 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  ASP B  24 "
            pdb=" N   ASP B  24 "
            pdb=" C   ASP B  24 "
            pdb=" CB  ASP B  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.42e-01
  ... (remaining 2117 not shown)

  Planarity restraints: 1338
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  42 "   -0.035 5.00e-02 4.00e+02   5.25e-02 4.41e+00
        pdb=" N   PRO E  43 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO E  43 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO E  43 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  79 "   -0.029 5.00e-02 4.00e+02   4.41e-02 3.11e+00
        pdb=" N   PRO C  80 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I 100 "   -0.024 2.00e-02 2.50e+03   1.02e-02 3.10e+00
        pdb=" N9   DG I 100 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DG I 100 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I 100 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DG I 100 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I 100 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I 100 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1   DG I 100 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I 100 "    0.004 2.00e-02 2.50e+03
        pdb=" N2   DG I 100 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DG I 100 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I 100 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1335 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 5221
        2.98 -     3.46: 11113
        3.46 -     3.94: 25205
        3.94 -     4.42: 27880
        4.42 -     4.90: 36781
  Nonbonded interactions: 106200
  Sorted by model distance:
  nonbonded pdb=" O5'  DA I 124 "
            pdb=" O4'  DA I 124 "
     model   vdw
     2.505 2.432
  nonbonded pdb=" CB  GLU A  97 "
            pdb=" OE1 GLU A  97 "
     model   vdw
     2.539 2.752
  nonbonded pdb=" O5'  DG J  23 "
            pdb=" O4'  DG J  23 "
     model   vdw
     2.551 2.432
  nonbonded pdb=" O   LEU A  60 "
            pdb=" OE1 GLU A  97 "
     model   vdw
     2.557 3.040
  nonbonded pdb=" N   ARG D  31 "
            pdb=" N   SER D  32 "
     model   vdw
     2.573 2.560
  ... (remaining 106195 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' and (resid 38 through 128 or resid 130 through 133))
  selection = (chain 'E' and (resid 38 through 128 or resid 130 through 133))
}
ncs_group {
  reference = (chain 'B' and resid 22 through 101)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and (resid 32 through 81 or resid 83 through 124))
  selection = (chain 'H' and (resid 32 through 81 or resid 83 through 124))
}

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=0.45 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:             4.780
  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:          0.290
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.040
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.010
  Internal consistency checks:             0.000
  Total:   25.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
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   0.048  12861  Z= 0.551
  Angle     :  0.794  10.977  18633  Z= 0.688
  Chirality :  0.046   0.282   2120
  Planarity :  0.005   0.059   1338
  Dihedral  : 28.595 144.540   5566
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 21.39 %
    Favored  : 78.29 %
  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:  1.88 (0.30), residues: 743
  helix:  1.96 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.79 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  86 
 TYR   0.014   0.002   TYR B  88 
 PHE   0.008   0.002   PHE E  67 
 HIS   0.005   0.001   HIS E  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00637 /  0.55 (12861)
  covalent geometry    : angle       0.79427 /  0.69 (18633)
  hydrogen bonds       : bond        0.10033 /  6.64 (  782)
  hydrogen bonds       : angle       3.68555 /  2.48 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 155
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8758 (tt0) cc_final: 0.8537 (tt0)
REVERT: B   93 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7473 (mp10)
REVERT: C   36 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8683 (mmtp)
REVERT: C   73 ASN cc_start: 0.8773 (t0) cc_final: 0.8500 (t0)
REVERT: D  108 LYS cc_start: 0.8734 (mtpp) cc_final: 0.8376 (mtmm)
REVERT: E   73 GLU cc_start: 0.8649 (tt0) cc_final: 0.8428 (tt0)
REVERT: G   73 ASN cc_start: 0.8709 (t0) cc_final: 0.8107 (t0)
REVERT: H   68 ASP cc_start: 0.8952 (t0) cc_final: 0.8697 (t0)
REVERT: H   99 ARG cc_start: 0.8721 (mtm-85) cc_final: 0.8391 (mtt90)
REVERT: H  108 LYS cc_start: 0.8615 (mtpp) cc_final: 0.8177 (mttt)
  outliers start: 2
  outliers final: 0
  residues processed: 155
  average time/residue: 0.8666
  time to fit residues: 141.7385
Evaluate side-chains
  154 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
E  68 GLN
G  73 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.102140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.070179 restraints weight = 36515.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 1.91
r_work: 0.2781 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2769
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2769 r_free = 0.2769    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2769 r_free = 0.2769    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2769
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8781
moved from start:          0.0351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12861  Z= 0.158
  Angle     :  0.661   9.320  18633  Z= 0.392
  Chirality :  0.048   0.266   2120
  Planarity :  0.004   0.048   1338
  Dihedral  : 30.775 145.308   4066
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 19.97 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.42 (0.30), residues: 743
  helix:  2.35 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.61 (0.40), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  86 
 TYR   0.012   0.001   TYR D  40 
 PHE   0.012   0.002   PHE E  67 
 HIS   0.003   0.001   HIS E  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.16 (12861)
  covalent geometry    : angle       0.66063 /  0.39 (18633)
  hydrogen bonds       : bond        0.04893 /  3.29 (  782)
  hydrogen bonds       : angle       3.26072 /  2.21 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 153
  time to evaluate  : 0.317 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8629 (mtp85)
REVERT: C   36 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8652 (mmtp)
REVERT: C   73 ASN cc_start: 0.8755 (t0) cc_final: 0.8477 (t0)
REVERT: D  108 LYS cc_start: 0.8687 (mtpp) cc_final: 0.8337 (mtmm)
REVERT: F   92 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8494 (ttp80)
REVERT: G   73 ASN cc_start: 0.8669 (t0) cc_final: 0.8053 (t0)
REVERT: H   34 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7791 (tptp)
REVERT: H   68 ASP cc_start: 0.8951 (t0) cc_final: 0.8690 (t0)
REVERT: H   99 ARG cc_start: 0.8707 (mtm-85) cc_final: 0.8391 (mtt90)
  outliers start: 10
  outliers final: 1
  residues processed: 157
  average time/residue: 0.8424
  time to fit residues: 139.5227
Evaluate side-chains
  157 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 153
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue   34 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 77 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   overall best weight:    2.7386

-------------------------------------------------------------------------------
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 = 0.3562 r_free = 0.3562 target = 0.100829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.068709 restraints weight = 36972.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 1.91
r_work: 0.2744 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2737
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2737 r_free = 0.2737    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2736 r_free = 0.2736    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2736
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8802
moved from start:          0.0576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  12861  Z= 0.251
  Angle     :  0.665   7.231  18633  Z= 0.386
  Chirality :  0.048   0.253   2120
  Planarity :  0.004   0.050   1338
  Dihedral  : 31.054 146.206   4063
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 19.65 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.43 (0.30), residues: 743
  helix:  2.35 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.68 (0.39), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  86 
 TYR   0.011   0.002   TYR C  57 
 PHE   0.011   0.002   PHE E  67 
 HIS   0.005   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00522 /  0.25 (12861)
  covalent geometry    : angle       0.66474 /  0.39 (18633)
  hydrogen bonds       : bond        0.05060 /  3.38 (  782)
  hydrogen bonds       : angle       3.08236 /  2.09 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 155
  time to evaluate  : 0.266 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8609 (mtp85)
REVERT: B   93 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7549 (mp10)
REVERT: C   73 ASN cc_start: 0.8773 (t0) cc_final: 0.8509 (t160)
REVERT: G   64 GLU cc_start: 0.8634 (tt0) cc_final: 0.8395 (tm-30)
REVERT: G   73 ASN cc_start: 0.8696 (t0) cc_final: 0.8076 (t0)
REVERT: H   34 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7795 (tptp)
REVERT: H   68 ASP cc_start: 0.9042 (t0) cc_final: 0.8777 (t0)
REVERT: H   99 ARG cc_start: 0.8722 (mtm-85) cc_final: 0.8410 (mtt90)
  outliers start: 10
  outliers final: 3
  residues processed: 160
  average time/residue: 0.8555
  time to fit residues: 144.5835
Evaluate side-chains
  160 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 154
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   34 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 85 optimal weight:   30.0000
   chunk 12 optimal weight:    0.2980
   chunk 89 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 78 optimal weight:   10.0000
   chunk 47 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 104 GLN
E  85 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.101733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.069360 restraints weight = 41129.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 2.01
r_work: 0.2752 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2751
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2751
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8794
moved from start:          0.0639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  12861  Z= 0.148
  Angle     :  0.655  10.402  18633  Z= 0.379
  Chirality :  0.046   0.260   2120
  Planarity :  0.004   0.045   1338
  Dihedral  : 31.105 146.628   4063
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.54 %
    Favored  : 79.08 %
  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:  2.69 (0.31), residues: 743
  helix:  2.54 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.59 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  86 
 TYR   0.013   0.002   TYR D  40 
 PHE   0.012   0.002   PHE A  67 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.15 (12861)
  covalent geometry    : angle       0.65520 /  0.38 (18633)
  hydrogen bonds       : bond        0.04496 /  3.00 (  782)
  hydrogen bonds       : angle       3.04805 /  2.07 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 151
  time to evaluate  : 0.301 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8589 (mtp85)
REVERT: B   93 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7545 (mp10)
REVERT: C   73 ASN cc_start: 0.8763 (t0) cc_final: 0.8507 (t0)
REVERT: D  108 LYS cc_start: 0.8652 (mtpp) cc_final: 0.8286 (mtmm)
REVERT: F   92 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8483 (ttp80)
REVERT: G   64 GLU cc_start: 0.8629 (tt0) cc_final: 0.8391 (tm-30)
REVERT: G   73 ASN cc_start: 0.8678 (t0) cc_final: 0.8132 (t0)
REVERT: G   75 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8792 (mttm)
REVERT: H   34 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7799 (tptp)
REVERT: H   99 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8364 (mtt90)
  outliers start: 15
  outliers final: 6
  residues processed: 157
  average time/residue: 0.9208
  time to fit residues: 152.2222
Evaluate side-chains
  161 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 150
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain H residue  105 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 92 optimal weight:    9.9990
   chunk 30 optimal weight:    0.6980
   chunk 66 optimal weight:    0.7980
   chunk 96 optimal weight:   10.0000
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.102077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.069882 restraints weight = 36865.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.91
r_work: 0.2770 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2764
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2764 r_free = 0.2764    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2764 r_free = 0.2764    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2764
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8788
moved from start:          0.0640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12861  Z= 0.152
  Angle     :  0.638   7.037  18633  Z= 0.372
  Chirality :  0.046   0.230   2120
  Planarity :  0.004   0.044   1338
  Dihedral  : 31.097 146.384   4063
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 19.49 %
    Favored  : 78.92 %
  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:  2.71 (0.31), residues: 743
  helix:  2.55 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.56 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  42 
 TYR   0.010   0.001   TYR D  40 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.15 (12861)
  covalent geometry    : angle       0.63844 /  0.37 (18633)
  hydrogen bonds       : bond        0.04183 /  2.79 (  782)
  hydrogen bonds       : angle       3.01141 /  2.04 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 152
  time to evaluate  : 0.346 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8573 (mtp85)
REVERT: B   93 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7539 (mp10)
REVERT: C   36 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8613 (mmtm)
REVERT: C   73 ASN cc_start: 0.8766 (t0) cc_final: 0.8506 (t0)
REVERT: D  108 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8341 (mtmm)
REVERT: F   92 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8477 (ttp80)
REVERT: G   64 GLU cc_start: 0.8618 (tt0) cc_final: 0.8388 (tm-30)
REVERT: G   73 ASN cc_start: 0.8674 (t0) cc_final: 0.8022 (t0)
REVERT: H   34 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7805 (tptp)
REVERT: H   99 ARG cc_start: 0.8682 (mtm-85) cc_final: 0.8338 (mtt90)
  outliers start: 10
  outliers final: 5
  residues processed: 157
  average time/residue: 0.9316
  time to fit residues: 154.1288
Evaluate side-chains
  161 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 152
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   34 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    9.9990
   chunk 82 optimal weight:   10.0000
   chunk 90 optimal weight:    9.9990
   chunk 57 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 97 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    1.5588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.101720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.069329 restraints weight = 44012.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 2.08
r_work: 0.2749 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2748
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2748
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8795
moved from start:          0.0736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12861  Z= 0.176
  Angle     :  0.636   7.136  18633  Z= 0.369
  Chirality :  0.045   0.227   2120
  Planarity :  0.004   0.044   1338
  Dihedral  : 31.143 145.954   4063
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.86 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.75 (0.31), residues: 743
  helix:  2.59 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.56 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  42 
 TYR   0.011   0.001   TYR D  40 
 PHE   0.011   0.002   PHE A  67 
 HIS   0.003   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.18 (12861)
  covalent geometry    : angle       0.63555 /  0.37 (18633)
  hydrogen bonds       : bond        0.04223 /  2.81 (  782)
  hydrogen bonds       : angle       2.94911 /  2.00 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 152
  time to evaluate  : 0.319 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8599 (mtp85)
REVERT: B   93 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7577 (mp10)
REVERT: C   36 LYS cc_start: 0.8984 (mmmm) cc_final: 0.8657 (mmtp)
REVERT: C   73 ASN cc_start: 0.8768 (t0) cc_final: 0.8487 (t160)
REVERT: D  108 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8330 (mtmm)
REVERT: F   92 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8482 (ttp80)
REVERT: G   64 GLU cc_start: 0.8632 (tt0) cc_final: 0.8384 (tm-30)
REVERT: G   73 ASN cc_start: 0.8675 (t0) cc_final: 0.8110 (t0)
REVERT: G   75 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8796 (mttm)
REVERT: H   34 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7808 (tptp)
REVERT: H   99 ARG cc_start: 0.8703 (mtm-85) cc_final: 0.8355 (mtt90)
  outliers start: 15
  outliers final: 4
  residues processed: 157
  average time/residue: 0.9397
  time to fit residues: 155.5115
Evaluate side-chains
  161 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 152
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   34 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 97 optimal weight:   10.0000
   chunk 87 optimal weight:   30.0000
   chunk 27 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 80 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    2.0986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
C 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.100936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.068616 restraints weight = 33042.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 1.82
r_work: 0.2754 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2746
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2746
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.0821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12861  Z= 0.205
  Angle     :  0.652   7.241  18633  Z= 0.373
  Chirality :  0.046   0.226   2120
  Planarity :  0.004   0.044   1338
  Dihedral  : 31.290 146.937   4063
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.70 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.70 (0.30), residues: 743
  helix:  2.55 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.60 (0.39), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  42 
 TYR   0.011   0.002   TYR B  88 
 PHE   0.010   0.002   PHE A  67 
 HIS   0.004   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00417 /  0.21 (12861)
  covalent geometry    : angle       0.65195 /  0.37 (18633)
  hydrogen bonds       : bond        0.04675 /  3.12 (  782)
  hydrogen bonds       : angle       2.92841 /  1.98 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.350 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8578 (mtp85)
REVERT: B   93 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7590 (mp10)
REVERT: C   73 ASN cc_start: 0.8770 (t0) cc_final: 0.8504 (t160)
REVERT: D  108 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8355 (mtmm)
REVERT: F   92 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8479 (ttp80)
REVERT: G   64 GLU cc_start: 0.8604 (tt0) cc_final: 0.8359 (tm-30)
REVERT: G   73 ASN cc_start: 0.8693 (t0) cc_final: 0.8107 (t0)
REVERT: G   75 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8811 (mttm)
REVERT: H   99 ARG cc_start: 0.8689 (mtm-85) cc_final: 0.8374 (mtt90)
  outliers start: 16
  outliers final: 6
  residues processed: 159
  average time/residue: 0.9217
  time to fit residues: 154.5966
Evaluate side-chains
  162 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 152
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 91 optimal weight:    9.9990
   chunk 81 optimal weight:   10.0000
   chunk 96 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9980
   chunk 90 optimal weight:    9.9990
   chunk 78 optimal weight:    9.9990
   chunk 21 optimal weight:    0.7980
   chunk 97 optimal weight:   10.0000
   chunk 39 optimal weight:    0.5980
   chunk 88 optimal weight:   20.0000
   overall best weight:    2.8784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  75 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.100273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.067955 restraints weight = 40897.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 1.97
r_work: 0.2721 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2718
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8822
moved from start:          0.0964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  12861  Z= 0.259
  Angle     :  0.696   7.397  18633  Z= 0.389
  Chirality :  0.049   0.252   2120
  Planarity :  0.005   0.045   1338
  Dihedral  : 31.480 148.385   4063
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.02 %
    Favored  : 78.61 %
  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:  2.50 (0.30), residues: 743
  helix:  2.41 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.68 (0.39), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  42 
 TYR   0.013   0.002   TYR A  54 
 PHE   0.010   0.002   PHE E  67 
 HIS   0.005   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00549 /  0.26 (12861)
  covalent geometry    : angle       0.69566 /  0.39 (18633)
  hydrogen bonds       : bond        0.05334 /  3.57 (  782)
  hydrogen bonds       : angle       2.97361 /  2.02 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 152
  time to evaluate  : 0.216 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8598 (mtp85)
REVERT: B   93 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7683 (mp10)
REVERT: C   73 ASN cc_start: 0.8785 (t0) cc_final: 0.8523 (t160)
REVERT: D  108 LYS cc_start: 0.8733 (mtpp) cc_final: 0.8404 (mtmm)
REVERT: E   73 GLU cc_start: 0.8690 (tt0) cc_final: 0.8421 (tt0)
REVERT: F   92 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8489 (ttp80)
REVERT: G   64 GLU cc_start: 0.8662 (tt0) cc_final: 0.8402 (tm-30)
REVERT: G   73 ASN cc_start: 0.8718 (t0) cc_final: 0.8109 (t0)
REVERT: G   75 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8807 (mttm)
REVERT: H   68 ASP cc_start: 0.8984 (t0) cc_final: 0.8739 (t0)
REVERT: H   99 ARG cc_start: 0.8739 (mtm-85) cc_final: 0.8422 (mtt90)
  outliers start: 15
  outliers final: 7
  residues processed: 158
  average time/residue: 0.8594
  time to fit residues: 143.1430
Evaluate side-chains
  163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 152
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 85 optimal weight:   30.0000
   chunk 58 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 98 optimal weight:   10.0000
   chunk 97 optimal weight:   10.0000
   chunk 92 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   overall best weight:    1.2582

-------------------------------------------------------------------------------
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 = 0.3558 r_free = 0.3558 target = 0.100680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.068705 restraints weight = 27372.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 1.66
r_work: 0.2766 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.2619 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2607
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2607 r_free = 0.2607    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2607 r_free = 0.2607    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2607
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8863
moved from start:          0.0937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  12861  Z= 0.170
  Angle     :  0.683   9.273  18633  Z= 0.385
  Chirality :  0.047   0.265   2120
  Planarity :  0.004   0.043   1338
  Dihedral  : 31.489 148.332   4063
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 20.13 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.60 (0.31), residues: 743
  helix:  2.48 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.64 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  42 
 TYR   0.011   0.002   TYR D  40 
 PHE   0.011   0.002   PHE A  67 
 HIS   0.004   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.17 (12861)
  covalent geometry    : angle       0.68316 /  0.38 (18633)
  hydrogen bonds       : bond        0.04972 /  3.32 (  782)
  hydrogen bonds       : angle       2.97609 /  2.02 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.327 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8641 (mtp85)
REVERT: C   73 ASN cc_start: 0.8789 (t0) cc_final: 0.8524 (t160)
REVERT: D  108 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8427 (mtmm)
REVERT: E   73 GLU cc_start: 0.8800 (tt0) cc_final: 0.8550 (tt0)
REVERT: F   92 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8530 (ttp80)
REVERT: G   64 GLU cc_start: 0.8769 (tt0) cc_final: 0.8501 (tm-30)
REVERT: G   73 ASN cc_start: 0.8733 (t0) cc_final: 0.8118 (t0)
REVERT: G   75 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8830 (mttm)
REVERT: H   68 ASP cc_start: 0.9077 (t0) cc_final: 0.8822 (t0)
REVERT: H   99 ARG cc_start: 0.8797 (mtm-85) cc_final: 0.8490 (mtt90)
  outliers start: 12
  outliers final: 6
  residues processed: 156
  average time/residue: 0.9358
  time to fit residues: 153.7610
Evaluate side-chains
  161 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 152
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 65 optimal weight:    0.2980
   chunk 1 optimal weight:    0.4980
   chunk 89 optimal weight:   10.0000
   chunk 59 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 93 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.3562 r_free = 0.3562 target = 0.100981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.068658 restraints weight = 38085.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 1.93
r_work: 0.2745 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2736
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2736 r_free = 0.2736    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2736 r_free = 0.2736    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2736
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8807
moved from start:          0.0948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12861  Z= 0.169
  Angle     :  0.672   7.578  18633  Z= 0.379
  Chirality :  0.047   0.261   2120
  Planarity :  0.004   0.045   1338
  Dihedral  : 31.486 148.338   4063
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 20.44 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.61 (0.30), residues: 743
  helix:  2.49 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.62 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  42 
 TYR   0.012   0.002   TYR D  40 
 PHE   0.011   0.001   PHE A  67 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.17 (12861)
  covalent geometry    : angle       0.67203 /  0.38 (18633)
  hydrogen bonds       : bond        0.04716 /  3.15 (  782)
  hydrogen bonds       : angle       2.95765 /  2.01 ( 1943)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 153
  time to evaluate  : 0.396 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8579 (mtp85)
REVERT: C   36 LYS cc_start: 0.8978 (mmmm) cc_final: 0.8657 (mmtp)
REVERT: C   73 ASN cc_start: 0.8774 (t0) cc_final: 0.8505 (t160)
REVERT: D  108 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8389 (mtmm)
REVERT: E   73 GLU cc_start: 0.8695 (tt0) cc_final: 0.8490 (tt0)
REVERT: F   92 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8471 (ttp80)
REVERT: G   64 GLU cc_start: 0.8647 (tt0) cc_final: 0.8387 (tm-30)
REVERT: G   73 ASN cc_start: 0.8705 (t0) cc_final: 0.8093 (t0)
REVERT: G   75 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8798 (mttm)
REVERT: H   68 ASP cc_start: 0.8986 (t0) cc_final: 0.8729 (t0)
REVERT: H   99 ARG cc_start: 0.8699 (mtm-85) cc_final: 0.8385 (mtt90)
  outliers start: 10
  outliers final: 6
  residues processed: 158
  average time/residue: 0.9592
  time to fit residues: 159.7068
Evaluate side-chains
  162 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 153
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:   30.0000
   chunk 80 optimal weight:   10.0000
   chunk 10 optimal weight:    0.6980
   chunk 91 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 73 optimal weight:   30.0000
   chunk 20 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    1.6584

-------------------------------------------------------------------------------
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 = 0.3560 r_free = 0.3560 target = 0.100697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.068691 restraints weight = 34913.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 1.84
r_work: 0.2753 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2746
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2746
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8804
moved from start:          0.0942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12861  Z= 0.183
  Angle     :  0.672   7.693  18633  Z= 0.378
  Chirality :  0.047   0.270   2120
  Planarity :  0.004   0.044   1338
  Dihedral  : 31.478 148.145   4063
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 20.44 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.62 (0.31), residues: 743
  helix:  2.50 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.63 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  42 
 TYR   0.011   0.002   TYR D  40 
 PHE   0.010   0.002   PHE A  67 
 HIS   0.004   0.001   HIS D  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.18 (12861)
  covalent geometry    : angle       0.67161 /  0.38 (18633)
  hydrogen bonds       : bond        0.04642 /  3.10 (  782)
  hydrogen bonds       : angle       2.94813 /  2.00 ( 1943)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4848.67 seconds
wall clock time: 83 minutes 6.56 seconds (4986.56 seconds total)