Starting phenix.real_space_refine
on Thu Mar  5 13:15:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9r5w_53596/03_2026/9r5w_53596.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9r5w_53596/03_2026/9r5w_53596.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9r5w_53596/03_2026/9r5w_53596.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9r5w_53596/03_2026/9r5w_53596.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9r5w_53596/03_2026/9r5w_53596.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9r5w_53596/03_2026/9r5w_53596.cif"
  }
  resolution = 3.8
  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=   0.001 sd=   0.028
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: 6
    Type Number    sf(0)   Gaussians
     P     323      5.49       5
     S      10      5.16       5
     C    6835      2.51       5
     N    2340      2.21       5
     O    2983      1.98       5
     H    9763      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 22254
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "I"
      Number of atoms: 5129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 5129
          Classifications: {'DNA': 162}
          Modifications used: {'3*END': 1}
          Link IDs: {'rna3p': 161}
    Chain: "J"
      Number of atoms: 5146
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 5146
          Classifications: {'DNA': 162}
          Modifications used: {'3*END': 1, '5*END': 1}
          Link IDs: {'rna3p': 161}
    Chain: "A"
      Number of atoms: 1622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 1622
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "B"
      Number of atoms: 1314
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 1314
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 1642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 1642
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "D"
      Number of atoms: 1492
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 1492
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 1620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 1620
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "F"
      Number of atoms: 1298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 1298
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "G"
      Number of atoms: 1537
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 1537
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "H"
      Number of atoms: 1454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 1454
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.47, per 1000 atoms: 0.16
  Number of scatterers: 22254
  At special positions: 0
  Unit cell: (77.55, 151.25, 132.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      10     16.00
     P     323     15.00
     O    2983      8.00
     N    2340      7.00
     C    6835      6.00
     H    9763      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.62
  Conformation dependent library (CDL) restraints added in 433.2 milliseconds
  

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1378

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 9 sheets defined
      73.0% alpha, 2.7% beta
      158 base pairs and 256 stacking pairs defined.
    Time for finding SS restraints: 4.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 4.136A  pdb=" N   LEU A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.664A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.863A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.881A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLN A 125 " --> pdb=" O   PRO A 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
      removed outlier: 3.868A  pdb=" N   ARG B  40 " --> pdb=" O   ARG B  36 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   GLY B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLY B  42 " --> pdb=" O   ALA B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.580A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ASN B  64 " --> pdb=" O   VAL B  60 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   HIS B  75 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.572A  pdb=" N   ARG B  92 " --> pdb=" O   TYR B  88 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
      removed outlier: 3.970A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ARG C  35 " --> pdb=" O   HIS C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 74
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.984A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLN C  84 " --> pdb=" O   PRO C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.606A  pdb=" N   ASN C  94 " --> pdb=" O   ASP C  90 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   LEU C  96 " --> pdb=" O   GLU C  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 46
      removed outlier: 3.708A  pdb=" N   VAL D  38 " --> pdb=" O   TYR D  34 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   TYR D  39 " --> pdb=" O   ALA D  35 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LYS D  40 " --> pdb=" O   ILE D  36 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 98
    Processing helix  chain 'D' and resid 102 through 120
      removed outlier: 3.643A  pdb=" N   SER D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ALA D 114 " --> pdb=" O   GLU D 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 57
      removed outlier: 3.605A  pdb=" N   GLU E  50 " --> pdb=" O   VAL E  46 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   SER E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.527A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LYS E  79 " --> pdb=" O   ALA E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.797A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.858A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLN E 125 " --> pdb=" O   PRO E 121 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 3.569A  pdb=" N   ARG F  40 " --> pdb=" O   ARG F  36 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLY F  41 " --> pdb=" O   LEU F  37 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLY F  42 " --> pdb=" O   ALA F  38 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.996A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   HIS F  75 " --> pdb=" O   THR F  71 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.508A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.590A  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
      removed outlier: 3.635A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.630A  pdb=" N   TYR G  50 " --> pdb=" O   GLY G  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.882A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
      removed outlier: 3.619A  pdb=" N   ASN G  94 " --> pdb=" O   ASP G  90 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LYS G  95 " --> pdb=" O   GLU G  91 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   LEU G  96 " --> pdb=" O   GLU G  92 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 3.535A  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 120
      removed outlier: 4.038A  pdb=" N   ALA H 104 " --> pdb=" O   PRO H 100 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LYS H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.368A  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
      removed outlier: 3.511A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.307A  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: 6.982A  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 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 7.207A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.097A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 6.905A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    358 hydrogen bonds defined for protein.
    1068 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      406 hydrogen bonds
      812 hydrogen bond angles
      0 basepair planarities
      158 basepair parallelities
      256 stacking parallelities
  Total time for adding SS restraints: 5.35

  Time building geometry restraints manager: 2.36 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 9763
        1.03 -     1.22: 70
        1.22 -     1.42: 5553
        1.42 -     1.61: 7726
        1.61 -     1.80: 28
  Bond restraints: 23140
  Sorted by residual:
  bond pdb=" N   ARG A  42 "
       pdb=" CA  ARG A  42 "
    ideal  model  delta    sigma   weight residual
    1.453  1.491 -0.038 1.64e-02 3.72e+03 5.43e+00
  bond pdb=" N   ARG C  71 "
       pdb=" CA  ARG C  71 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.025 1.23e-02 6.61e+03 4.09e+00
  bond pdb=" C   PRO G  80 "
       pdb=" O   PRO G  80 "
    ideal  model  delta    sigma   weight residual
    1.237  1.257 -0.019 1.26e-02 6.30e+03 2.30e+00
  bond pdb=" N3   DC I  19 "
       pdb=" C4   DC I  19 "
    ideal  model  delta    sigma   weight residual
    1.334  1.306  0.028 2.00e-02 2.50e+03 2.00e+00
  bond pdb=" CA  PRO G  80 "
       pdb=" C   PRO G  80 "
    ideal  model  delta    sigma   weight residual
    1.517  1.538 -0.021 1.46e-02 4.69e+03 1.98e+00
  ... (remaining 23135 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.11: 40976
        2.11 -     4.22: 939
        4.22 -     6.33: 12
        6.33 -     8.43: 2
        8.43 -    10.54: 4
  Bond angle restraints: 41933
  Sorted by residual:
  angle pdb=" OP1  DT I -72 "
        pdb=" P    DT I -72 "
        pdb=" OP2  DT I -72 "
      ideal   model   delta    sigma   weight residual
     120.00  109.46   10.54 3.00e+00 1.11e-01 1.23e+01
  angle pdb=" OP1  DC I -73 "
        pdb=" P    DC I -73 "
        pdb=" OP2  DC I -73 "
      ideal   model   delta    sigma   weight residual
     120.00  109.62   10.38 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" O3'  DC I -73 "
        pdb=" P    DT I -72 "
        pdb=" OP1  DT I -72 "
      ideal   model   delta    sigma   weight residual
     108.00  117.83   -9.83 3.00e+00 1.11e-01 1.07e+01
  angle pdb=" CB  LYS B  31 "
        pdb=" CG  LYS B  31 "
        pdb=" CD  LYS B  31 "
      ideal   model   delta    sigma   weight residual
     111.30  118.75   -7.45 2.30e+00 1.89e-01 1.05e+01
  angle pdb=" C3'  DT J -17 "
        pdb=" O3'  DT J -17 "
        pdb=" P    DC J -16 "
      ideal   model   delta    sigma   weight residual
     120.20  124.99   -4.79 1.50e+00 4.44e-01 1.02e+01
  ... (remaining 41928 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.20: 6622
       17.20 -    34.39: 1191
       34.39 -    51.59: 1212
       51.59 -    68.78: 488
       68.78 -    85.98: 11
  Dihedral angle restraints: 9524
    sinusoidal: 7124
      harmonic: 2400
  Sorted by residual:
  dihedral pdb=" CA  PRO H 100 "
           pdb=" C   PRO H 100 "
           pdb=" N   GLY H 101 "
           pdb=" CA  GLY H 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.03   18.97     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  ARG E  63 "
           pdb=" C   ARG E  63 "
           pdb=" N   LYS E  64 "
           pdb=" CA  LYS E  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.92  -18.08     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  PRO H  47 "
           pdb=" C   PRO H  47 "
           pdb=" N   ASP H  48 "
           pdb=" CA  ASP H  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.43  -17.57     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 9521 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 2118
       0.083 -    0.166: 89
       0.166 -    0.250: 3
       0.250 -    0.333: 0
       0.333 -    0.416: 2
  Chirality restraints: 2212
  Sorted by residual:
  chirality pdb=" P    DT I -72 "
            pdb=" OP1  DT I -72 "
            pdb=" OP2  DT I -72 "
            pdb=" O5'  DT I -72 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.76   -0.42 2.00e-01 2.50e+01 4.33e+00
  chirality pdb=" P    DC I -73 "
            pdb=" OP1  DC I -73 "
            pdb=" OP2  DC I -73 "
            pdb=" O5'  DC I -73 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.74   -0.39 2.00e-01 2.50e+01 3.81e+00
  chirality pdb=" P    DC J -20 "
            pdb=" OP1  DC J -20 "
            pdb=" OP2  DC J -20 "
            pdb=" O5'  DC J -20 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.54   -0.20 2.00e-01 2.50e+01 9.55e-01
  ... (remaining 2209 not shown)

  Planarity restraints: 2310
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J -20 "    0.003 2.00e-02 2.50e+03   2.32e-02 1.48e+01
        pdb=" N1   DC J -20 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DC J -20 "    0.061 2.00e-02 2.50e+03
        pdb=" O2   DC J -20 "   -0.038 2.00e-02 2.50e+03
        pdb=" N3   DC J -20 "   -0.018 2.00e-02 2.50e+03
        pdb=" C4   DC J -20 "    0.017 2.00e-02 2.50e+03
        pdb=" N4   DC J -20 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5   DC J -20 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DC J -20 "   -0.001 2.00e-02 2.50e+03
        pdb=" H5   DC J -20 "   -0.006 2.00e-02 2.50e+03
        pdb=" H6   DC J -20 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  19 "   -0.017 2.00e-02 2.50e+03   1.73e-02 8.23e+00
        pdb=" N1   DC I  19 "    0.008 2.00e-02 2.50e+03
        pdb=" C2   DC I  19 "   -0.036 2.00e-02 2.50e+03
        pdb=" O2   DC I  19 "    0.038 2.00e-02 2.50e+03
        pdb=" N3   DC I  19 "   -0.011 2.00e-02 2.50e+03
        pdb=" C4   DC I  19 "    0.004 2.00e-02 2.50e+03
        pdb=" N4   DC I  19 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5   DC I  19 "    0.004 2.00e-02 2.50e+03
        pdb=" C6   DC I  19 "    0.004 2.00e-02 2.50e+03
        pdb=" H5   DC I  19 "    0.006 2.00e-02 2.50e+03
        pdb=" H6   DC I  19 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU H 103 "   -0.013 2.00e-02 2.50e+03   2.54e-02 6.46e+00
        pdb=" C   LEU H 103 "    0.044 2.00e-02 2.50e+03
        pdb=" O   LEU H 103 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ALA H 104 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 2307 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 853
        2.19 -     2.79: 36865
        2.79 -     3.40: 54052
        3.40 -     4.00: 75698
        4.00 -     4.60: 113984
  Nonbonded interactions: 281452
  Sorted by model distance:
  nonbonded pdb=" HZ  PHE E 104 "
            pdb=" HG1 THR F  54 "
     model   vdw
     1.589 2.100
  nonbonded pdb=" OD1 ASN G  68 "
            pdb="HH21 ARG G  71 "
     model   vdw
     1.640 2.450
  nonbonded pdb=" O   ILE D  36 "
            pdb=" HZ3 LYS D  40 "
     model   vdw
     1.688 2.450
  nonbonded pdb=" OE2 GLU G  64 "
            pdb="HD21 ASN G  68 "
     model   vdw
     1.699 2.450
  nonbonded pdb=" OP1  DA I -44 "
            pdb="HH12 ARG C  32 "
     model   vdw
     1.709 2.450
  ... (remaining 281447 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 39 and (name N or name CA or name C or name O or name CB  \ 
or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name HA or name HB \ 
2 or name HB3)) or resid 40 through 133 or (resid 134 and (name N or name CA or  \ 
name C or name O or name CB or name H or name HA ))))
  selection = (chain 'E' and ((resid 39 and (name N or name CA or name C or name O or name CB  \ 
or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name HA or name HB \ 
2 or name HB3)) or resid 40 through 134))
}
ncs_group {
  reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB  \ 
or name HA )) or resid 24 through 102))
  selection = (chain 'F' and ((resid 23 and (name N or name CA or name C or name O or name CB  \ 
or name HA )) or resid 24 through 102))
}
ncs_group {
  reference = (chain 'C' and resid 14 through 109)
  selection = (chain 'G' and resid 14 through 109)
}
ncs_group {
  reference = (chain 'D' and ((resid 30 and (name N or name CA or name C or name O or name CB  \ 
or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA o \ 
r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ 
E or name HH11 or name HH12 or name HH21 or name HH22)) or resid 31 through 120  \ 
or (resid 121 and (name N or name CA or name C or name O or name H ))))
  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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             23.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.110
  Extract box with map and model:          0.820
  Check model and map are aligned:         0.080
  Set scattering table:                    0.060
  Process input model:                     23.980
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.040
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
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      :  0.004   0.045  13377  Z= 0.212
  Angle     :  0.716  10.543  19463  Z= 0.442
  Chirality :  0.041   0.416   2212
  Planarity :  0.006   0.049   1343
  Dihedral  : 26.919  82.580   5801
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.34 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.33 %
    Favored  : 99.51 %
  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:  1.41 (0.29), residues: 726
  helix:  1.70 (0.23), residues: 460
  sheet:  None (None), residues: 0
  loop : -0.38 (0.35), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  96 
 TYR   0.011   0.001   TYR A  99 
 PHE   0.012   0.001   PHE B  61 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (13377)
  covalent geometry    : angle       0.71638 (19463)
  hydrogen bonds       : bond        0.14914 (  764)
  hydrogen bonds       : angle       4.97391 ( 1880)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   72 TYR cc_start: 0.6589 (m-80) cc_final: 0.6367 (m-80)
REVERT: B   91 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7825 (ttmm)
REVERT: E   42 ARG cc_start: 0.7880 (mtp180) cc_final: 0.7547 (mtp85)
REVERT: G   13 LYS cc_start: 0.7890 (tptp) cc_final: 0.7679 (tptp)
  outliers start: 1
  outliers final: 0
  residues processed: 91
  average time/residue: 0.3959
  time to fit residues: 44.2872
Evaluate side-chains
  84 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN
F  25 ASN
G  73 ASN
** H  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.135415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.110455 restraints weight = 47626.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.113560 restraints weight = 17740.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.115578 restraints weight = 9518.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.116737 restraints weight = 6605.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.117404 restraints weight = 5395.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13377  Z= 0.235
  Angle     :  0.667   6.462  19463  Z= 0.417
  Chirality :  0.042   0.147   2212
  Planarity :  0.005   0.060   1343
  Dihedral  : 29.666  77.588   4361
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  4.77 %
    Favored  : 94.08 %
  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:  1.87 (0.30), residues: 726
  helix:  2.15 (0.22), residues: 489
  sheet:  None (None), residues: 0
  loop : -0.72 (0.38), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG G  17 
 TYR   0.011   0.002   TYR A  41 
 PHE   0.009   0.002   PHE G  25 
 HIS   0.008   0.002   HIS H  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 (13377)
  covalent geometry    : angle       0.66656 (19463)
  hydrogen bonds       : bond        0.07227 (  764)
  hydrogen bonds       : angle       3.31436 ( 1880)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  118 TYR cc_start: 0.8215 (t80) cc_final: 0.8002 (t80)
REVERT: F   75 HIS cc_start: 0.7852 (t70) cc_final: 0.7185 (t70)
REVERT: F   92 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7938 (ttp80)
  outliers start: 7
  outliers final: 3
  residues processed: 89
  average time/residue: 0.3714
  time to fit residues: 41.1762
Evaluate side-chains
  87 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain F residue   92 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 94 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:    0.9990
   chunk 76 optimal weight:    0.2980
   chunk 100 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
G  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.138563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.113499 restraints weight = 48961.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.116903 restraints weight = 17312.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.119094 restraints weight = 8915.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.120290 restraints weight = 6077.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.121214 restraints weight = 4919.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  13377  Z= 0.207
  Angle     :  0.621   6.010  19463  Z= 0.391
  Chirality :  0.040   0.141   2212
  Planarity :  0.004   0.054   1343
  Dihedral  : 29.355  74.771   4361
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  6.41 %
    Favored  : 92.60 %
  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:  2.53 (0.31), residues: 726
  helix:  2.76 (0.23), residues: 490
  sheet:  None (None), residues: 0
  loop : -0.77 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  96 
 TYR   0.013   0.002   TYR H 118 
 PHE   0.010   0.001   PHE B  61 
 HIS   0.006   0.001   HIS H  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (13377)
  covalent geometry    : angle       0.62070 (19463)
  hydrogen bonds       : bond        0.06458 (  764)
  hydrogen bonds       : angle       3.05538 ( 1880)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   75 HIS cc_start: 0.8067 (t70) cc_final: 0.7506 (t70)
  outliers start: 6
  outliers final: 2
  residues processed: 85
  average time/residue: 0.4177
  time to fit residues: 43.6994
Evaluate side-chains
  84 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue  112 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 90 optimal weight:    0.9980
   chunk 99 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 82 optimal weight:    0.5980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
H  44 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.135493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.110095 restraints weight = 48458.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.113424 restraints weight = 16982.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.115590 restraints weight = 8882.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.116804 restraints weight = 6128.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.117521 restraints weight = 4987.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.3628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  13377  Z= 0.241
  Angle     :  0.633   6.288  19463  Z= 0.397
  Chirality :  0.042   0.137   2212
  Planarity :  0.005   0.046   1343
  Dihedral  : 29.280  73.226   4361
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  7.57 %
    Favored  : 90.62 %
  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:  2.30 (0.31), residues: 726
  helix:  2.63 (0.23), residues: 489
  sheet:  None (None), residues: 0
  loop : -0.94 (0.38), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  96 
 TYR   0.011   0.002   TYR E  99 
 PHE   0.009   0.002   PHE B  61 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 (13377)
  covalent geometry    : angle       0.63284 (19463)
  hydrogen bonds       : bond        0.07021 (  764)
  hydrogen bonds       : angle       3.10692 ( 1880)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.8541 (mtm180) cc_final: 0.8265 (mtm180)
REVERT: F   92 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.8044 (ttp80)
  outliers start: 11
  outliers final: 5
  residues processed: 90
  average time/residue: 0.4028
  time to fit residues: 44.8010
Evaluate side-chains
  89 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain F residue   92 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 102 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.135078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.109518 restraints weight = 47902.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.112832 restraints weight = 17011.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.114999 restraints weight = 8920.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.116200 restraints weight = 6177.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 63)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.117058 restraints weight = 5058.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.3886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  13377  Z= 0.242
  Angle     :  0.627   6.200  19463  Z= 0.393
  Chirality :  0.042   0.139   2212
  Planarity :  0.005   0.050   1343
  Dihedral  : 29.159  73.247   4361
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  9.70 %
    Favored  : 89.14 %
  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:  2.25 (0.31), residues: 726
  helix:  2.58 (0.23), residues: 490
  sheet:  None (None), residues: 0
  loop : -0.96 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  96 
 TYR   0.010   0.001   TYR A  41 
 PHE   0.009   0.001   PHE B  61 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 (13377)
  covalent geometry    : angle       0.62706 (19463)
  hydrogen bonds       : bond        0.06855 (  764)
  hydrogen bonds       : angle       3.09585 ( 1880)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.8538 (mtm180) cc_final: 0.8297 (mtm180)
REVERT: C   38 ASN cc_start: 0.7650 (m110) cc_final: 0.7439 (m110)
REVERT: F   27 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7860 (mp10)
REVERT: F   75 HIS cc_start: 0.8101 (t70) cc_final: 0.7139 (t70)
REVERT: F   92 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8051 (ttp80)
  outliers start: 7
  outliers final: 4
  residues processed: 92
  average time/residue: 0.3811
  time to fit residues: 43.7436
Evaluate side-chains
  92 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ARG
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain F residue   92 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
C 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.133807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.107938 restraints weight = 48183.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.111206 restraints weight = 17357.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.113337 restraints weight = 9237.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.114608 restraints weight = 6446.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.115285 restraints weight = 5297.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.4248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037  13377  Z= 0.273
  Angle     :  0.648   6.359  19463  Z= 0.405
  Chirality :  0.044   0.142   2212
  Planarity :  0.005   0.047   1343
  Dihedral  : 29.142  75.228   4361
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  :  9.05 %
    Favored  : 88.49 %
  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:  1.99 (0.31), residues: 726
  helix:  2.39 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -1.19 (0.37), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  96 
 TYR   0.013   0.002   TYR A  41 
 PHE   0.010   0.002   PHE D  62 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00597 (13377)
  covalent geometry    : angle       0.64762 (19463)
  hydrogen bonds       : bond        0.07497 (  764)
  hydrogen bonds       : angle       3.23784 ( 1880)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.8574 (mtm180) cc_final: 0.8325 (mtm180)
REVERT: F   27 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7939 (mp10)
REVERT: F   92 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8100 (ttp80)
REVERT: H   79 HIS cc_start: 0.8081 (t70) cc_final: 0.7738 (t-170)
  outliers start: 15
  outliers final: 9
  residues processed: 96
  average time/residue: 0.4119
  time to fit residues: 48.4285
Evaluate side-chains
  99 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ARG
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain F residue   92 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 91 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 94 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.135546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.109733 restraints weight = 48036.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.113037 restraints weight = 17278.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.115155 restraints weight = 9144.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.116459 restraints weight = 6377.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.117119 restraints weight = 5218.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.4310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13377  Z= 0.210
  Angle     :  0.615   6.089  19463  Z= 0.385
  Chirality :  0.040   0.143   2212
  Planarity :  0.004   0.059   1343
  Dihedral  : 29.074  75.447   4361
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  9.54 %
    Favored  : 88.65 %
  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:  2.25 (0.31), residues: 726
  helix:  2.63 (0.23), residues: 490
  sheet:  None (None), residues: 0
  loop : -1.08 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  83 
 TYR   0.008   0.001   TYR A  41 
 PHE   0.008   0.001   PHE D  62 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 (13377)
  covalent geometry    : angle       0.61471 (19463)
  hydrogen bonds       : bond        0.06518 (  764)
  hydrogen bonds       : angle       3.03749 ( 1880)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   27 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7926 (mp10)
REVERT: F   92 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8076 (ttp80)
REVERT: H   79 HIS cc_start: 0.8074 (t70) cc_final: 0.7754 (t-170)
  outliers start: 11
  outliers final: 4
  residues processed: 92
  average time/residue: 0.3790
  time to fit residues: 43.3452
Evaluate side-chains
  92 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ARG
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain F residue   92 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.132083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.106025 restraints weight = 47804.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.109275 restraints weight = 17340.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.111396 restraints weight = 9287.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.112568 restraints weight = 6520.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.113122 restraints weight = 5380.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.4582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.040  13377  Z= 0.318
  Angle     :  0.674   6.311  19463  Z= 0.420
  Chirality :  0.047   0.153   2212
  Planarity :  0.005   0.052   1343
  Dihedral  : 29.171  77.301   4361
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 10.69 %
    Favored  : 87.66 %
  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:  1.79 (0.31), residues: 726
  helix:  2.22 (0.23), residues: 502
  sheet:  None (None), residues: 0
  loop : -1.29 (0.38), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  83 
 TYR   0.015   0.002   TYR D  37 
 PHE   0.010   0.002   PHE D  62 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00703 (13377)
  covalent geometry    : angle       0.67371 (19463)
  hydrogen bonds       : bond        0.08228 (  764)
  hydrogen bonds       : angle       3.40753 ( 1880)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: F   27 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8015 (mp10)
REVERT: F   92 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8124 (ttp80)
  outliers start: 10
  outliers final: 8
  residues processed: 94
  average time/residue: 0.3935
  time to fit residues: 45.4591
Evaluate side-chains
  96 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ARG
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain F residue   92 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.9386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.134929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.109003 restraints weight = 47966.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.112296 restraints weight = 17223.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.114450 restraints weight = 9175.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.115633 restraints weight = 6410.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 58)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.116512 restraints weight = 5276.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.4622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  13377  Z= 0.221
  Angle     :  0.626   6.129  19463  Z= 0.391
  Chirality :  0.041   0.137   2212
  Planarity :  0.005   0.066   1343
  Dihedral  : 29.071  77.482   4361
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 11.02 %
    Favored  : 87.50 %
  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:  2.07 (0.31), residues: 726
  helix:  2.44 (0.23), residues: 491
  sheet:  None (None), residues: 0
  loop : -1.04 (0.38), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H  83 
 TYR   0.008   0.001   TYR A  41 
 PHE   0.009   0.001   PHE D  62 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (13377)
  covalent geometry    : angle       0.62595 (19463)
  hydrogen bonds       : bond        0.06712 (  764)
  hydrogen bonds       : angle       3.08553 ( 1880)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.7330 (mtp) cc_final: 0.7074 (mtp)
REVERT: F   27 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8043 (mp10)
REVERT: F   92 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8095 (ttp80)
  outliers start: 9
  outliers final: 6
  residues processed: 93
  average time/residue: 0.3946
  time to fit residues: 45.5871
Evaluate side-chains
  93 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ARG
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain F residue   92 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.135126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.109611 restraints weight = 48284.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.112739 restraints weight = 17918.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.114794 restraints weight = 9738.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.115892 restraints weight = 6889.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.116593 restraints weight = 5718.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.4679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  13377  Z= 0.220
  Angle     :  0.620   6.047  19463  Z= 0.387
  Chirality :  0.041   0.151   2212
  Planarity :  0.005   0.060   1343
  Dihedral  : 29.061  77.813   4361
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 11.35 %
    Favored  : 87.50 %
  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:  2.11 (0.31), residues: 726
  helix:  2.50 (0.23), residues: 491
  sheet:  None (None), residues: 0
  loop : -1.09 (0.38), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  83 
 TYR   0.009   0.001   TYR A  41 
 PHE   0.008   0.001   PHE D  62 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 (13377)
  covalent geometry    : angle       0.61965 (19463)
  hydrogen bonds       : bond        0.06569 (  764)
  hydrogen bonds       : angle       3.03478 ( 1880)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.7278 (mtp) cc_final: 0.7028 (mtp)
REVERT: F   27 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7991 (mp10)
REVERT: F   92 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8083 (ttp80)
  outliers start: 7
  outliers final: 6
  residues processed: 91
  average time/residue: 0.3904
  time to fit residues: 44.0130
Evaluate side-chains
  93 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ARG
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain F residue   92 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 66 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 81 optimal weight:    0.2980
   chunk 90 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
H  44 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.137552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.111742 restraints weight = 48056.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.115063 restraints weight = 17216.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 68)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.117238 restraints weight = 9131.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.118464 restraints weight = 6337.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.119313 restraints weight = 5189.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.4749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13377  Z= 0.187
  Angle     :  0.596   6.078  19463  Z= 0.374
  Chirality :  0.039   0.130   2212
  Planarity :  0.004   0.055   1343
  Dihedral  : 29.007  78.135   4361
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 11.35 %
    Favored  : 87.50 %
  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:  2.40 (0.32), residues: 726
  helix:  2.77 (0.23), residues: 490
  sheet:  None (None), residues: 0
  loop : -1.10 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  83 
 TYR   0.007   0.001   TYR A  41 
 PHE   0.008   0.001   PHE B  61 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (13377)
  covalent geometry    : angle       0.59590 (19463)
  hydrogen bonds       : bond        0.05612 (  764)
  hydrogen bonds       : angle       2.81197 ( 1880)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4196.43 seconds
wall clock time: 71 minutes 53.96 seconds (4313.96 seconds total)