Starting phenix.real_space_refine
on Tue Mar  3 16:31:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wvx_32861/03_2026/7wvx_32861.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wvx_32861/03_2026/7wvx_32861.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wvx_32861/03_2026/7wvx_32861.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wvx_32861/03_2026/7wvx_32861.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wvx_32861/03_2026/7wvx_32861.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wvx_32861/03_2026/7wvx_32861.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    4554      2.51       5
     N    1197      2.21       5
     O    1267      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7070
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "L"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 114
          Classifications: {'peptide': 15}
          Link IDs: {'PTRANS': 1, 'TRANS': 13}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 2331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2331
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 13, 'TRANS': 285}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 1680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1680
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 2, 'TRANS': 212}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 5, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "B"
      Number of atoms: 2557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2557
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 36
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 30
    Chain: "C"
      Number of atoms: 388
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 388
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
  Time building chain proxies: 1.56, per 1000 atoms: 0.22
  Number of scatterers: 7070
  At special positions: 0
  Unit cell: (114.95, 119.13, 85.69, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1267      8.00
     N    1197      7.00
     C    4554      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  98 " - pdb=" SG  CYS R 176 " distance=2.03

  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: 0.68
  Conformation dependent library (CDL) restraints added in 272.2 milliseconds
  

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1726

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 9 sheets defined
      48.6% alpha, 16.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'R' and resid 21 through 55
      Proline residue:  R  29  - end of helix
      removed outlier: 3.752A  pdb=" N   MET R  55 " --> pdb=" O   ALA R  51 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 58 through 86
      removed outlier: 3.699A  pdb=" N   THR R  77 " --> pdb=" O   SER R  73 " (cutoff:3.500A)
      Proline residue:  R  79  - end of helix
    Processing helix  chain 'R' and resid 94 through 129
    Processing helix  chain 'R' and resid 129 through 137
    Processing helix  chain 'R' and resid 138 through 163
      removed outlier: 3.784A  pdb=" N   GLY R 148 " --> pdb=" O   LYS R 144 " (cutoff:3.500A)
      Proline residue:  R 149  - end of helix
      Proline residue:  R 159  - end of helix
    Processing helix  chain 'R' and resid 180 through 185
      removed outlier: 3.922A  pdb=" N   GLY R 185 " --> pdb=" O   ALA R 181 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 186 through 209
    Processing helix  chain 'R' and resid 210 through 232
    Processing helix  chain 'R' and resid 237 through 267
      Proline residue:  R 256  - end of helix
    Processing helix  chain 'R' and resid 267 through 274
    Processing helix  chain 'R' and resid 278 through 303
      removed outlier: 3.835A  pdb=" N   ILE R 282 " --> pdb=" O   LYS R 278 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   ASN R 285 " --> pdb=" O   ASP R 281 " (cutoff:3.500A)
      Proline residue:  R 286  - end of helix
      Proline residue:  R 299  - end of helix
    Processing helix  chain 'R' and resid 306 through 317
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.799A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 52
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 4.118A  pdb=" N   TRP A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 217
    Processing helix  chain 'A' and resid 229 through 231
      No H-bonds generated for 'chain 'A' and resid 229 through 231'
    Processing helix  chain 'A' and resid 242 through 256
    Processing helix  chain 'A' and resid 257 through 261
      removed outlier: 3.958A  pdb=" N   THR A 261 " --> pdb=" O   LYS A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 280
      removed outlier: 3.818A  pdb=" N   GLU A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   THR A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 312
      removed outlier: 4.234A  pdb=" N   SER A 302 " --> pdb=" O   ASP A 298 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASN A 312 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.647A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 11 through 25
      removed outlier: 4.332A  pdb=" N   MET C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLU C  22 " --> pdb=" O   GLN C  18 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ALA C  23 " --> pdb=" O   LEU C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.564A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 48
    Processing sheet with id=AA1, first strand: chain 'R' and resid 167 through 168
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 192
      removed outlier: 6.234A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 198 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   PHE A 200 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      removed outlier: 8.841A  pdb=" N   ALA A 221 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 8.311A  pdb=" N   ALA A 227 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 4.057A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.518A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.686A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.670A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151
      removed outlier: 6.512A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.711A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.498A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278
      removed outlier: 6.388A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    387 hydrogen bonds defined for protein.
    1119 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: 0.97

  Time building geometry restraints manager: 0.88 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: 2252
        1.34 -     1.46: 1339
        1.46 -     1.58: 3553
        1.58 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 7218
  Sorted by residual:
  bond pdb=" SD  FME L   1 "
       pdb=" CE  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.805  1.751  0.054 2.00e-02 2.50e+03 7.27e+00
  bond pdb=" CG  FME L   1 "
       pdb=" SD  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.817  1.770  0.047 2.00e-02 2.50e+03 5.54e+00
  bond pdb=" N   FME L   1 "
       pdb=" CN  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.335  1.377 -0.042 2.00e-02 2.50e+03 4.36e+00
  bond pdb=" C   LEU R 212 "
       pdb=" N   PRO R 213 "
    ideal  model  delta    sigma   weight residual
    1.336  1.350 -0.014 1.20e-02 6.94e+03 1.34e+00
  bond pdb=" N   FME L   1 "
       pdb=" CA  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.436  0.022 1.90e-02 2.77e+03 1.31e+00
  ... (remaining 7213 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 9645
        1.56 -     3.13: 118
        3.13 -     4.69: 29
        4.69 -     6.25: 6
        6.25 -     7.81: 1
  Bond angle restraints: 9799
  Sorted by residual:
  angle pdb=" C   ASP A 329 "
        pdb=" N   THR A 330 "
        pdb=" CA  THR A 330 "
      ideal   model   delta    sigma   weight residual
     122.46  125.84   -3.38 1.41e+00 5.03e-01 5.76e+00
  angle pdb=" C   PHE R 161 "
        pdb=" N   LEU R 162 "
        pdb=" CA  LEU R 162 "
      ideal   model   delta    sigma   weight residual
     122.53  118.15    4.38 1.92e+00 2.71e-01 5.20e+00
  angle pdb=" CA  LEU R 162 "
        pdb=" CB  LEU R 162 "
        pdb=" CG  LEU R 162 "
      ideal   model   delta    sigma   weight residual
     116.30  124.11   -7.81 3.50e+00 8.16e-02 4.98e+00
  angle pdb=" CA  TRP R  95 "
        pdb=" CB  TRP R  95 "
        pdb=" CG  TRP R  95 "
      ideal   model   delta    sigma   weight residual
     113.60  117.82   -4.22 1.90e+00 2.77e-01 4.94e+00
  angle pdb=" C   PHE C  61 "
        pdb=" N   ARG C  62 "
        pdb=" CA  ARG C  62 "
      ideal   model   delta    sigma   weight residual
     121.70  125.20   -3.50 1.80e+00 3.09e-01 3.78e+00
  ... (remaining 9794 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.28: 3894
       17.28 -    34.56: 282
       34.56 -    51.83: 61
       51.83 -    69.11: 2
       69.11 -    86.39: 2
  Dihedral angle restraints: 4241
    sinusoidal: 1582
      harmonic: 2659
  Sorted by residual:
  dihedral pdb=" CG  ARG R 137 "
           pdb=" CD  ARG R 137 "
           pdb=" NE  ARG R 137 "
           pdb=" CZ  ARG R 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.63  -44.63     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" CG  ARG B  22 "
           pdb=" CD  ARG B  22 "
           pdb=" NE  ARG B  22 "
           pdb=" CZ  ARG B  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -137.47  -42.53     2      1.50e+01 4.44e-03 9.75e+00
  dihedral pdb=" CA  LYS C  14 "
           pdb=" CB  LYS C  14 "
           pdb=" CG  LYS C  14 "
           pdb=" CD  LYS C  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.00   56.00     3      1.50e+01 4.44e-03 9.38e+00
  ... (remaining 4238 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 719
       0.029 -    0.058: 263
       0.058 -    0.087: 112
       0.087 -    0.115: 53
       0.115 -    0.144: 7
  Chirality restraints: 1154
  Sorted by residual:
  chirality pdb=" CB  ILE R 101 "
            pdb=" CA  ILE R 101 "
            pdb=" CG1 ILE R 101 "
            pdb=" CG2 ILE R 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.20e-01
  chirality pdb=" CA  ILE B  81 "
            pdb=" N   ILE B  81 "
            pdb=" C   ILE B  81 "
            pdb=" CB  ILE B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  chirality pdb=" CA  PRO R 187 "
            pdb=" N   PRO R 187 "
            pdb=" C   PRO R 187 "
            pdb=" CB  PRO R 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.16e-01
  ... (remaining 1151 not shown)

  Planarity restraints: 1223
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 148 "    0.033 5.00e-02 4.00e+02   5.05e-02 4.08e+00
        pdb=" N   PRO R 149 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO R 149 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO R 149 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 186 "    0.032 5.00e-02 4.00e+02   4.89e-02 3.83e+00
        pdb=" N   PRO R 187 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO R 187 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO R 187 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.031 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO B 236 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1220 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1451
        2.78 -     3.31: 6959
        3.31 -     3.84: 12150
        3.84 -     4.37: 14439
        4.37 -     4.90: 24954
  Nonbonded interactions: 59953
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 310 "
            pdb=" NZ  LYS B 337 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" OD1 ASP B 290 "
            pdb=" NH1 ARG B 314 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" OD1 ASN A 270 "
            pdb=" OG1 THR A 325 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   MET B 325 "
            pdb=" ND2 ASN B 340 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" NE2 HIS B 225 "
            pdb=" OG1 THR B 243 "
     model   vdw
     2.324 3.120
  ... (remaining 59948 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.170
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.340
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
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      :  0.002   0.054   7219  Z= 0.113
  Angle     :  0.493   7.814   9801  Z= 0.267
  Chirality :  0.040   0.144   1154
  Planarity :  0.004   0.051   1223
  Dihedral  : 12.148  86.390   2512
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.28), residues: 903
  helix:  1.86 (0.25), residues: 407
  sheet:  0.42 (0.42), residues: 158
  loop : -0.95 (0.31), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 190 
 TYR   0.005   0.001   TYR A 231 
 PHE   0.009   0.001   PHE B 199 
 TRP   0.028   0.001   TRP R  95 
 HIS   0.002   0.000   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 7218)
  covalent geometry    : angle       0.49248 ( 9799)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       1.29289 (    2)
  hydrogen bonds       : bond        0.19609 (  387)
  hydrogen bonds       : angle       6.86167 ( 1119)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.242 
Fit side-chains
REVERT: R   65 LEU cc_start: 0.8050 (tt) cc_final: 0.7831 (tm)
REVERT: A  194 ASP cc_start: 0.7448 (m-30) cc_final: 0.7237 (m-30)
  outliers start: 0
  outliers final: 1
  residues processed: 132
  average time/residue: 0.5342
  time to fit residues: 74.3328
Evaluate side-chains
  114 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  129 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 189 HIS
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.155511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.120610 restraints weight = 8059.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.91
r_work: 0.3275 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7219  Z= 0.156
  Angle     :  0.552   7.629   9801  Z= 0.289
  Chirality :  0.042   0.141   1154
  Planarity :  0.005   0.086   1223
  Dihedral  :  4.186  45.949    977
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.86 %
    Favored  : 87.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.28), residues: 903
  helix:  1.80 (0.25), residues: 422
  sheet:  0.09 (0.37), residues: 187
  loop : -0.65 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 123 
 TYR   0.011   0.001   TYR R 221 
 PHE   0.013   0.002   PHE A 197 
 TRP   0.023   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 7218)
  covalent geometry    : angle       0.55072 ( 9799)
  SS BOND              : bond        0.00354 (    1)
  SS BOND              : angle       2.50744 (    2)
  hydrogen bonds       : bond        0.04022 (  387)
  hydrogen bonds       : angle       5.12129 ( 1119)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.322 
Fit side-chains
REVERT: R   65 LEU cc_start: 0.8333 (tt) cc_final: 0.8088 (tm)
REVERT: R  224 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7702 (mt)
REVERT: R  238 ARG cc_start: 0.8274 (tmt90) cc_final: 0.7899 (tpt-90)
REVERT: R  304 PHE cc_start: 0.8153 (m-10) cc_final: 0.7946 (m-10)
REVERT: A   33 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8225 (mm-30)
REVERT: A  194 ASP cc_start: 0.8384 (m-30) cc_final: 0.8121 (m-30)
REVERT: A  350 LYS cc_start: 0.8108 (mtmt) cc_final: 0.7774 (mtpt)
REVERT: B  220 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7593 (mt0)
REVERT: C   21 MET cc_start: 0.3449 (OUTLIER) cc_final: 0.2557 (ppp)
  outliers start: 13
  outliers final: 6
  residues processed: 133
  average time/residue: 0.5325
  time to fit residues: 74.9557
Evaluate side-chains
  124 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   41 VAL
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  224 ILE
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain C residue   21 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 48 optimal weight:    0.3980
   chunk 83 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 77 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.151380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.116902 restraints weight = 8090.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.87
r_work: 0.3225 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7219  Z= 0.152
  Angle     :  0.543   9.350   9801  Z= 0.282
  Chirality :  0.042   0.144   1154
  Planarity :  0.004   0.061   1223
  Dihedral  :  4.098  42.646    975
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.68 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.28), residues: 903
  helix:  1.63 (0.25), residues: 424
  sheet: -0.06 (0.38), residues: 178
  loop : -0.71 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 209 
 TYR   0.007   0.001   TYR R 221 
 PHE   0.012   0.001   PHE A 197 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 7218)
  covalent geometry    : angle       0.54266 ( 9799)
  SS BOND              : bond        0.00064 (    1)
  SS BOND              : angle       2.16817 (    2)
  hydrogen bonds       : bond        0.03907 (  387)
  hydrogen bonds       : angle       5.10013 ( 1119)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.321 
Fit side-chains
REVERT: R  238 ARG cc_start: 0.8322 (tmt90) cc_final: 0.8069 (tpt-90)
REVERT: A   33 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8252 (mm-30)
REVERT: A  194 ASP cc_start: 0.8411 (m-30) cc_final: 0.8132 (m-30)
REVERT: A  209 ARG cc_start: 0.8342 (ttp80) cc_final: 0.8103 (ttm110)
REVERT: A  350 LYS cc_start: 0.8138 (mtmt) cc_final: 0.7785 (mtpt)
REVERT: B   52 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8297 (mtp85)
REVERT: B  220 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7649 (mt0)
  outliers start: 19
  outliers final: 7
  residues processed: 136
  average time/residue: 0.5531
  time to fit residues: 79.2680
Evaluate side-chains
  121 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  174 THR
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  220 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   chunk 2 optimal weight:    0.6980
   chunk 82 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
R 294 ASN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 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 = 0.3720 r_free = 0.3720 target = 0.145623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.109506 restraints weight = 8094.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 1.93
r_work: 0.3129 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   7219  Z= 0.207
  Angle     :  0.589   8.231   9801  Z= 0.310
  Chirality :  0.044   0.147   1154
  Planarity :  0.005   0.073   1223
  Dihedral  :  4.387  43.867    975
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 16.89 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.27), residues: 903
  helix:  1.52 (0.25), residues: 419
  sheet: -0.39 (0.35), residues: 189
  loop : -0.85 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 209 
 TYR   0.011   0.001   TYR B  59 
 PHE   0.029   0.002   PHE R  37 
 TRP   0.012   0.002   TRP B  82 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 7218)
  covalent geometry    : angle       0.58741 ( 9799)
  SS BOND              : bond        0.00012 (    1)
  SS BOND              : angle       2.71920 (    2)
  hydrogen bonds       : bond        0.04115 (  387)
  hydrogen bonds       : angle       5.33907 ( 1119)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: R   42 LEU cc_start: 0.8364 (mp) cc_final: 0.7665 (tm)
REVERT: R  238 ARG cc_start: 0.8341 (tmt90) cc_final: 0.8066 (ttm-80)
REVERT: R  304 PHE cc_start: 0.8383 (m-10) cc_final: 0.8159 (m-10)
REVERT: R  312 ARG cc_start: 0.6703 (mtp85) cc_final: 0.6338 (mtp85)
REVERT: A   29 LYS cc_start: 0.8324 (ttmm) cc_final: 0.8115 (ttmt)
REVERT: A   33 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8224 (mm-30)
REVERT: A  350 LYS cc_start: 0.8292 (mtmt) cc_final: 0.7919 (mtpt)
REVERT: B   52 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8099 (mtp85)
REVERT: B  219 ARG cc_start: 0.8056 (ttm170) cc_final: 0.7526 (mtt90)
REVERT: B  220 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7663 (mt0)
REVERT: B  312 ASP cc_start: 0.8327 (m-30) cc_final: 0.8065 (m-30)
REVERT: C   46 LYS cc_start: 0.8420 (mptt) cc_final: 0.8094 (pmtt)
  outliers start: 27
  outliers final: 11
  residues processed: 135
  average time/residue: 0.5088
  time to fit residues: 72.6262
Evaluate side-chains
  129 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  113 VAL
Chi-restraints excluded: chain R residue  174 THR
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  342 ASP
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  220 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 63 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9980
   chunk 31 optimal weight:    0.3980
   chunk 45 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 88 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.147591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.112093 restraints weight = 8027.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 1.91
r_work: 0.3165 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.3388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7219  Z= 0.150
  Angle     :  0.548   7.669   9801  Z= 0.285
  Chirality :  0.042   0.146   1154
  Planarity :  0.004   0.049   1223
  Dihedral  :  4.205  41.393    975
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 19.03 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.27), residues: 903
  helix:  1.45 (0.25), residues: 425
  sheet: -0.56 (0.34), residues: 189
  loop : -0.67 (0.35), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 209 
 TYR   0.010   0.001   TYR R 221 
 PHE   0.019   0.001   PHE R  37 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 7218)
  covalent geometry    : angle       0.54749 ( 9799)
  SS BOND              : bond        0.00024 (    1)
  SS BOND              : angle       2.15719 (    2)
  hydrogen bonds       : bond        0.03745 (  387)
  hydrogen bonds       : angle       5.18120 ( 1119)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.255 
Fit side-chains
REVERT: R   42 LEU cc_start: 0.8351 (mp) cc_final: 0.7657 (tm)
REVERT: R  238 ARG cc_start: 0.8262 (tmt90) cc_final: 0.8026 (ttm-80)
REVERT: R  304 PHE cc_start: 0.8315 (m-10) cc_final: 0.8070 (m-10)
REVERT: A   33 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8242 (mm-30)
REVERT: A  209 ARG cc_start: 0.8349 (ttp80) cc_final: 0.8127 (ttm110)
REVERT: A  350 LYS cc_start: 0.8310 (mtmt) cc_final: 0.7924 (mtpt)
REVERT: B   52 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8117 (mtp85)
REVERT: B  220 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7595 (mt0)
REVERT: C   46 LYS cc_start: 0.8414 (mptt) cc_final: 0.8085 (pmtt)
  outliers start: 19
  outliers final: 9
  residues processed: 127
  average time/residue: 0.4804
  time to fit residues: 64.9746
Evaluate side-chains
  123 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  340 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 22 optimal weight:    0.0770
   chunk 8 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 82 optimal weight:    0.4980
   chunk 42 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.149378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.114043 restraints weight = 8058.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.91
r_work: 0.3188 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7219  Z= 0.130
  Angle     :  0.532   7.931   9801  Z= 0.277
  Chirality :  0.041   0.146   1154
  Planarity :  0.004   0.049   1223
  Dihedral  :  4.082  39.988    975
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 19.97 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.27), residues: 903
  helix:  1.61 (0.25), residues: 419
  sheet: -0.55 (0.34), residues: 187
  loop : -0.72 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 209 
 TYR   0.013   0.001   TYR B 124 
 PHE   0.015   0.001   PHE R  37 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7218)
  covalent geometry    : angle       0.53144 ( 9799)
  SS BOND              : bond        0.00063 (    1)
  SS BOND              : angle       1.95099 (    2)
  hydrogen bonds       : bond        0.03603 (  387)
  hydrogen bonds       : angle       5.07295 ( 1119)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.188 
Fit side-chains
REVERT: R   42 LEU cc_start: 0.8372 (mp) cc_final: 0.7682 (tm)
REVERT: R  238 ARG cc_start: 0.8350 (tmt90) cc_final: 0.8121 (ttm-80)
REVERT: R  304 PHE cc_start: 0.8274 (m-10) cc_final: 0.8054 (m-10)
REVERT: A   33 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8181 (mm-30)
REVERT: A  209 ARG cc_start: 0.8338 (ttp80) cc_final: 0.8110 (ttm110)
REVERT: A  350 LYS cc_start: 0.8383 (mtmt) cc_final: 0.8017 (mtpt)
REVERT: B  226 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8174 (mt-10)
REVERT: B  243 THR cc_start: 0.8638 (p) cc_final: 0.8400 (p)
  outliers start: 17
  outliers final: 6
  residues processed: 127
  average time/residue: 0.5240
  time to fit residues: 70.2214
Evaluate side-chains
  111 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  112 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 66 optimal weight:    0.0670
   chunk 28 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 45 optimal weight:    0.2980
   chunk 76 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0970
   chunk 25 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    0.3916

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.151408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.116461 restraints weight = 7920.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 1.91
r_work: 0.3225 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.3370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7219  Z= 0.118
  Angle     :  0.524   7.793   9801  Z= 0.271
  Chirality :  0.041   0.142   1154
  Planarity :  0.004   0.049   1223
  Dihedral  :  3.839  21.408    975
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 20.38 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.28), residues: 903
  helix:  1.68 (0.25), residues: 421
  sheet: -0.47 (0.36), residues: 180
  loop : -0.70 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R  54 
 TYR   0.017   0.001   TYR B 124 
 PHE   0.014   0.001   PHE R  37 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 7218)
  covalent geometry    : angle       0.52354 ( 9799)
  SS BOND              : bond        0.00091 (    1)
  SS BOND              : angle       1.75646 (    2)
  hydrogen bonds       : bond        0.03448 (  387)
  hydrogen bonds       : angle       4.93919 ( 1119)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.277 
Fit side-chains
REVERT: R  238 ARG cc_start: 0.8326 (tmt90) cc_final: 0.8008 (tpt170)
REVERT: R  304 PHE cc_start: 0.8220 (m-10) cc_final: 0.7982 (m-10)
REVERT: A   33 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8165 (mm-30)
REVERT: A  194 ASP cc_start: 0.8382 (m-30) cc_final: 0.8082 (m-30)
REVERT: A  350 LYS cc_start: 0.8532 (mtmt) cc_final: 0.8181 (mtpt)
REVERT: B  226 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8189 (mt-10)
REVERT: C   46 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8178 (pmtt)
  outliers start: 18
  outliers final: 9
  residues processed: 122
  average time/residue: 0.4546
  time to fit residues: 59.1516
Evaluate side-chains
  115 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  340 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0170
   chunk 52 optimal weight:   10.0000
   chunk 3 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 50 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 ASN
** B 340 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 = 0.3775 r_free = 0.3775 target = 0.151082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.115739 restraints weight = 7892.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.89
r_work: 0.3212 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3076 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.3484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7219  Z= 0.138
  Angle     :  0.539   7.695   9801  Z= 0.278
  Chirality :  0.042   0.146   1154
  Planarity :  0.004   0.049   1223
  Dihedral  :  3.886  24.967    975
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 21.58 %
    Favored  : 76.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.27), residues: 903
  helix:  1.63 (0.25), residues: 422
  sheet: -0.50 (0.35), residues: 187
  loop : -0.79 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R  54 
 TYR   0.015   0.001   TYR B 124 
 PHE   0.013   0.001   PHE A 197 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7218)
  covalent geometry    : angle       0.53855 ( 9799)
  SS BOND              : bond        0.00079 (    1)
  SS BOND              : angle       1.99427 (    2)
  hydrogen bonds       : bond        0.03559 (  387)
  hydrogen bonds       : angle       5.02598 ( 1119)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.227 
Fit side-chains
REVERT: R   42 LEU cc_start: 0.8380 (mp) cc_final: 0.7701 (tm)
REVERT: R  238 ARG cc_start: 0.8313 (tmt90) cc_final: 0.8005 (tpt170)
REVERT: R  304 PHE cc_start: 0.8275 (m-10) cc_final: 0.8016 (m-10)
REVERT: A   33 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8193 (mm-30)
REVERT: A  350 LYS cc_start: 0.8542 (mtmt) cc_final: 0.8190 (mtpt)
REVERT: B  226 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8244 (mt-10)
REVERT: C   46 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8197 (pmtt)
  outliers start: 11
  outliers final: 8
  residues processed: 115
  average time/residue: 0.4733
  time to fit residues: 57.9329
Evaluate side-chains
  112 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  186 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 53 optimal weight:   10.0000
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.148053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.113101 restraints weight = 8022.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 1.88
r_work: 0.3169 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3031 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.3649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7219  Z= 0.159
  Angle     :  0.555   7.120   9801  Z= 0.288
  Chirality :  0.042   0.147   1154
  Planarity :  0.004   0.049   1223
  Dihedral  :  4.035  26.781    975
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 20.64 %
    Favored  : 76.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.27), residues: 903
  helix:  1.59 (0.25), residues: 420
  sheet: -0.60 (0.34), residues: 189
  loop : -0.78 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R  54 
 TYR   0.019   0.001   TYR B 124 
 PHE   0.013   0.001   PHE A 197 
 TRP   0.010   0.001   TRP B  99 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 7218)
  covalent geometry    : angle       0.55440 ( 9799)
  SS BOND              : bond        0.00007 (    1)
  SS BOND              : angle       2.20852 (    2)
  hydrogen bonds       : bond        0.03696 (  387)
  hydrogen bonds       : angle       5.14673 ( 1119)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.185 
Fit side-chains
REVERT: R  143 MET cc_start: 0.7711 (mtt) cc_final: 0.7345 (mtt)
REVERT: R  243 LEU cc_start: 0.7920 (tt) cc_final: 0.7502 (mp)
REVERT: R  304 PHE cc_start: 0.8376 (m-10) cc_final: 0.8050 (m-10)
REVERT: A   33 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8200 (mm-30)
REVERT: A  350 LYS cc_start: 0.8461 (mtmt) cc_final: 0.8093 (mtpt)
REVERT: B  226 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8306 (mt-10)
  outliers start: 18
  outliers final: 8
  residues processed: 128
  average time/residue: 0.4517
  time to fit residues: 61.6951
Evaluate side-chains
  116 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  186 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 59 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 84 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.144236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.109451 restraints weight = 8108.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.84
r_work: 0.3124 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.3953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   7219  Z= 0.218
  Angle     :  0.624   7.142   9801  Z= 0.322
  Chirality :  0.044   0.153   1154
  Planarity :  0.004   0.049   1223
  Dihedral  :  4.398  31.703    975
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 22.52 %
    Favored  : 75.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.27), residues: 903
  helix:  1.37 (0.25), residues: 425
  sheet: -0.80 (0.34), residues: 188
  loop : -0.96 (0.34), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 209 
 TYR   0.019   0.001   TYR B 124 
 PHE   0.016   0.002   PHE A 197 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 7218)
  covalent geometry    : angle       0.62279 ( 9799)
  SS BOND              : bond        0.00130 (    1)
  SS BOND              : angle       2.72794 (    2)
  hydrogen bonds       : bond        0.04046 (  387)
  hydrogen bonds       : angle       5.37423 ( 1119)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.282 
Fit side-chains
REVERT: R   42 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7806 (tm)
REVERT: R  304 PHE cc_start: 0.8442 (m-10) cc_final: 0.8078 (m-10)
REVERT: A   33 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8179 (mm-30)
REVERT: A  350 LYS cc_start: 0.8433 (mtmt) cc_final: 0.8075 (mtpt)
REVERT: B  226 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8289 (mt-10)
REVERT: B  243 THR cc_start: 0.8694 (p) cc_final: 0.8458 (p)
REVERT: C   46 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8153 (pmtt)
  outliers start: 13
  outliers final: 9
  residues processed: 116
  average time/residue: 0.4692
  time to fit residues: 58.0652
Evaluate side-chains
  116 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  186 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 78 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 22 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.147453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.113089 restraints weight = 8058.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 1.85
r_work: 0.3185 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.3857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7219  Z= 0.154
  Angle     :  0.580   8.072   9801  Z= 0.297
  Chirality :  0.042   0.151   1154
  Planarity :  0.004   0.048   1223
  Dihedral  :  4.227  27.632    975
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 22.52 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.27), residues: 903
  helix:  1.41 (0.25), residues: 426
  sheet: -0.69 (0.34), residues: 186
  loop : -0.86 (0.34), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 209 
 TYR   0.022   0.001   TYR B 124 
 PHE   0.011   0.001   PHE A 197 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 7218)
  covalent geometry    : angle       0.57967 ( 9799)
  SS BOND              : bond        0.00146 (    1)
  SS BOND              : angle       2.12790 (    2)
  hydrogen bonds       : bond        0.03697 (  387)
  hydrogen bonds       : angle       5.21393 ( 1119)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2822.31 seconds
wall clock time: 48 minutes 45.75 seconds (2925.75 seconds total)