Starting phenix.real_space_refine
on Sat Aug 23 17:54:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vfy_43194/08_2025/8vfy_43194.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vfy_43194/08_2025/8vfy_43194.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vfy_43194/08_2025/8vfy_43194.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vfy_43194/08_2025/8vfy_43194.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vfy_43194/08_2025/8vfy_43194.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vfy_43194/08_2025/8vfy_43194.cif"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     342      5.49       5
     S      21      5.16       5
     C    7786      2.51       5
     N    2611      2.21       5
     O    3286      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14046
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 799
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 799
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 927
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 927
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 5, 'TRANS': 114}
    Chain: "H"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 3501
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 3501
          Classifications: {'DNA': 171}
          Link IDs: {'rna3p': 170}
    Chain: "J"
      Number of atoms: 3510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 3510
          Classifications: {'DNA': 171}
          Link IDs: {'rna3p': 170}
    Chain: "O"
      Number of atoms: 856
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 856
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 7, 'TRANS': 94}
  Time building chain proxies: 2.76, per 1000 atoms: 0.20
  Number of scatterers: 14046
  At special positions: 0
  Unit cell: (84.48, 118.8, 192.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      21     16.00
     P     342     15.00
     O    3286      8.00
     N    2611      7.00
     C    7786      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.88
  Conformation dependent library (CDL) restraints added in 391.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1648

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 11 sheets defined
      68.1% alpha, 3.2% beta
      171 base pairs and 306 stacking pairs defined.
    Time for finding SS restraints: 2.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.618A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 40
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.742A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.370A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.549A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 56
      removed outlier: 3.537A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.809A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.637A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.507A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.323A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.527A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 123
      removed outlier: 3.561A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   VAL H 111 " --> pdb=" O   ALA H 107 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 174 through 186
    Processing helix  chain 'O' and resid 192 through 204
    Processing helix  chain 'O' and resid 205 through 209
      removed outlier: 3.690A  pdb=" N   GLN O 209 " --> pdb=" O   TYR O 206 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 210 through 225
      removed outlier: 4.029A  pdb=" N   TRP O 214 " --> pdb=" O   ASN O 210 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.804A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.521A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.486A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.723A  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: 7.520A  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: 7.468A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'O' and resid 228 through 231

    436 hydrogen bonds defined for protein.
    1278 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      417 hydrogen bonds
      834 hydrogen bond angles
      0 basepair planarities
      171 basepair parallelities
      306 stacking parallelities
  Total time for adding SS restraints: 2.56

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2566
        1.33 -     1.45: 4879
        1.45 -     1.57: 6846
        1.57 -     1.69: 682
        1.69 -     1.81: 35
  Bond restraints: 15008
  Sorted by residual:
  bond pdb=" N   HIS O 168 "
       pdb=" CA  HIS O 168 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.14e+00
  bond pdb=" N   LYS D  30 "
       pdb=" CA  LYS D  30 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.03e+00
  bond pdb=" N   ALA C  10 "
       pdb=" CA  ALA C  10 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.01e+00
  bond pdb=" N   LYS H  30 "
       pdb=" CA  LYS H  30 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.97e+00
  bond pdb=" N   LYS B  20 "
       pdb=" CA  LYS B  20 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.92e+00
  ... (remaining 15003 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 20049
        1.17 -     2.33: 1297
        2.33 -     3.50: 345
        3.50 -     4.66: 34
        4.66 -     5.83: 6
  Bond angle restraints: 21731
  Sorted by residual:
  angle pdb=" C2'  DT J  55 "
        pdb=" C1'  DT J  55 "
        pdb=" N1   DT J  55 "
      ideal   model   delta    sigma   weight residual
     113.50  117.99   -4.49 1.50e+00 4.44e-01 8.98e+00
  angle pdb=" C2'  DT I 140 "
        pdb=" C1'  DT I 140 "
        pdb=" N1   DT I 140 "
      ideal   model   delta    sigma   weight residual
     113.50  117.92   -4.42 1.50e+00 4.44e-01 8.69e+00
  angle pdb=" C2'  DC I 110 "
        pdb=" C1'  DC I 110 "
        pdb=" N1   DC I 110 "
      ideal   model   delta    sigma   weight residual
     113.50  117.76   -4.26 1.50e+00 4.44e-01 8.07e+00
  angle pdb=" C2'  DT I 161 "
        pdb=" C1'  DT I 161 "
        pdb=" N1   DT I 161 "
      ideal   model   delta    sigma   weight residual
     113.50  117.59   -4.09 1.50e+00 4.44e-01 7.43e+00
  angle pdb=" C2'  DT I  69 "
        pdb=" C1'  DT I  69 "
        pdb=" N1   DT I  69 "
      ideal   model   delta    sigma   weight residual
     113.50  117.55   -4.05 1.50e+00 4.44e-01 7.29e+00
  ... (remaining 21726 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.36: 6504
       31.36 -    62.73: 1665
       62.73 -    94.09: 52
       94.09 -   125.46: 0
      125.46 -   156.82: 2
  Dihedral angle restraints: 8223
    sinusoidal: 5666
      harmonic: 2557
  Sorted by residual:
  dihedral pdb=" C4'  DG J 127 "
           pdb=" C3'  DG J 127 "
           pdb=" O3'  DG J 127 "
           pdb=" P    DG J 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   63.18  156.82     1      3.50e+01 8.16e-04 1.50e+01
  dihedral pdb=" C4'  DC J  93 "
           pdb=" C3'  DC J  93 "
           pdb=" O3'  DC J  93 "
           pdb=" P    DC J  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   68.58  151.42     1      3.50e+01 8.16e-04 1.47e+01
  dihedral pdb=" CA  LYS O 237 "
           pdb=" C   LYS O 237 "
           pdb=" N   PRO O 238 "
           pdb=" CA  PRO O 238 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.38   17.62     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 8220 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1616
       0.032 -    0.064: 525
       0.064 -    0.095: 263
       0.095 -    0.127: 38
       0.127 -    0.159: 5
  Chirality restraints: 2447
  Sorted by residual:
  chirality pdb=" CA  ILE B  29 "
            pdb=" N   ILE B  29 "
            pdb=" C   ILE B  29 "
            pdb=" CB  ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.32e-01
  chirality pdb=" CA  ILE F  29 "
            pdb=" N   ILE F  29 "
            pdb=" C   ILE F  29 "
            pdb=" CB  ILE F  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.99e-01
  chirality pdb=" CA  ILE G 111 "
            pdb=" N   ILE G 111 "
            pdb=" C   ILE G 111 "
            pdb=" CB  ILE G 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.59e-01
  ... (remaining 2444 not shown)

  Planarity restraints: 1565
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS O 237 "   -0.048 5.00e-02 4.00e+02   7.30e-02 8.53e+00
        pdb=" N   PRO O 238 "    0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO O 238 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO O 238 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I 140 "    0.038 2.00e-02 2.50e+03   1.78e-02 7.88e+00
        pdb=" N1   DT I 140 "   -0.036 2.00e-02 2.50e+03
        pdb=" C2   DT I 140 "   -0.008 2.00e-02 2.50e+03
        pdb=" O2   DT I 140 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DT I 140 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DT I 140 "    0.002 2.00e-02 2.50e+03
        pdb=" O4   DT I 140 "    0.015 2.00e-02 2.50e+03
        pdb=" C5   DT I 140 "    0.002 2.00e-02 2.50e+03
        pdb=" C7   DT I 140 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DT I 140 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO O 171 "    0.031 5.00e-02 4.00e+02   4.72e-02 3.56e+00
        pdb=" N   PRO O 172 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO O 172 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO O 172 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1562 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1294
        2.74 -     3.28: 12610
        3.28 -     3.82: 27731
        3.82 -     4.36: 32977
        4.36 -     4.90: 47101
  Nonbonded interactions: 121713
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D  90 "
            pdb=" OE1 GLU D  93 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   THR C  16 "
            pdb=" OG  SER C  19 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OH  TYR B  72 "
            pdb=" OE2 GLU D  76 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OH  TYR F  72 "
            pdb=" OE2 GLU H  76 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OH  TYR B  98 "
            pdb=" OD2 ASP H  68 "
     model   vdw
     2.275 3.040
  ... (remaining 121708 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 10 through 118)
}
ncs_group {
  reference = chain 'D'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.850
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
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      :  0.005   0.047  15008  Z= 0.212
  Angle     :  0.678   5.829  21731  Z= 0.427
  Chirality :  0.039   0.159   2447
  Planarity :  0.005   0.073   1565
  Dihedral  : 26.421 156.825   6575
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.74 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.21 %
    Favored  : 98.52 %
  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 aren not related in a simple way.
  whole:  2.05 (0.29), residues: 863
  helix:  2.21 (0.22), residues: 577
  sheet: -1.65 (1.37), residues: 12
  loop : -0.34 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  42 
 TYR   0.007   0.001   TYR G  57 
 PHE   0.007   0.001   PHE E 104 
 TRP   0.007   0.001   TRP O 214 
 HIS   0.003   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 (15008)
  covalent geometry    : angle       0.67754 (21731)
  hydrogen bonds       : bond        0.09755 (  853)
  hydrogen bonds       : angle       3.64263 ( 2112)

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 184
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8872 (p) cc_final: 0.8313 (t)
REVERT: A   76 GLN cc_start: 0.8172 (mt0) cc_final: 0.7704 (mt0)
REVERT: B   85 ASP cc_start: 0.9143 (m-30) cc_final: 0.8911 (m-30)
REVERT: C   90 ASP cc_start: 0.8325 (t0) cc_final: 0.8071 (t0)
REVERT: C   95 LYS cc_start: 0.9288 (ttpt) cc_final: 0.9063 (tttm)
REVERT: D  108 LYS cc_start: 0.8240 (ptmm) cc_final: 0.8016 (ptpp)
REVERT: E   79 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8520 (mtpm)
REVERT: G  120 THR cc_start: 0.8473 (p) cc_final: 0.8052 (p)
REVERT: H   59 MET cc_start: 0.9127 (tpp) cc_final: 0.8898 (tpt)
REVERT: H  113 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8341 (tt0)
REVERT: H  115 THR cc_start: 0.9240 (m) cc_final: 0.9030 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 186
  average time/residue: 0.7854
  time to fit residues: 155.3356
Evaluate side-chains
  117 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   88 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:   30.0000
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    9.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 ASN
D  47 GLN
E  68 GLN
** H  63 ASN ** 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 = 0.3931 r_free = 0.3931 target = 0.104892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.068730 restraints weight = 35709.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.05
r_work: 0.3097 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.1504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  15008  Z= 0.236
  Angle     :  0.633   6.564  21731  Z= 0.378
  Chirality :  0.037   0.147   2447
  Planarity :  0.005   0.076   1565
  Dihedral  : 30.470 150.966   4803
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.32 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.23 %
    Favored  : 84.35 %
  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 aren not related in a simple way.
  whole:  2.14 (0.28), residues: 863
  helix:  2.18 (0.21), residues: 585
  sheet: -1.59 (1.32), residues: 12
  loop : -0.12 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  99 
 TYR   0.015   0.002   TYR H  40 
 PHE   0.012   0.002   PHE O 254 
 TRP   0.020   0.003   TRP O 199 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 (15008)
  covalent geometry    : angle       0.63286 (21731)
  hydrogen bonds       : bond        0.04433 (  853)
  hydrogen bonds       : angle       3.03263 ( 2112)

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8253 (mt0) cc_final: 0.7786 (mt0)
REVERT: C   13 LYS cc_start: 0.9147 (tppp) cc_final: 0.8842 (tppp)
REVERT: C   90 ASP cc_start: 0.8304 (t0) cc_final: 0.8062 (t0)
REVERT: C   91 GLU cc_start: 0.7810 (tp30) cc_final: 0.7607 (tp30)
REVERT: D   63 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8182 (m-40)
REVERT: D  108 LYS cc_start: 0.8162 (ptmm) cc_final: 0.7900 (ptpp)
REVERT: E   77 ASP cc_start: 0.8917 (m-30) cc_final: 0.8663 (t0)
REVERT: G   90 ASP cc_start: 0.8616 (t70) cc_final: 0.8329 (t0)
REVERT: H   59 MET cc_start: 0.9155 (tpp) cc_final: 0.8821 (tpt)
REVERT: H  113 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8412 (tt0)
REVERT: O  190 MET cc_start: 0.6387 (ttp) cc_final: 0.5640 (tpp)
REVERT: O  253 MET cc_start: 0.6135 (tpt) cc_final: 0.5757 (tpp)
  outliers start: 18
  outliers final: 12
  residues processed: 130
  average time/residue: 0.7464
  time to fit residues: 103.3813
Evaluate side-chains
  121 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 72 optimal weight:    0.7980
   chunk 17 optimal weight:    8.9990
   chunk 36 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0970
   chunk 4 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.1580

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 ASN
G 104 GLN
H  49 HIS
** H  63 ASN ** 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 = 0.3921 r_free = 0.3921 target = 0.105821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.069442 restraints weight = 35921.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.26
r_work: 0.3093 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  15008  Z= 0.193
  Angle     :  0.605   9.631  21731  Z= 0.363
  Chirality :  0.035   0.147   2447
  Planarity :  0.005   0.077   1565
  Dihedral  : 30.394 149.193   4803
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.09 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.84 %
    Favored  : 83.00 %
  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 aren not related in a simple way.
  whole:  2.33 (0.28), residues: 863
  helix:  2.27 (0.21), residues: 588
  sheet: -1.51 (1.34), residues: 12
  loop :  0.09 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  86 
 TYR   0.015   0.002   TYR H  40 
 PHE   0.013   0.001   PHE O 254 
 TRP   0.009   0.001   TRP O 199 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (15008)
  covalent geometry    : angle       0.60523 (21731)
  hydrogen bonds       : bond        0.03963 (  853)
  hydrogen bonds       : angle       2.84815 ( 2112)

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8196 (mt0) cc_final: 0.7685 (mt0)
REVERT: C   91 GLU cc_start: 0.7829 (tp30) cc_final: 0.7615 (tm-30)
REVERT: D   57 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8934 (mtpt)
REVERT: D   63 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8110 (m-40)
REVERT: D   71 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8238 (mt-10)
REVERT: D  108 LYS cc_start: 0.8082 (ptmm) cc_final: 0.7800 (ptpp)
REVERT: E   63 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7893 (mmm160)
REVERT: E   77 ASP cc_start: 0.8962 (m-30) cc_final: 0.8720 (t0)
REVERT: F   24 ASP cc_start: 0.8266 (t0) cc_final: 0.7967 (t0)
REVERT: F   79 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7935 (ttmm)
REVERT: G   90 ASP cc_start: 0.8474 (t70) cc_final: 0.8206 (t0)
REVERT: G  119 LYS cc_start: 0.8569 (mptt) cc_final: 0.8275 (mmtt)
REVERT: H   31 ARG cc_start: 0.8383 (pmt170) cc_final: 0.7830 (ptt90)
REVERT: H   59 MET cc_start: 0.9167 (tpp) cc_final: 0.8596 (tpt)
REVERT: H  113 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8425 (tt0)
REVERT: O  190 MET cc_start: 0.6677 (ttp) cc_final: 0.6288 (tpp)
  outliers start: 16
  outliers final: 7
  residues processed: 132
  average time/residue: 0.7360
  time to fit residues: 103.5477
Evaluate side-chains
  123 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   57 LYS
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain E residue   63 ARG
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 112 optimal weight:    0.7980
   chunk 75 optimal weight:   10.0000
   chunk 108 optimal weight:   20.0000
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
B  25 ASN
C  38 ASN
H  63 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.104212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.067926 restraints weight = 35795.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 2.06
r_work: 0.3081 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  15008  Z= 0.244
  Angle     :  0.632   7.991  21731  Z= 0.375
  Chirality :  0.037   0.144   2447
  Planarity :  0.005   0.078   1565
  Dihedral  : 30.765 150.877   4803
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.43 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 15.79 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.28), residues: 863
  helix:  2.15 (0.21), residues: 584
  sheet: -1.30 (1.32), residues: 12
  loop : -0.10 (0.37), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  86 
 TYR   0.017   0.002   TYR B  88 
 PHE   0.008   0.001   PHE E  67 
 TRP   0.005   0.001   TRP O 214 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 (15008)
  covalent geometry    : angle       0.63166 (21731)
  hydrogen bonds       : bond        0.04312 (  853)
  hydrogen bonds       : angle       2.96748 ( 2112)

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8667 (p) cc_final: 0.8252 (t)
REVERT: A   76 GLN cc_start: 0.8184 (mt0) cc_final: 0.7697 (mt0)
REVERT: C   64 GLU cc_start: 0.7970 (tp30) cc_final: 0.7680 (mm-30)
REVERT: C   91 GLU cc_start: 0.7940 (tp30) cc_final: 0.7704 (tm-30)
REVERT: C   92 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8147 (mt-10)
REVERT: D   63 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8060 (m-40)
REVERT: D   71 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8295 (mt-10)
REVERT: D  108 LYS cc_start: 0.8266 (ptmm) cc_final: 0.7985 (ptpp)
REVERT: E   77 ASP cc_start: 0.8961 (m-30) cc_final: 0.8709 (t0)
REVERT: F   24 ASP cc_start: 0.8244 (t0) cc_final: 0.8035 (t0)
REVERT: G   90 ASP cc_start: 0.8497 (t70) cc_final: 0.8239 (t0)
REVERT: G   95 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8683 (ttpp)
REVERT: G  116 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8900 (mt)
REVERT: H   31 ARG cc_start: 0.8279 (pmt170) cc_final: 0.7873 (ptt90)
REVERT: H  101 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8739 (mm)
REVERT: H  113 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8475 (tt0)
REVERT: O  190 MET cc_start: 0.6676 (ttp) cc_final: 0.6199 (tpp)
  outliers start: 24
  outliers final: 11
  residues processed: 130
  average time/residue: 0.7580
  time to fit residues: 104.9706
Evaluate side-chains
  123 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 2 optimal weight:    0.5980
   chunk 72 optimal weight:    0.6980
   chunk 85 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 89 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0370
   chunk 117 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.106410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.070083 restraints weight = 35581.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.27
r_work: 0.3111 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15008  Z= 0.157
  Angle     :  0.602   8.790  21731  Z= 0.360
  Chirality :  0.035   0.175   2447
  Planarity :  0.004   0.079   1565
  Dihedral  : 30.612 148.837   4803
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.09 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.87 %
    Favored  : 81.11 %
  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 aren not related in a simple way.
  whole:  2.36 (0.28), residues: 863
  helix:  2.29 (0.21), residues: 590
  sheet: -1.09 (1.39), residues: 12
  loop :  0.06 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  86 
 TYR   0.026   0.001   TYR B  88 
 PHE   0.011   0.001   PHE E  67 
 TRP   0.027   0.003   TRP O 199 
 HIS   0.002   0.000   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (15008)
  covalent geometry    : angle       0.60172 (21731)
  hydrogen bonds       : bond        0.03711 (  853)
  hydrogen bonds       : angle       2.77218 ( 2112)

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8514 (mm-30)
REVERT: A   97 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7987 (mt-10)
REVERT: C   13 LYS cc_start: 0.9153 (tppp) cc_final: 0.8899 (tppp)
REVERT: C   91 GLU cc_start: 0.7851 (tp30) cc_final: 0.7581 (tm-30)
REVERT: D   63 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.7992 (m-40)
REVERT: D  108 LYS cc_start: 0.8025 (ptmm) cc_final: 0.7709 (ptpp)
REVERT: E   77 ASP cc_start: 0.8974 (m-30) cc_final: 0.8691 (t0)
REVERT: F   24 ASP cc_start: 0.8323 (t0) cc_final: 0.8096 (t0)
REVERT: G   90 ASP cc_start: 0.8293 (t70) cc_final: 0.7922 (t0)
REVERT: G  116 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8774 (mt)
REVERT: H   31 ARG cc_start: 0.8207 (pmt170) cc_final: 0.7921 (ptt90)
REVERT: H  113 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8407 (tt0)
  outliers start: 15
  outliers final: 6
  residues processed: 135
  average time/residue: 0.7438
  time to fit residues: 107.3405
Evaluate side-chains
  121 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 15 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 87 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C  38 ASN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.103423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.066996 restraints weight = 35772.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 2.05
r_work: 0.3066 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061  15008  Z= 0.290
  Angle     :  0.661   7.509  21731  Z= 0.389
  Chirality :  0.038   0.177   2447
  Planarity :  0.005   0.079   1565
  Dihedral  : 30.999 151.546   4803
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.43 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 20.24 %
    Favored  : 78.00 %
  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 aren not related in a simple way.
  whole:  1.96 (0.28), residues: 863
  helix:  2.03 (0.21), residues: 584
  sheet: -1.28 (1.37), residues: 12
  loop : -0.16 (0.37), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  86 
 TYR   0.026   0.002   TYR B  88 
 PHE   0.008   0.001   PHE H  65 
 TRP   0.007   0.002   TRP O 199 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00662 (15008)
  covalent geometry    : angle       0.66077 (21731)
  hydrogen bonds       : bond        0.04542 (  853)
  hydrogen bonds       : angle       3.11387 ( 2112)

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8189 (mt-10)
REVERT: C   64 GLU cc_start: 0.7976 (tp30) cc_final: 0.7715 (mm-30)
REVERT: C   91 GLU cc_start: 0.7950 (tp30) cc_final: 0.7709 (tm-30)
REVERT: D   63 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8069 (m-40)
REVERT: D   71 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8261 (mt-10)
REVERT: D  108 LYS cc_start: 0.8227 (ptmm) cc_final: 0.7919 (ptpp)
REVERT: E   77 ASP cc_start: 0.8986 (m-30) cc_final: 0.8695 (t0)
REVERT: G   90 ASP cc_start: 0.8463 (t70) cc_final: 0.8224 (t0)
REVERT: G  116 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8818 (mt)
REVERT: H   40 TYR cc_start: 0.8908 (m-80) cc_final: 0.8643 (m-80)
REVERT: H   76 GLU cc_start: 0.9144 (tp30) cc_final: 0.8812 (mm-30)
REVERT: H  113 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8450 (tt0)
REVERT: O  190 MET cc_start: 0.6768 (ttp) cc_final: 0.6347 (tpp)
  outliers start: 13
  outliers final: 8
  residues processed: 122
  average time/residue: 0.8273
  time to fit residues: 107.5915
Evaluate side-chains
  121 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 79 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0570
   chunk 80 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 114 optimal weight:    9.9990
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C  38 ASN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.106576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.070371 restraints weight = 35468.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 2.31
r_work: 0.3117 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  15008  Z= 0.160
  Angle     :  0.607  11.892  21731  Z= 0.360
  Chirality :  0.034   0.162   2447
  Planarity :  0.004   0.080   1565
  Dihedral  : 30.568 148.680   4803
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.32 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 20.51 %
    Favored  : 78.27 %
  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 aren not related in a simple way.
  whole:  2.34 (0.28), residues: 863
  helix:  2.28 (0.21), residues: 589
  sheet: -1.20 (1.38), residues: 12
  loop :  0.05 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  86 
 TYR   0.029   0.001   TYR B  88 
 PHE   0.013   0.001   PHE E  67 
 TRP   0.007   0.001   TRP O 214 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (15008)
  covalent geometry    : angle       0.60663 (21731)
  hydrogen bonds       : bond        0.03648 (  853)
  hydrogen bonds       : angle       2.74340 ( 2112)

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8411 (p) cc_final: 0.8059 (t)
REVERT: C   91 GLU cc_start: 0.7901 (tp30) cc_final: 0.7678 (tm-30)
REVERT: D   63 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8071 (m-40)
REVERT: D   71 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8196 (mt-10)
REVERT: D  108 LYS cc_start: 0.8085 (ptmm) cc_final: 0.7763 (ptpp)
REVERT: E   77 ASP cc_start: 0.8958 (m-30) cc_final: 0.8697 (t0)
REVERT: F   24 ASP cc_start: 0.8293 (t0) cc_final: 0.7926 (t0)
REVERT: G   90 ASP cc_start: 0.8360 (t70) cc_final: 0.8057 (t0)
REVERT: G  116 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8691 (mt)
REVERT: H   40 TYR cc_start: 0.8645 (m-80) cc_final: 0.8302 (m-80)
REVERT: O  190 MET cc_start: 0.6665 (ttp) cc_final: 0.6260 (tpp)
  outliers start: 9
  outliers final: 4
  residues processed: 125
  average time/residue: 0.8431
  time to fit residues: 112.1626
Evaluate side-chains
  122 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 116
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 115 optimal weight:   10.0000
   chunk 109 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 114 optimal weight:    6.9990
   chunk 89 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0570
   chunk 16 optimal weight:    0.0040
   chunk 48 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.9112

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 168 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.106194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.070101 restraints weight = 35488.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.26
r_work: 0.3110 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  15008  Z= 0.175
  Angle     :  0.603   8.369  21731  Z= 0.359
  Chirality :  0.034   0.164   2447
  Planarity :  0.004   0.080   1565
  Dihedral  : 30.594 149.507   4803
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.20 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 21.46 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.28), residues: 863
  helix:  2.30 (0.21), residues: 590
  sheet: -1.00 (1.41), residues: 12
  loop :  0.07 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  86 
 TYR   0.034   0.001   TYR B  88 
 PHE   0.011   0.001   PHE E  67 
 TRP   0.008   0.001   TRP O 214 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (15008)
  covalent geometry    : angle       0.60324 (21731)
  hydrogen bonds       : bond        0.03648 (  853)
  hydrogen bonds       : angle       2.78271 ( 2112)

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8402 (p) cc_final: 0.8057 (t)
REVERT: C   50 TYR cc_start: 0.8954 (t80) cc_final: 0.8702 (t80)
REVERT: D   63 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8074 (m-40)
REVERT: D   71 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8216 (mt-10)
REVERT: D  108 LYS cc_start: 0.8033 (ptmm) cc_final: 0.7713 (ptpp)
REVERT: E   77 ASP cc_start: 0.8970 (m-30) cc_final: 0.8729 (t0)
REVERT: F   24 ASP cc_start: 0.8226 (t0) cc_final: 0.7968 (t0)
REVERT: G   90 ASP cc_start: 0.8359 (t70) cc_final: 0.8090 (t0)
REVERT: G  116 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8635 (mt)
REVERT: H   31 ARG cc_start: 0.8220 (pmt170) cc_final: 0.7741 (ttp-170)
REVERT: H   40 TYR cc_start: 0.8765 (m-80) cc_final: 0.8465 (m-80)
REVERT: O  190 MET cc_start: 0.6753 (ttp) cc_final: 0.6180 (tpp)
REVERT: O  215 GLN cc_start: 0.7087 (pp30) cc_final: 0.6879 (pp30)
  outliers start: 8
  outliers final: 5
  residues processed: 123
  average time/residue: 0.7868
  time to fit residues: 103.1682
Evaluate side-chains
  121 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   chunk 112 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 109 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 116 optimal weight:   20.0000
   chunk 56 optimal weight:    0.6980
   chunk 110 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.106058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.069956 restraints weight = 35671.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 2.28
r_work: 0.3128 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  15008  Z= 0.186
  Angle     :  0.624  11.804  21731  Z= 0.366
  Chirality :  0.035   0.168   2447
  Planarity :  0.004   0.080   1565
  Dihedral  : 30.614 149.573   4803
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.32 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 22.13 %
    Favored  : 76.65 %
  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 aren not related in a simple way.
  whole:  2.30 (0.28), residues: 863
  helix:  2.23 (0.21), residues: 590
  sheet: -0.97 (1.40), residues: 12
  loop :  0.05 (0.38), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  86 
 TYR   0.036   0.002   TYR B  88 
 PHE   0.010   0.001   PHE E  67 
 TRP   0.007   0.001   TRP O 214 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (15008)
  covalent geometry    : angle       0.62440 (21731)
  hydrogen bonds       : bond        0.03722 (  853)
  hydrogen bonds       : angle       2.81441 ( 2112)

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8329 (p) cc_final: 0.8011 (t)
REVERT: C   50 TYR cc_start: 0.9037 (t80) cc_final: 0.8781 (t80)
REVERT: D   63 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8085 (m-40)
REVERT: D   71 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8205 (mt-10)
REVERT: D  108 LYS cc_start: 0.8059 (ptmm) cc_final: 0.7728 (ptpp)
REVERT: E   77 ASP cc_start: 0.8964 (m-30) cc_final: 0.8728 (t0)
REVERT: G   90 ASP cc_start: 0.8366 (t70) cc_final: 0.8067 (t0)
REVERT: G  116 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8699 (mt)
REVERT: H   31 ARG cc_start: 0.8286 (pmt170) cc_final: 0.7663 (ttp-170)
REVERT: H   40 TYR cc_start: 0.8768 (m-80) cc_final: 0.8477 (m-80)
REVERT: H  113 GLU cc_start: 0.8374 (tt0) cc_final: 0.7970 (tm-30)
REVERT: H  115 THR cc_start: 0.9221 (m) cc_final: 0.9008 (p)
REVERT: O  190 MET cc_start: 0.6654 (ttp) cc_final: 0.6244 (tpp)
REVERT: O  253 MET cc_start: 0.5454 (tpt) cc_final: 0.1631 (mtt)
  outliers start: 9
  outliers final: 6
  residues processed: 122
  average time/residue: 0.8038
  time to fit residues: 104.4200
Evaluate side-chains
  123 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0030
   chunk 13 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.106533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.070518 restraints weight = 35438.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 2.27
r_work: 0.3138 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  15008  Z= 0.164
  Angle     :  0.632  12.874  21731  Z= 0.367
  Chirality :  0.034   0.198   2447
  Planarity :  0.004   0.080   1565
  Dihedral  : 30.595 149.358   4803
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.20 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 22.40 %
    Favored  : 76.52 %
  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 aren not related in a simple way.
  whole:  2.34 (0.28), residues: 863
  helix:  2.26 (0.21), residues: 590
  sheet: -1.02 (1.38), residues: 12
  loop :  0.09 (0.38), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  86 
 TYR   0.045   0.002   TYR B  88 
 PHE   0.010   0.001   PHE E  67 
 TRP   0.007   0.002   TRP O 199 
 HIS   0.002   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (15008)
  covalent geometry    : angle       0.63225 (21731)
  hydrogen bonds       : bond        0.03632 (  853)
  hydrogen bonds       : angle       2.78360 ( 2112)

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8280 (p) cc_final: 0.7973 (t)
REVERT: C   50 TYR cc_start: 0.8991 (t80) cc_final: 0.8746 (t80)
REVERT: D   63 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8061 (m-40)
REVERT: D   71 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8193 (mt-10)
REVERT: D  108 LYS cc_start: 0.8095 (ptmm) cc_final: 0.7753 (ptpp)
REVERT: E   77 ASP cc_start: 0.8963 (m-30) cc_final: 0.8725 (t0)
REVERT: F   24 ASP cc_start: 0.8131 (t0) cc_final: 0.7841 (t0)
REVERT: G   90 ASP cc_start: 0.8352 (t70) cc_final: 0.8048 (t0)
REVERT: H   31 ARG cc_start: 0.8266 (pmt170) cc_final: 0.7647 (ttp-170)
REVERT: H   40 TYR cc_start: 0.8738 (m-80) cc_final: 0.8401 (m-80)
REVERT: H   76 GLU cc_start: 0.9160 (tp30) cc_final: 0.8868 (mm-30)
REVERT: H  113 GLU cc_start: 0.8358 (tt0) cc_final: 0.7962 (tm-30)
REVERT: H  115 THR cc_start: 0.9224 (m) cc_final: 0.9012 (p)
REVERT: O  190 MET cc_start: 0.6624 (ttp) cc_final: 0.6215 (tpp)
REVERT: O  253 MET cc_start: 0.5309 (tpt) cc_final: 0.1405 (mtt)
  outliers start: 8
  outliers final: 5
  residues processed: 121
  average time/residue: 0.8666
  time to fit residues: 111.8479
Evaluate side-chains
  119 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 58 optimal weight:    0.5980
   chunk 69 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 55 optimal weight:    0.4980
   chunk 60 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.106987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.071155 restraints weight = 35336.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.28
r_work: 0.3134 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  15008  Z= 0.162
  Angle     :  0.631  11.511  21731  Z= 0.368
  Chirality :  0.034   0.181   2447
  Planarity :  0.004   0.080   1565
  Dihedral  : 30.514 149.009   4803
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.20 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 22.54 %
    Favored  : 76.25 %
  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 aren not related in a simple way.
  whole:  2.37 (0.28), residues: 863
  helix:  2.28 (0.21), residues: 590
  sheet: -1.07 (1.38), residues: 12
  loop :  0.11 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  86 
 TYR   0.045   0.002   TYR B  88 
 PHE   0.011   0.001   PHE E  67 
 TRP   0.009   0.002   TRP O 214 
 HIS   0.002   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (15008)
  covalent geometry    : angle       0.63063 (21731)
  hydrogen bonds       : bond        0.03567 (  853)
  hydrogen bonds       : angle       2.78438 ( 2112)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5114.50 seconds
wall clock time: 87 minutes 27.16 seconds (5247.16 seconds total)