Starting phenix.real_space_refine
on Fri Aug 22 19:18:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8umc_42375/08_2025/8umc_42375.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8umc_42375/08_2025/8umc_42375.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8umc_42375/08_2025/8umc_42375.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8umc_42375/08_2025/8umc_42375.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8umc_42375/08_2025/8umc_42375.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8umc_42375/08_2025/8umc_42375.cif"
  }
  resolution = 2.5
  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=   0.021
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
     Mn      2      7.51       5
     S      54      5.16       5
     C    4564      2.51       5
     N    1270      2.21       5
     O    1308      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 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: 7198
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 322, 2630
          Classifications: {'peptide': 322}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 307}
    Chain: "B"
      Number of atoms: 968
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 968
          Classifications: {'peptide': 123}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 114}
    Chain: "C"
      Number of atoms: 2630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 322, 2630
          Classifications: {'peptide': 322}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 307}
    Chain: "D"
      Number of atoms: 968
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 968
          Classifications: {'peptide': 123}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 114}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.68, per 1000 atoms: 0.23
  Number of scatterers: 7198
  At special positions: 0
  Unit cell: (107.06, 80.8, 82.82, 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)
     Mn      2     24.99
     S      54     16.00
     O    1308      8.00
     N    1270      7.00
     C    4564      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: 0.57
  Conformation dependent library (CDL) restraints added in 305.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1644

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 9 sheets defined
      43.5% alpha, 17.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 21
    Processing helix  chain 'A' and resid 25 through 36
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 56 through 71
    Processing helix  chain 'A' and resid 92 through 111
      removed outlier: 3.563A  pdb=" N   GLU A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ASP A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 129
    Processing helix  chain 'A' and resid 129 through 137
    Processing helix  chain 'A' and resid 152 through 164
      removed outlier: 3.770A  pdb=" N   ARG A 164 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 180
      removed outlier: 3.860A  pdb=" N   THR A 180 " --> pdb=" O   GLY A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 194
    Processing helix  chain 'A' and resid 197 through 210
    Processing helix  chain 'A' and resid 213 through 225
    Processing helix  chain 'A' and resid 227 through 240
      removed outlier: 4.030A  pdb=" N   LEU A 237 " --> pdb=" O   ALA A 233 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   ARG A 238 " --> pdb=" O   ALA A 234 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   HIS A 239 " --> pdb=" O   GLU A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 250
    Processing helix  chain 'A' and resid 279 through 286
    Processing helix  chain 'A' and resid 309 through 325
    Processing helix  chain 'B' and resid 34 through 36
      No H-bonds generated for 'chain 'B' and resid 34 through 36'
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 65 through 69
      removed outlier: 4.367A  pdb=" N   ASP B  68 " --> pdb=" O   ALA B  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 15 through 21
    Processing helix  chain 'C' and resid 25 through 37
    Processing helix  chain 'C' and resid 44 through 49
    Processing helix  chain 'C' and resid 56 through 71
      removed outlier: 3.658A  pdb=" N   TYR C  60 " --> pdb=" O   ASP C  56 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASP C  61 " --> pdb=" O   ASP C  57 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 111
      removed outlier: 3.659A  pdb=" N   ASP C 103 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ARG C 109 " --> pdb=" O   ARG C 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 129
    Processing helix  chain 'C' and resid 129 through 137
      removed outlier: 3.685A  pdb=" N   SER C 136 " --> pdb=" O   HIS C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 152 through 162
    Processing helix  chain 'C' and resid 176 through 179
    Processing helix  chain 'C' and resid 184 through 194
    Processing helix  chain 'C' and resid 197 through 211
    Processing helix  chain 'C' and resid 213 through 224
    Processing helix  chain 'C' and resid 227 through 240
      removed outlier: 3.996A  pdb=" N   LEU C 237 " --> pdb=" O   ALA C 233 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   ARG C 238 " --> pdb=" O   ALA C 234 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   HIS C 239 " --> pdb=" O   GLU C 235 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 250
      removed outlier: 3.526A  pdb=" N   GLU C 250 " --> pdb=" O   ARG C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 251 through 255
    Processing helix  chain 'C' and resid 279 through 287
    Processing helix  chain 'C' and resid 298 through 303
    Processing helix  chain 'C' and resid 309 through 325
    Processing helix  chain 'D' and resid 49 through 51
      No H-bonds generated for 'chain 'D' and resid 49 through 51'
    Processing helix  chain 'D' and resid 65 through 67
      No H-bonds generated for 'chain 'D' and resid 65 through 67'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 174
      removed outlier: 6.093A  pdb=" N   ILE A 115 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   GLU A 143 " --> pdb=" O   ILE A 115 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   VAL A 117 " --> pdb=" O   GLU A 143 " (cutoff:3.500A)
      removed outlier: 9.727A  pdb=" N   VAL A 114 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL A  75 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   ARG A 116 " --> pdb=" O   VAL A  75 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   HIS A  77 " --> pdb=" O   ARG A 116 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   ILE A  41 " --> pdb=" O   VAL A  75 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   HIS A  77 " --> pdb=" O   ILE A  41 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   SER A  43 " --> pdb=" O   HIS A  77 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLY A  40 " --> pdb=" O   ARG A   8 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   LYS A   7 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   SER A 294 " --> pdb=" O   LYS A   7 " (cutoff:3.500A)
      removed outlier: 7.612A  pdb=" N   GLY A   9 " --> pdb=" O   SER A 294 " (cutoff:3.500A)
      removed outlier: 8.388A  pdb=" N   TYR A 296 " --> pdb=" O   GLY A   9 " (cutoff:3.500A)
      removed outlier: 8.631A  pdb=" N   SER A  11 " --> pdb=" O   TYR A 296 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   VAL A 258 " --> pdb=" O   ALA A 293 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   GLU A 295 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ALA A 260 " --> pdb=" O   GLU A 295 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 15
    Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 23
    Processing sheet with id=AA4, first strand: chain 'B' and resid 31 through 32
    Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 48
      removed outlier: 4.707A  pdb=" N   VAL B  41 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   GLY B  94 " --> pdb=" O   LEU B 123 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 170 through 174
      removed outlier: 6.707A  pdb=" N   LEU C 140 " --> pdb=" O   GLY C 171 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ILE C 173 " --> pdb=" O   LEU C 140 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   LEU C 142 " --> pdb=" O   ILE C 173 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   ILE C 115 " --> pdb=" O   GLY C 141 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   GLU C 143 " --> pdb=" O   ILE C 115 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   VAL C 117 " --> pdb=" O   GLU C 143 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   ILE C  41 " --> pdb=" O   VAL C  75 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   HIS C  77 " --> pdb=" O   ILE C  41 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   SER C  43 " --> pdb=" O   HIS C  77 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLY C  40 " --> pdb=" O   ARG C   8 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   LYS C   7 " --> pdb=" O   LEU C 292 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   SER C 294 " --> pdb=" O   LYS C   7 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   GLY C   9 " --> pdb=" O   SER C 294 " (cutoff:3.500A)
      removed outlier: 8.371A  pdb=" N   TYR C 296 " --> pdb=" O   GLY C   9 " (cutoff:3.500A)
      removed outlier: 8.331A  pdb=" N   SER C  11 " --> pdb=" O   TYR C 296 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 13 through 15
      removed outlier: 3.543A  pdb=" N   THR D  84 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 31 through 32
    Processing sheet with id=AA9, first strand: chain 'D' and resid 46 through 47
      removed outlier: 3.529A  pdb=" N   GLU D  46 " --> pdb=" O   VAL D  43 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL D  43 " --> pdb=" O   GLU D  46 " (cutoff:3.500A)

    305 hydrogen bonds defined for protein.
    834 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.80

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2438
        1.34 -     1.46: 1331
        1.46 -     1.57: 3499
        1.57 -     1.69: 0
        1.69 -     1.81: 100
  Bond restraints: 7368
  Sorted by residual:
  bond pdb=" N   VAL A 101 "
       pdb=" CA  VAL A 101 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.036 1.19e-02 7.06e+03 9.01e+00
  bond pdb=" N   ILE A 104 "
       pdb=" CA  ILE A 104 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 7.76e+00
  bond pdb=" N   ASP A 266 "
       pdb=" CA  ASP A 266 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.34e-02 5.57e+03 7.07e+00
  bond pdb=" N   GLN C 268 "
       pdb=" CA  GLN C 268 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.18e-02 7.18e+03 6.98e+00
  bond pdb=" N   HIS A 145 "
       pdb=" CA  HIS A 145 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.18e-02 7.18e+03 6.86e+00
  ... (remaining 7363 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 9339
        1.26 -     2.53: 487
        2.53 -     3.79: 104
        3.79 -     5.05: 21
        5.05 -     6.32: 3
  Bond angle restraints: 9954
  Sorted by residual:
  angle pdb=" N   PRO A 147 "
        pdb=" CA  PRO A 147 "
        pdb=" CB  PRO A 147 "
      ideal   model   delta    sigma   weight residual
     103.25   96.93    6.32 1.05e+00 9.07e-01 3.62e+01
  angle pdb=" CA  ILE A 302 "
        pdb=" C   ILE A 302 "
        pdb=" O   ILE A 302 "
      ideal   model   delta    sigma   weight residual
     122.63  118.54    4.09 8.70e-01 1.32e+00 2.21e+01
  angle pdb=" N   MET C 320 "
        pdb=" CA  MET C 320 "
        pdb=" C   MET C 320 "
      ideal   model   delta    sigma   weight residual
     111.14  106.07    5.07 1.08e+00 8.57e-01 2.20e+01
  angle pdb=" CA  ASP C 266 "
        pdb=" C   ASP C 266 "
        pdb=" O   ASP C 266 "
      ideal   model   delta    sigma   weight residual
     122.01  118.23    3.78 1.05e+00 9.07e-01 1.30e+01
  angle pdb=" CA  ASP A 266 "
        pdb=" C   ASP A 266 "
        pdb=" O   ASP A 266 "
      ideal   model   delta    sigma   weight residual
     122.01  118.28    3.73 1.05e+00 9.07e-01 1.26e+01
  ... (remaining 9949 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.28: 4078
       26.28 -    52.56: 288
       52.56 -    78.84: 47
       78.84 -   105.12: 10
      105.12 -   131.40: 1
  Dihedral angle restraints: 4424
    sinusoidal: 1862
      harmonic: 2562
  Sorted by residual:
  dihedral pdb=" CA  ALA A 146 "
           pdb=" C   ALA A 146 "
           pdb=" N   PRO A 147 "
           pdb=" CA  PRO A 147 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   48.60  131.40     0      5.00e+00 4.00e-02 6.91e+02
  dihedral pdb=" CA  ARG C 193 "
           pdb=" C   ARG C 193 "
           pdb=" N   GLN C 194 "
           pdb=" CA  GLN C 194 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.55   18.45     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  ARG C 105 "
           pdb=" C   ARG C 105 "
           pdb=" N   HIS C 106 "
           pdb=" CA  HIS C 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.20   17.80     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 4421 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 801
       0.049 -    0.098: 192
       0.098 -    0.147: 55
       0.147 -    0.197: 6
       0.197 -    0.246: 2
  Chirality restraints: 1056
  Sorted by residual:
  chirality pdb=" CA  MET C 320 "
            pdb=" N   MET C 320 "
            pdb=" C   MET C 320 "
            pdb=" CB  MET C 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CA  ARG A 102 "
            pdb=" N   ARG A 102 "
            pdb=" C   ARG A 102 "
            pdb=" CB  ARG A 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  VAL B  15 "
            pdb=" N   VAL B  15 "
            pdb=" C   VAL B  15 "
            pdb=" CB  VAL B  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.17e-01
  ... (remaining 1053 not shown)

  Planarity restraints: 1310
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 210 "    0.313 9.50e-02 1.11e+02   1.40e-01 1.21e+01
        pdb=" NE  ARG A 210 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 210 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 210 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 210 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 254 "    0.248 9.50e-02 1.11e+02   1.11e-01 7.56e+00
        pdb=" NE  ARG A 254 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 254 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 254 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 254 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 270 "    0.178 9.50e-02 1.11e+02   7.99e-02 4.29e+00
        pdb=" NE  ARG A 270 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 270 "    0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 270 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 270 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1307 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.62: 113
        2.62 -     3.19: 6478
        3.19 -     3.76: 11573
        3.76 -     4.33: 17203
        4.33 -     4.90: 27913
  Nonbonded interactions: 63280
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  27 "
            pdb=" OH  TYR B 108 "
     model   vdw
     2.045 3.040
  nonbonded pdb=" OH  TYR D  28 "
            pdb=" OH  TYR D 108 "
     model   vdw
     2.048 3.040
  nonbonded pdb=" OE1 GLU A 295 "
            pdb="MN    MN A 401 "
     model   vdw
     2.101 2.320
  nonbonded pdb=" OE1 GLU C 295 "
            pdb="MN    MN C 401 "
     model   vdw
     2.115 2.320
  nonbonded pdb=" O   LYS C 261 "
            pdb=" OH  TYR C 276 "
     model   vdw
     2.133 3.040
  ... (remaining 63275 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             1.280
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.490
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
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   0.039   7368  Z= 0.289
  Angle     :  0.683   6.318   9954  Z= 0.420
  Chirality :  0.048   0.246   1056
  Planarity :  0.007   0.140   1310
  Dihedral  : 17.532 131.399   2780
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 19.51 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -0.80 (0.28), residues: 882
  helix:  0.14 (0.28), residues: 344
  sheet: -1.05 (0.42), residues: 154
  loop : -0.79 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 270 
 TYR   0.014   0.001   TYR A  13 
 PHE   0.012   0.002   PHE C  20 
 TRP   0.007   0.001   TRP A 242 
 HIS   0.006   0.001   HIS C 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 7368)
  covalent geometry    : angle       0.68272 ( 9954)
  hydrogen bonds       : bond        0.15222 (  305)
  hydrogen bonds       : angle       6.77669 (  834)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 214
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  241 ASN cc_start: 0.8181 (p0) cc_final: 0.7918 (p0)
  outliers start: 9
  outliers final: 5
  residues processed: 221
  average time/residue: 0.5501
  time to fit residues: 127.3280
Evaluate side-chains
  214 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 209
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   27 GLU
Chi-restraints excluded: chain C residue   54 ASN
Chi-restraints excluded: chain D residue   62 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0870
   chunk 65 optimal weight:    0.0670
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.3980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0870
   overall best weight:    0.2474

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.135522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.126252 restraints weight = 9064.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 1.30
r_work: 0.3611 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3482 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.1432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7368  Z= 0.122
  Angle     :  0.549   5.017   9954  Z= 0.287
  Chirality :  0.043   0.168   1056
  Planarity :  0.004   0.052   1310
  Dihedral  :  5.414  62.848   1004
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.77 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -0.18 (0.29), residues: 882
  helix:  0.78 (0.29), residues: 334
  sheet: -0.97 (0.43), residues: 154
  loop : -0.42 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 270 
 TYR   0.013   0.001   TYR D  28 
 PHE   0.011   0.001   PHE A 150 
 TRP   0.006   0.001   TRP B  75 
 HIS   0.004   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7368)
  covalent geometry    : angle       0.54879 ( 9954)
  hydrogen bonds       : bond        0.03450 (  305)
  hydrogen bonds       : angle       5.36960 (  834)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 219
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 LYS cc_start: 0.8126 (mptt) cc_final: 0.7908 (mttp)
REVERT: A   61 ASP cc_start: 0.7513 (m-30) cc_final: 0.7247 (m-30)
REVERT: C  241 ASN cc_start: 0.8101 (p0) cc_final: 0.7875 (p0)
REVERT: C  308 VAL cc_start: 0.8492 (t) cc_final: 0.8284 (p)
REVERT: D   29 ARG cc_start: 0.8598 (ptt90) cc_final: 0.8373 (ptt90)
  outliers start: 27
  outliers final: 12
  residues processed: 231
  average time/residue: 0.5319
  time to fit residues: 128.9053
Evaluate side-chains
  219 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 207
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  161 PHE
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   54 ASN
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  126 MET
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain C residue  303 GLN
Chi-restraints excluded: chain D residue   40 ASP
Chi-restraints excluded: chain D residue   43 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 57 optimal weight:    0.2980
   chunk 24 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 60 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 241 ASN
C  96 GLN
C 313 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.133079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.123638 restraints weight = 8939.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 1.29
r_work: 0.3581 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3453 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7368  Z= 0.180
  Angle     :  0.578   5.345   9954  Z= 0.299
  Chirality :  0.044   0.164   1056
  Planarity :  0.005   0.104   1310
  Dihedral  :  5.350  57.544   1000
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 21.06 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -0.12 (0.29), residues: 882
  helix:  0.86 (0.29), residues: 334
  sheet: -1.12 (0.42), residues: 162
  loop : -0.29 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 102 
 TYR   0.009   0.001   TYR C  13 
 PHE   0.014   0.002   PHE C  20 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.003   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 7368)
  covalent geometry    : angle       0.57780 ( 9954)
  hydrogen bonds       : bond        0.03582 (  305)
  hydrogen bonds       : angle       5.20106 (  834)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 211
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 LYS cc_start: 0.8156 (mptt) cc_final: 0.7917 (mttp)
REVERT: A   61 ASP cc_start: 0.7522 (m-30) cc_final: 0.7222 (m-30)
REVERT: C   49 MET cc_start: 0.8559 (mtt) cc_final: 0.8224 (mtt)
REVERT: C  203 TYR cc_start: 0.8206 (t80) cc_final: 0.7837 (t80)
REVERT: C  241 ASN cc_start: 0.8137 (p0) cc_final: 0.7903 (p0)
  outliers start: 30
  outliers final: 14
  residues processed: 228
  average time/residue: 0.6052
  time to fit residues: 144.1542
Evaluate side-chains
  222 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 208
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  158 HIS
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   54 ASN
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  243 SER
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain D residue   40 ASP
Chi-restraints excluded: chain D residue  111 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0030
   chunk 80 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 74 optimal weight:    0.2980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.4590

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 241 ASN
C  96 GLN
C 303 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.134430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.124934 restraints weight = 9064.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 1.31
r_work: 0.3595 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3467 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7368  Z= 0.147
  Angle     :  0.556   5.435   9954  Z= 0.288
  Chirality :  0.043   0.159   1056
  Planarity :  0.005   0.104   1310
  Dihedral  :  5.205  53.061   1000
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 20.41 %
    Favored  : 75.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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:  0.03 (0.29), residues: 882
  helix:  0.99 (0.29), residues: 334
  sheet: -1.03 (0.43), residues: 166
  loop : -0.22 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 102 
 TYR   0.016   0.001   TYR A  13 
 PHE   0.012   0.001   PHE C  20 
 TRP   0.008   0.001   TRP A  63 
 HIS   0.003   0.001   HIS C 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 7368)
  covalent geometry    : angle       0.55618 ( 9954)
  hydrogen bonds       : bond        0.03300 (  305)
  hydrogen bonds       : angle       5.07737 (  834)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 217
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 LYS cc_start: 0.8126 (mptt) cc_final: 0.7892 (mttp)
REVERT: A   28 ASP cc_start: 0.8117 (m-30) cc_final: 0.7815 (m-30)
REVERT: A   61 ASP cc_start: 0.7505 (m-30) cc_final: 0.7279 (m-30)
REVERT: A  300 ARG cc_start: 0.7970 (ptp-170) cc_final: 0.7768 (ptp-170)
REVERT: C  161 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7841 (t80)
REVERT: C  187 MET cc_start: 0.8101 (mtt) cc_final: 0.7793 (mtp)
REVERT: C  241 ASN cc_start: 0.8099 (p0) cc_final: 0.7892 (p0)
REVERT: C  284 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8689 (mtmm)
  outliers start: 32
  outliers final: 19
  residues processed: 235
  average time/residue: 0.5720
  time to fit residues: 140.9016
Evaluate side-chains
  234 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 213
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  158 HIS
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   44 ASP
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   54 ASN
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  161 PHE
Chi-restraints excluded: chain C residue  243 SER
Chi-restraints excluded: chain C residue  284 LYS
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain D residue   40 ASP
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  123 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 87 optimal weight:    0.0050
   chunk 16 optimal weight:    0.0470
   chunk 35 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0980
   chunk 48 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.3492

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 241 ASN
A 303 GLN
C  96 GLN
C 303 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.135078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.125646 restraints weight = 8972.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 1.31
r_work: 0.3609 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3482 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7368  Z= 0.129
  Angle     :  0.550   6.008   9954  Z= 0.284
  Chirality :  0.043   0.156   1056
  Planarity :  0.005   0.105   1310
  Dihedral  :  5.027  47.649   1000
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 23.00 %
    Favored  : 74.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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:  0.19 (0.30), residues: 882
  helix:  1.11 (0.29), residues: 334
  sheet: -0.98 (0.43), residues: 166
  loop : -0.09 (0.34), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 102 
 TYR   0.009   0.001   TYR D  28 
 PHE   0.018   0.001   PHE A  59 
 TRP   0.010   0.001   TRP A  63 
 HIS   0.003   0.001   HIS C 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7368)
  covalent geometry    : angle       0.55004 ( 9954)
  hydrogen bonds       : bond        0.03083 (  305)
  hydrogen bonds       : angle       4.98131 (  834)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 215
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A    7 LYS cc_start: 0.8104 (mptt) cc_final: 0.7876 (mttp)
REVERT: A   28 ASP cc_start: 0.8100 (m-30) cc_final: 0.7804 (m-30)
REVERT: A   61 ASP cc_start: 0.7538 (m-30) cc_final: 0.7307 (m-30)
REVERT: A  246 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7714 (mmm160)
REVERT: B   29 ARG cc_start: 0.8644 (ptt90) cc_final: 0.8301 (ptt-90)
REVERT: C  187 MET cc_start: 0.8103 (mtt) cc_final: 0.7844 (mtm)
REVERT: C  203 TYR cc_start: 0.8181 (t80) cc_final: 0.7872 (t80)
REVERT: C  232 ARG cc_start: 0.8294 (ttp80) cc_final: 0.8017 (ttm110)
  outliers start: 23
  outliers final: 15
  residues processed: 230
  average time/residue: 0.6260
  time to fit residues: 150.3070
Evaluate side-chains
  224 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 208
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  158 HIS
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   44 ASP
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain D residue   38 THR
Chi-restraints excluded: chain D residue   40 ASP
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  123 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 60 optimal weight:    0.0030
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 199 HIS
A 241 ASN
C  96 GLN
C 303 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.133383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.123782 restraints weight = 9080.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 1.32
r_work: 0.3574 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3445 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7368  Z= 0.197
  Angle     :  0.591   6.013   9954  Z= 0.305
  Chirality :  0.045   0.154   1056
  Planarity :  0.005   0.095   1310
  Dihedral  :  5.139  48.205    998
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 23.39 %
    Favored  : 72.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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:  0.21 (0.29), residues: 882
  helix:  1.04 (0.29), residues: 334
  sheet: -0.74 (0.45), residues: 154
  loop : -0.13 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 102 
 TYR   0.017   0.002   TYR D 108 
 PHE   0.016   0.002   PHE C  20 
 TRP   0.010   0.001   TRP A  63 
 HIS   0.005   0.001   HIS C 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 7368)
  covalent geometry    : angle       0.59079 ( 9954)
  hydrogen bonds       : bond        0.03449 (  305)
  hydrogen bonds       : angle       5.05336 (  834)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 211
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8172 (mptt) cc_final: 0.7925 (mttp)
REVERT: A   61 ASP cc_start: 0.7556 (m-30) cc_final: 0.7304 (m-30)
REVERT: A  246 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7790 (mmm160)
REVERT: A  300 ARG cc_start: 0.7960 (ptp-170) cc_final: 0.7756 (ptp-170)
REVERT: C  203 TYR cc_start: 0.8234 (t80) cc_final: 0.7948 (t80)
REVERT: C  205 ARG cc_start: 0.8187 (mtp180) cc_final: 0.7912 (mtm180)
REVERT: C  232 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8088 (ttm110)
  outliers start: 31
  outliers final: 18
  residues processed: 230
  average time/residue: 0.5484
  time to fit residues: 132.1984
Evaluate side-chains
  230 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 211
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  158 HIS
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   44 ASP
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  161 PHE
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain D residue   38 THR
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  123 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 66 optimal weight:    0.0770
   chunk 72 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0870
   chunk 59 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0970
   chunk 0 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.3314

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 244 ASN
A 303 GLN
C  96 GLN
C 241 ASN
C 303 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.135068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.125601 restraints weight = 9101.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 1.32
r_work: 0.3606 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3479 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7368  Z= 0.129
  Angle     :  0.548   6.111   9954  Z= 0.283
  Chirality :  0.043   0.153   1056
  Planarity :  0.005   0.088   1310
  Dihedral  :  4.915  43.665    998
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 25.45 %
    Favored  : 71.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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:  0.27 (0.30), residues: 882
  helix:  1.16 (0.29), residues: 334
  sheet: -0.91 (0.43), residues: 166
  loop : -0.03 (0.34), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 102 
 TYR   0.017   0.001   TYR D 108 
 PHE   0.013   0.001   PHE A  80 
 TRP   0.011   0.001   TRP A  63 
 HIS   0.003   0.001   HIS C 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7368)
  covalent geometry    : angle       0.54780 ( 9954)
  hydrogen bonds       : bond        0.02996 (  305)
  hydrogen bonds       : angle       4.96348 (  834)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 212
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: A    7 LYS cc_start: 0.8113 (mptt) cc_final: 0.7873 (mttp)
REVERT: A   61 ASP cc_start: 0.7571 (m-30) cc_final: 0.7318 (m-30)
REVERT: A  246 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7718 (mmm160)
REVERT: B   29 ARG cc_start: 0.8532 (ptm-80) cc_final: 0.8221 (ptt-90)
REVERT: C   48 MET cc_start: 0.8687 (mtt) cc_final: 0.8222 (mtt)
REVERT: C   49 MET cc_start: 0.8382 (mtt) cc_final: 0.7735 (mtt)
REVERT: C  203 TYR cc_start: 0.8182 (t80) cc_final: 0.7872 (t80)
REVERT: C  232 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8112 (ttm110)
REVERT: C  236 MET cc_start: 0.8809 (mtt) cc_final: 0.8392 (mtt)
  outliers start: 23
  outliers final: 17
  residues processed: 226
  average time/residue: 0.5775
  time to fit residues: 136.6812
Evaluate side-chains
  226 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 208
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  158 HIS
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   54 ASN
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  161 PHE
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain D residue   40 ASP
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  123 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0000
   chunk 59 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0970
   chunk 43 optimal weight:    0.6980
   chunk 3 optimal weight:    0.1980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.3182

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 145 HIS
C  96 GLN
C 303 GLN
C 313 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.136244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.126785 restraints weight = 9092.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 1.32
r_work: 0.3616 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3489 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7368  Z= 0.125
  Angle     :  0.548   5.581   9954  Z= 0.282
  Chirality :  0.043   0.152   1056
  Planarity :  0.005   0.085   1310
  Dihedral  :  4.829  43.039    998
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 24.55 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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:  0.30 (0.30), residues: 882
  helix:  1.21 (0.29), residues: 334
  sheet: -0.88 (0.43), residues: 166
  loop : -0.06 (0.34), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 102 
 TYR   0.017   0.001   TYR A  13 
 PHE   0.013   0.001   PHE A  80 
 TRP   0.010   0.001   TRP A  63 
 HIS   0.004   0.001   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 7368)
  covalent geometry    : angle       0.54808 ( 9954)
  hydrogen bonds       : bond        0.02945 (  305)
  hydrogen bonds       : angle       4.88550 (  834)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 212
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 LYS cc_start: 0.8101 (mptt) cc_final: 0.7861 (mttp)
REVERT: A   52 PHE cc_start: 0.7598 (t80) cc_final: 0.7223 (t80)
REVERT: A   61 ASP cc_start: 0.7569 (m-30) cc_final: 0.7327 (m-30)
REVERT: A  232 ARG cc_start: 0.8380 (ttm170) cc_final: 0.8068 (ttp80)
REVERT: A  246 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7728 (mmm160)
REVERT: B   29 ARG cc_start: 0.8539 (ptm-80) cc_final: 0.8225 (ptt-90)
REVERT: C   49 MET cc_start: 0.8392 (mtt) cc_final: 0.7742 (mtt)
REVERT: C  187 MET cc_start: 0.7999 (mtt) cc_final: 0.7736 (mtp)
REVERT: C  203 TYR cc_start: 0.8195 (t80) cc_final: 0.7947 (t80)
REVERT: C  232 ARG cc_start: 0.8385 (ttp80) cc_final: 0.8133 (ttm110)
  outliers start: 25
  outliers final: 20
  residues processed: 228
  average time/residue: 0.5760
  time to fit residues: 137.6161
Evaluate side-chains
  230 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 209
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  158 HIS
Chi-restraints excluded: chain A residue  161 PHE
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   54 ASN
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  161 PHE
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain D residue   40 ASP
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  123 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 68 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 145 HIS
C  96 GLN
C 241 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.134483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.124945 restraints weight = 8965.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 1.31
r_work: 0.3592 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3466 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7368  Z= 0.185
  Angle     :  0.594   5.913   9954  Z= 0.306
  Chirality :  0.045   0.151   1056
  Planarity :  0.005   0.082   1310
  Dihedral  :  5.027  43.948    998
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 25.32 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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:  0.17 (0.29), residues: 882
  helix:  1.14 (0.29), residues: 334
  sheet: -0.95 (0.43), residues: 168
  loop : -0.16 (0.34), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 102 
 TYR   0.019   0.002   TYR D 108 
 PHE   0.016   0.002   PHE A  80 
 TRP   0.011   0.001   TRP A  63 
 HIS   0.005   0.001   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 7368)
  covalent geometry    : angle       0.59404 ( 9954)
  hydrogen bonds       : bond        0.03331 (  305)
  hydrogen bonds       : angle       4.97908 (  834)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 208
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A    7 LYS cc_start: 0.8175 (mptt) cc_final: 0.7923 (mttp)
REVERT: A   61 ASP cc_start: 0.7558 (m-30) cc_final: 0.7299 (m-30)
REVERT: A  246 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7784 (mmm160)
REVERT: B   29 ARG cc_start: 0.8563 (ptm-80) cc_final: 0.8220 (ptt-90)
REVERT: C   48 MET cc_start: 0.8652 (mtt) cc_final: 0.8250 (mtt)
REVERT: C  187 MET cc_start: 0.8073 (mtt) cc_final: 0.7790 (mtp)
REVERT: C  203 TYR cc_start: 0.8239 (t80) cc_final: 0.7978 (t80)
REVERT: C  232 ARG cc_start: 0.8406 (ttp80) cc_final: 0.8205 (ttm110)
  outliers start: 27
  outliers final: 19
  residues processed: 223
  average time/residue: 0.5644
  time to fit residues: 131.9601
Evaluate side-chains
  226 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 206
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  158 HIS
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  161 PHE
Chi-restraints excluded: chain C residue  176 MET
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain D residue   40 ASP
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  123 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 86 optimal weight:    0.5980
   chunk 48 optimal weight:    0.4980
   chunk 76 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 145 HIS
A 244 ASN
C  96 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.135062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.125519 restraints weight = 9044.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 1.32
r_work: 0.3593 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3466 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7368  Z= 0.186
  Angle     :  0.608   8.717   9954  Z= 0.312
  Chirality :  0.045   0.151   1056
  Planarity :  0.005   0.082   1310
  Dihedral  :  5.065  44.080    998
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 25.32 %
    Favored  : 71.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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:  0.17 (0.30), residues: 882
  helix:  1.13 (0.29), residues: 334
  sheet: -0.95 (0.43), residues: 168
  loop : -0.16 (0.34), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 102 
 TYR   0.019   0.002   TYR D 108 
 PHE   0.017   0.002   PHE A  80 
 TRP   0.013   0.001   TRP A  63 
 HIS   0.005   0.001   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 7368)
  covalent geometry    : angle       0.60758 ( 9954)
  hydrogen bonds       : bond        0.03312 (  305)
  hydrogen bonds       : angle       4.95594 (  834)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 205
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8181 (mptt) cc_final: 0.7931 (mttp)
REVERT: A   42 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6857 (tm-30)
REVERT: A   61 ASP cc_start: 0.7516 (m-30) cc_final: 0.7265 (m-30)
REVERT: A  246 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7788 (mmm160)
REVERT: B   29 ARG cc_start: 0.8572 (ptm-80) cc_final: 0.8262 (ptt-90)
REVERT: C   48 MET cc_start: 0.8662 (mtt) cc_final: 0.8265 (mtt)
REVERT: C  187 MET cc_start: 0.8078 (mtt) cc_final: 0.7805 (mtp)
REVERT: C  203 TYR cc_start: 0.8240 (t80) cc_final: 0.7964 (t80)
  outliers start: 25
  outliers final: 17
  residues processed: 220
  average time/residue: 0.5694
  time to fit residues: 131.4648
Evaluate side-chains
  230 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 211
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  158 HIS
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  176 MET
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain D residue   40 ASP
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  123 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 8 optimal weight:    0.4980
   chunk 42 optimal weight:    0.6980
   chunk 76 optimal weight:    0.7980
   chunk 41 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 48 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 145 HIS
A 244 ASN
C  96 GLN
C 241 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.135261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.125747 restraints weight = 9060.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 1.33
r_work: 0.3595 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3466 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7368  Z= 0.187
  Angle     :  0.615   6.850   9954  Z= 0.316
  Chirality :  0.045   0.151   1056
  Planarity :  0.005   0.081   1310
  Dihedral  :  5.078  43.970    998
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 26.23 %
    Favored  : 70.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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:  0.14 (0.30), residues: 882
  helix:  1.10 (0.29), residues: 334
  sheet: -0.94 (0.43), residues: 168
  loop : -0.17 (0.34), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 102 
 TYR   0.019   0.002   TYR D 108 
 PHE   0.018   0.002   PHE A  80 
 TRP   0.014   0.001   TRP A  63 
 HIS   0.005   0.001   HIS A 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 7368)
  covalent geometry    : angle       0.61505 ( 9954)
  hydrogen bonds       : bond        0.03331 (  305)
  hydrogen bonds       : angle       4.97126 (  834)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2991.88 seconds
wall clock time: 51 minutes 32.32 seconds (3092.32 seconds total)