Starting phenix.real_space_refine
on Thu Jul  2 04:34:43 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8bms_16124/07_2026/8bms_16124.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bms_16124/07_2026/8bms_16124.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8bms_16124/07_2026/8bms_16124.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8bms_16124/07_2026/8bms_16124.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bms_16124/07_2026/8bms_16124.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bms_16124/07_2026/8bms_16124.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bms_16124/07_2026/8bms_16124.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bms_16124/07_2026/8bms_16124.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.096
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      26      5.16       5
     C    4173      2.51       5
     N    1080      2.21       5
     O    1283      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6570
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2133
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 13, 'TRANS': 264}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2183
          Classifications: {'peptide': 281}
          Link IDs: {'PTRANS': 14, 'TRANS': 266}
    Chain: "C"
      Number of atoms: 2118
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 2118
          Classifications: {'peptide': 263}
          Link IDs: {'PTRANS': 9, 'TRANS': 253}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 35
          Classifications: {'water': 35}
          Link IDs: {None: 34}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 28
          Classifications: {'water': 28}
          Link IDs: {None: 27}
    Chain: "C"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 9
          Classifications: {'water': 9}
          Link IDs: {None: 8}
  Time building chain proxies: 1.12, per 1000 atoms: 0.17
  Number of scatterers: 6570
  At special positions: 0
  Unit cell: (72.732, 75.24, 122.056, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      26     16.00
     P       6     15.00
     Mg      2     11.99
     O    1283      8.00
     N    1080      7.00
     C    4173      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: 0.52
  Conformation dependent library (CDL) restraints added in 347.6 milliseconds
  

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1528

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 4 sheets defined
      58.3% alpha, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 78 through 84
      removed outlier: 3.555A  pdb=" N   GLU A  84 " --> pdb=" O   TRP A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 96
    Processing helix  chain 'A' and resid 101 through 113
      removed outlier: 4.453A  pdb=" N   GLY A 109 " --> pdb=" O   ASP A 105 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   LEU A 110 " --> pdb=" O   VAL A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 131
      removed outlier: 3.815A  pdb=" N   LYS A 122 " --> pdb=" O   PRO A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 137
      removed outlier: 3.937A  pdb=" N   ALA A 137 " --> pdb=" O   ALA A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 159
      removed outlier: 3.537A  pdb=" N   ILE A 157 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 194
    Processing helix  chain 'A' and resid 203 through 209
      removed outlier: 3.605A  pdb=" N   GLY A 209 " --> pdb=" O   GLU A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 231
    Processing helix  chain 'A' and resid 233 through 240
    Processing helix  chain 'A' and resid 245 through 257
    Processing helix  chain 'A' and resid 267 through 281
      removed outlier: 3.535A  pdb=" N   LYS A 281 " --> pdb=" O   GLN A 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 54
      removed outlier: 3.742A  pdb=" N   ASN B  54 " --> pdb=" O   MET B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 86
    Processing helix  chain 'B' and resid 93 through 97
    Processing helix  chain 'B' and resid 102 through 114
      removed outlier: 4.464A  pdb=" N   GLY B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
    Processing helix  chain 'B' and resid 117 through 132
    Processing helix  chain 'B' and resid 135 through 141
      removed outlier: 3.721A  pdb=" N   ILE B 139 " --> pdb=" O   ASP B 136 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   GLU B 140 " --> pdb=" O   ASP B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 161
    Processing helix  chain 'B' and resid 177 through 193
    Processing helix  chain 'B' and resid 204 through 212
      removed outlier: 3.515A  pdb=" N   VAL B 208 " --> pdb=" O   ASN B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 233
    Processing helix  chain 'B' and resid 235 through 242
    Processing helix  chain 'B' and resid 247 through 260
    Processing helix  chain 'B' and resid 269 through 282
    Processing helix  chain 'C' and resid 14 through 19
      removed outlier: 3.884A  pdb=" N   ARG C  18 " --> pdb=" O   THR C  14 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 36
      removed outlier: 3.675A  pdb=" N   PHE C  36 " --> pdb=" O   ILE C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 57
    Processing helix  chain 'C' and resid 61 through 87
      Proline residue:  C  71  - end of helix
    Processing helix  chain 'C' and resid 102 through 130
    Processing helix  chain 'C' and resid 131 through 143
    Processing helix  chain 'C' and resid 144 through 148
    Processing helix  chain 'C' and resid 152 through 184
      removed outlier: 4.165A  pdb=" N   VAL C 167 " --> pdb=" O   ALA C 163 " (cutoff:3.500A)
      Proline residue:  C 168  - end of helix
      removed outlier: 3.608A  pdb=" N   ARG C 184 " --> pdb=" O   ALA C 180 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 201
    Processing helix  chain 'C' and resid 203 through 225
      removed outlier: 3.558A  pdb=" N   SER C 219 " --> pdb=" O   ALA C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 261
      removed outlier: 3.887A  pdb=" N   VAL C 249 " --> pdb=" O   ASP C 245 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU C 255 " --> pdb=" O   TYR C 251 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   THR C 256 " --> pdb=" O   CYS C 252 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 30
      removed outlier: 5.636A  pdb=" N   SER A  24 " --> pdb=" O   VAL A  11 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   VAL A  11 " --> pdb=" O   SER A  24 " (cutoff:3.500A)
      removed outlier: 7.390A  pdb=" N   PHE A  28 " --> pdb=" O   SER A   7 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   SER A   7 " --> pdb=" O   PHE A  28 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   ILE A  30 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   ILE A   5 " --> pdb=" O   ILE A  30 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 89
      removed outlier: 6.668A  pdb=" N   THR A  36 " --> pdb=" O   SER A 199 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ASP A 217 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      removed outlier: 5.172A  pdb=" N   LEU A 221 " --> pdb=" O   ASP A 217 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 30
      removed outlier: 6.150A  pdb=" N   TYR B  10 " --> pdb=" O   GLY B  22 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ASP B  24 " --> pdb=" O   VAL B   8 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   VAL B   8 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   LEU B  26 " --> pdb=" O   GLU B   6 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU B   6 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   PHE B  28 " --> pdb=" O   LYS B   4 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   LYS B   4 " --> pdb=" O   PHE B  28 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   VAL B   8 " --> pdb=" O   SER B  61 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   SER B  61 " --> pdb=" O   VAL B   8 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 90
      removed outlier: 6.373A  pdb=" N   SER B  88 " --> pdb=" O   CYS B 168 " (cutoff:3.500A)
      removed outlier: 7.763A  pdb=" N   ASP B 170 " --> pdb=" O   SER B  88 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   ALA B  90 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   ILE B 167 " --> pdb=" O   ILE B 199 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   VAL B 201 " --> pdb=" O   ILE B 167 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU B 169 " --> pdb=" O   VAL B 201 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   PHE B  35 " --> pdb=" O   ASP B 214 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   LEU B 216 " --> pdb=" O   PHE B  35 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   ALA B  37 " --> pdb=" O   LEU B 216 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   LEU B 218 " --> pdb=" O   ALA B  37 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   VAL B  39 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LYS B 225 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   GLU B 219 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   LEU B 223 " --> pdb=" O   GLU B 219 " (cutoff:3.500A)

    348 hydrogen bonds defined for protein.
    1002 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: 0.67

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2078
        1.34 -     1.46: 1013
        1.46 -     1.57: 3479
        1.57 -     1.69: 10
        1.69 -     1.81: 50
  Bond restraints: 6630
  Sorted by residual:
  bond pdb=" CB  ASN B   7 "
       pdb=" CG  ASN B   7 "
    ideal  model  delta    sigma   weight residual
    1.516  1.550 -0.034 2.50e-02 1.60e+03 1.83e+00
  bond pdb=" CG1 ILE C  49 "
       pdb=" CD1 ILE C  49 "
    ideal  model  delta    sigma   weight residual
    1.513  1.465  0.048 3.90e-02 6.57e+02 1.51e+00
  bond pdb=" CA  ASN B   7 "
       pdb=" CB  ASN B   7 "
    ideal  model  delta    sigma   weight residual
    1.529  1.542 -0.013 1.58e-02 4.01e+03 6.59e-01
  bond pdb=" C   VAL C 201 "
       pdb=" N   PRO C 202 "
    ideal  model  delta    sigma   weight residual
    1.337  1.344 -0.007 9.80e-03 1.04e+04 5.69e-01
  bond pdb=" CG1 ILE A  88 "
       pdb=" CD1 ILE A  88 "
    ideal  model  delta    sigma   weight residual
    1.513  1.484  0.029 3.90e-02 6.57e+02 5.60e-01
  ... (remaining 6625 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 8807
        1.47 -     2.93: 144
        2.93 -     4.40: 28
        4.40 -     5.87: 12
        5.87 -     7.33: 3
  Bond angle restraints: 8994
  Sorted by residual:
  angle pdb=" CA  MET C 118 "
        pdb=" CB  MET C 118 "
        pdb=" CG  MET C 118 "
      ideal   model   delta    sigma   weight residual
     114.10  108.83    5.27 2.00e+00 2.50e-01 6.95e+00
  angle pdb=" CA  ASN B   7 "
        pdb=" CB  ASN B   7 "
        pdb=" CG  ASN B   7 "
      ideal   model   delta    sigma   weight residual
     112.60  114.79   -2.19 1.00e+00 1.00e+00 4.82e+00
  angle pdb=" N   VAL C 201 "
        pdb=" CA  VAL C 201 "
        pdb=" C   VAL C 201 "
      ideal   model   delta    sigma   weight residual
     108.88  113.61   -4.73 2.16e+00 2.14e-01 4.79e+00
  angle pdb=" CA  VAL C 201 "
        pdb=" C   VAL C 201 "
        pdb=" N   PRO C 202 "
      ideal   model   delta    sigma   weight residual
     118.88  122.22   -3.34 1.54e+00 4.22e-01 4.70e+00
  angle pdb=" N   PHE A 231 "
        pdb=" CA  PHE A 231 "
        pdb=" C   PHE A 231 "
      ideal   model   delta    sigma   weight residual
     109.81  114.54   -4.73 2.21e+00 2.05e-01 4.58e+00
  ... (remaining 8989 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 3595
       17.47 -    34.94: 294
       34.94 -    52.41: 50
       52.41 -    69.88: 13
       69.88 -    87.35: 5
  Dihedral angle restraints: 3957
    sinusoidal: 1592
      harmonic: 2365
  Sorted by residual:
  dihedral pdb=" CA  ARG B  84 "
           pdb=" C   ARG B  84 "
           pdb=" N   ARG B  85 "
           pdb=" CA  ARG B  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.84   17.16     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CG  ARG C 182 "
           pdb=" CD  ARG C 182 "
           pdb=" NE  ARG C 182 "
           pdb=" CZ  ARG C 182 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.23   42.77     2      1.50e+01 4.44e-03 9.84e+00
  dihedral pdb=" CB  GLU B  32 "
           pdb=" CG  GLU B  32 "
           pdb=" CD  GLU B  32 "
           pdb=" OE1 GLU B  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   84.98  -84.98     1      3.00e+01 1.11e-03 9.73e+00
  ... (remaining 3954 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 644
       0.029 -    0.059: 225
       0.059 -    0.088: 98
       0.088 -    0.117: 55
       0.117 -    0.147: 12
  Chirality restraints: 1034
  Sorted by residual:
  chirality pdb=" CA  ILE B 167 "
            pdb=" N   ILE B 167 "
            pdb=" C   ILE B 167 "
            pdb=" CB  ILE B 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.38e-01
  chirality pdb=" CA  ILE A 200 "
            pdb=" N   ILE A 200 "
            pdb=" C   ILE A 200 "
            pdb=" CB  ILE A 200 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.12e-01
  chirality pdb=" CA  MET C 118 "
            pdb=" N   MET C 118 "
            pdb=" C   MET C 118 "
            pdb=" CB  MET C 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.04e-01
  ... (remaining 1031 not shown)

  Planarity restraints: 1127
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 231 "   -0.038 5.00e-02 4.00e+02   5.72e-02 5.24e+00
        pdb=" N   PRO A 232 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 232 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 232 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 110 "   -0.028 5.00e-02 4.00e+02   4.22e-02 2.85e+00
        pdb=" N   PRO B 111 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 111 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 111 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  72 "    0.025 5.00e-02 4.00e+02   3.84e-02 2.36e+00
        pdb=" N   PRO B  73 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO B  73 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B  73 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1124 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 54
        2.55 -     3.13: 5081
        3.13 -     3.72: 10515
        3.72 -     4.31: 15344
        4.31 -     4.90: 25482
  Nonbonded interactions: 56476
  Sorted by model distance:
  nonbonded pdb=" O2B ATP A 301 "
            pdb="MG    MG A 302 "
     model   vdw
     1.956 2.170
  nonbonded pdb=" OG  SER B  47 "
            pdb="MG    MG B 302 "
     model   vdw
     1.958 2.170
  nonbonded pdb=" OE1 GLN A  91 "
            pdb="MG    MG A 302 "
     model   vdw
     1.991 2.170
  nonbonded pdb=" OE1 GLN B  92 "
            pdb="MG    MG B 302 "
     model   vdw
     2.028 2.170
  nonbonded pdb=" OG  SER A  47 "
            pdb="MG    MG A 302 "
     model   vdw
     2.043 2.170
  ... (remaining 56471 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:             3.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.980
  Find NCS groups from input model:        0.040
  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:5.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
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      :  0.003   0.048   6630  Z= 0.115
  Angle     :  0.522   7.334   8994  Z= 0.270
  Chirality :  0.041   0.147   1034
  Planarity :  0.004   0.057   1127
  Dihedral  : 13.556  87.345   2429
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.29), residues: 814
  helix:  1.57 (0.25), residues: 452
  sheet: -0.80 (0.52), residues: 74
  loop : -0.66 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 181 
 TYR   0.008   0.001   TYR B 162 
 PHE   0.011   0.001   PHE C  50 
 TRP   0.009   0.001   TRP B 128 
 HIS   0.002   0.000   HIS A  10 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.12 ( 6630)
  covalent geometry    : angle       0.52218 /  0.27 ( 8994)
  hydrogen bonds       : bond        0.14816 /  9.96 (  348)
  hydrogen bonds       : angle       5.51961 /  4.06 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7829 (tt0) cc_final: 0.7373 (tt0)
REVERT: A  184 ASP cc_start: 0.8172 (m-30) cc_final: 0.7873 (m-30)
REVERT: C  106 LEU cc_start: 0.5436 (tt) cc_final: 0.4988 (tm)
  outliers start: 0
  outliers final: 1
  residues processed: 114
  average time/residue: 0.4621
  time to fit residues: 55.3661
Evaluate side-chains
  91 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  189 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  10 HIS
B 243 HIS
C 181 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.160409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.121801 restraints weight = 6384.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 1.68
r_work: 0.3215 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.1032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   6630  Z= 0.191
  Angle     :  0.592   7.601   8994  Z= 0.301
  Chirality :  0.044   0.144   1034
  Planarity :  0.005   0.062   1127
  Dihedral  :  4.738  43.443    879
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  :  8.00 %
    Favored  : 89.57 %
  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: 814
  helix:  1.59 (0.24), residues: 448
  sheet: -0.57 (0.54), residues: 73
  loop : -0.48 (0.34), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 181 
 TYR   0.015   0.001   TYR C 251 
 PHE   0.013   0.001   PHE B 116 
 TRP   0.012   0.001   TRP A  80 
 HIS   0.007   0.001   HIS A  10 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00471 /  0.19 ( 6630)
  covalent geometry    : angle       0.59200 /  0.30 ( 8994)
  hydrogen bonds       : bond        0.04337 /  2.99 (  348)
  hydrogen bonds       : angle       4.55560 /  3.31 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A   62 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7751 (mm)
REVERT: A  180 GLU cc_start: 0.8134 (tt0) cc_final: 0.7613 (tt0)
REVERT: A  184 ASP cc_start: 0.8263 (m-30) cc_final: 0.7892 (m-30)
REVERT: A  264 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7163 (mt-10)
REVERT: B    4 LYS cc_start: 0.8166 (ttpt) cc_final: 0.7959 (ttpt)
REVERT: B   82 ASP cc_start: 0.7578 (t0) cc_final: 0.7114 (m-30)
REVERT: C  208 PHE cc_start: 0.6460 (OUTLIER) cc_final: 0.5987 (t80)
REVERT: C  231 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7301 (tm-30)
  outliers start: 17
  outliers final: 5
  residues processed: 102
  average time/residue: 0.4358
  time to fit residues: 46.8527
Evaluate side-chains
  101 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue    6 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  208 PHE
Chi-restraints excluded: chain C residue  231 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 12 optimal weight:    0.2980
   chunk 19 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 27 optimal weight:    0.6980
   chunk 32 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  10 HIS
B  77 ASN
B 226 HIS
B 243 HIS
C 189 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.160285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.122575 restraints weight = 6373.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 1.60
r_work: 0.3230 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.1116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6630  Z= 0.148
  Angle     :  0.536   7.505   8994  Z= 0.273
  Chirality :  0.042   0.143   1034
  Planarity :  0.005   0.060   1127
  Dihedral  :  4.580  41.217    877
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 10.29 %
    Favored  : 87.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.29), residues: 814
  helix:  1.67 (0.24), residues: 454
  sheet: -0.59 (0.54), residues: 73
  loop : -0.43 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 181 
 TYR   0.011   0.001   TYR C 251 
 PHE   0.012   0.001   PHE A 231 
 TRP   0.012   0.001   TRP B 128 
 HIS   0.005   0.001   HIS A  10 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.15 ( 6630)
  covalent geometry    : angle       0.53640 /  0.27 ( 8994)
  hydrogen bonds       : bond        0.03869 /  2.67 (  348)
  hydrogen bonds       : angle       4.36796 /  3.18 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A   62 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7792 (mm)
REVERT: A  180 GLU cc_start: 0.8124 (tt0) cc_final: 0.7649 (tt0)
REVERT: A  184 ASP cc_start: 0.8226 (m-30) cc_final: 0.7881 (m-30)
REVERT: A  264 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7182 (mt-10)
REVERT: B    4 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7857 (ttpt)
REVERT: B   82 ASP cc_start: 0.7542 (t0) cc_final: 0.7083 (m-30)
REVERT: C  208 PHE cc_start: 0.6474 (OUTLIER) cc_final: 0.6004 (t80)
  outliers start: 19
  outliers final: 8
  residues processed: 101
  average time/residue: 0.4275
  time to fit residues: 45.3744
Evaluate side-chains
  99 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  208 PHE
Chi-restraints excluded: chain C residue  259 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0270
   chunk 18 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.7240

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  10 HIS
B 243 HIS
C 189 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.160518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.122505 restraints weight = 6453.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 1.56
r_work: 0.3223 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.1250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6630  Z= 0.153
  Angle     :  0.539   7.399   8994  Z= 0.273
  Chirality :  0.043   0.144   1034
  Planarity :  0.005   0.062   1127
  Dihedral  :  4.585  41.751    877
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 11.86 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.29), residues: 814
  helix:  1.73 (0.24), residues: 454
  sheet: -0.66 (0.53), residues: 73
  loop : -0.46 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 181 
 TYR   0.011   0.001   TYR C 251 
 PHE   0.011   0.001   PHE A 231 
 TRP   0.012   0.001   TRP B 128 
 HIS   0.006   0.001   HIS A  10 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00376 /  0.15 ( 6630)
  covalent geometry    : angle       0.53922 /  0.27 ( 8994)
  hydrogen bonds       : bond        0.03739 /  2.58 (  348)
  hydrogen bonds       : angle       4.31642 /  3.14 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A   62 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7759 (mm)
REVERT: A  173 MET cc_start: 0.8939 (mtm) cc_final: 0.8696 (mtt)
REVERT: A  180 GLU cc_start: 0.8129 (tt0) cc_final: 0.7661 (tt0)
REVERT: A  184 ASP cc_start: 0.8227 (m-30) cc_final: 0.7890 (m-30)
REVERT: A  264 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7140 (mt-10)
REVERT: B   82 ASP cc_start: 0.7563 (t0) cc_final: 0.7090 (m-30)
REVERT: B  118 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7147 (mp0)
REVERT: C   87 MET cc_start: 0.4295 (mtt) cc_final: 0.4034 (pp-130)
REVERT: C  208 PHE cc_start: 0.6475 (OUTLIER) cc_final: 0.6016 (t80)
REVERT: C  231 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7298 (tm-30)
  outliers start: 17
  outliers final: 7
  residues processed: 98
  average time/residue: 0.4487
  time to fit residues: 46.2244
Evaluate side-chains
  99 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  208 PHE
Chi-restraints excluded: chain C residue  231 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 35 optimal weight:    0.2980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  10 HIS
B 243 HIS
C 189 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.161456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.122780 restraints weight = 6422.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 1.62
r_work: 0.3225 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6630  Z= 0.146
  Angle     :  0.531   7.480   8994  Z= 0.269
  Chirality :  0.043   0.148   1034
  Planarity :  0.005   0.061   1127
  Dihedral  :  4.536  41.245    877
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 12.57 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.29), residues: 814
  helix:  1.78 (0.24), residues: 454
  sheet: -0.67 (0.53), residues: 73
  loop : -0.47 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 181 
 TYR   0.011   0.001   TYR C 251 
 PHE   0.012   0.001   PHE A 231 
 TRP   0.011   0.001   TRP B 128 
 HIS   0.005   0.001   HIS A  10 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.15 ( 6630)
  covalent geometry    : angle       0.53059 /  0.27 ( 8994)
  hydrogen bonds       : bond        0.03631 /  2.51 (  348)
  hydrogen bonds       : angle       4.28706 /  3.12 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A   62 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7828 (mm)
REVERT: A  173 MET cc_start: 0.8933 (mtm) cc_final: 0.8686 (mtt)
REVERT: A  180 GLU cc_start: 0.8133 (tt0) cc_final: 0.7655 (tt0)
REVERT: A  184 ASP cc_start: 0.8219 (m-30) cc_final: 0.7879 (m-30)
REVERT: A  264 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7115 (mt-10)
REVERT: B   82 ASP cc_start: 0.7543 (t0) cc_final: 0.7060 (m-30)
REVERT: B  118 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7105 (mp0)
REVERT: C   87 MET cc_start: 0.4305 (mtt) cc_final: 0.3911 (pp-130)
REVERT: C  208 PHE cc_start: 0.6460 (OUTLIER) cc_final: 0.6016 (t80)
REVERT: C  231 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7273 (tm-30)
  outliers start: 19
  outliers final: 9
  residues processed: 104
  average time/residue: 0.4245
  time to fit residues: 46.5768
Evaluate side-chains
  106 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue    6 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  163 GLU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  208 PHE
Chi-restraints excluded: chain C residue  231 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 34 optimal weight:    0.1980
   chunk 76 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 64 optimal weight:    0.4980
   overall best weight:    0.7184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  10 HIS
B 243 HIS
C 181 GLN
C 189 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.161233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.122535 restraints weight = 6382.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.61
r_work: 0.3225 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.1350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6630  Z= 0.151
  Angle     :  0.540   7.409   8994  Z= 0.273
  Chirality :  0.043   0.155   1034
  Planarity :  0.005   0.062   1127
  Dihedral  :  4.541  41.666    877
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.14 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.29), residues: 814
  helix:  1.78 (0.24), residues: 455
  sheet: -0.64 (0.53), residues: 73
  loop : -0.48 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 181 
 TYR   0.012   0.001   TYR C 251 
 PHE   0.011   0.001   PHE A 231 
 TRP   0.011   0.001   TRP B 128 
 HIS   0.005   0.001   HIS A  10 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00373 /  0.15 ( 6630)
  covalent geometry    : angle       0.54027 /  0.27 ( 8994)
  hydrogen bonds       : bond        0.03646 /  2.52 (  348)
  hydrogen bonds       : angle       4.29081 /  3.13 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A   62 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7837 (mm)
REVERT: A  173 MET cc_start: 0.8937 (mtm) cc_final: 0.8701 (mtt)
REVERT: A  180 GLU cc_start: 0.8150 (tt0) cc_final: 0.7701 (tt0)
REVERT: A  184 ASP cc_start: 0.8225 (m-30) cc_final: 0.7887 (m-30)
REVERT: A  218 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8243 (m-30)
REVERT: A  264 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7035 (mt-10)
REVERT: B   82 ASP cc_start: 0.7577 (t0) cc_final: 0.7089 (m-30)
REVERT: B  120 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7736 (mt-10)
REVERT: B  214 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7471 (t70)
REVERT: C  208 PHE cc_start: 0.6498 (OUTLIER) cc_final: 0.6070 (t80)
REVERT: C  231 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7263 (tm-30)
  outliers start: 20
  outliers final: 9
  residues processed: 104
  average time/residue: 0.4007
  time to fit residues: 43.8763
Evaluate side-chains
  104 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue    6 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  163 GLU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  214 ASP
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  208 PHE
Chi-restraints excluded: chain C residue  231 GLU
Chi-restraints excluded: chain C residue  260 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   chunk 41 optimal weight:    0.4980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  10 HIS
B 243 HIS
C 189 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.161689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.122957 restraints weight = 6346.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 1.63
r_work: 0.3230 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6630  Z= 0.141
  Angle     :  0.533   8.110   8994  Z= 0.268
  Chirality :  0.043   0.159   1034
  Planarity :  0.005   0.060   1127
  Dihedral  :  4.490  40.747    877
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 13.43 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.29), residues: 814
  helix:  1.82 (0.24), residues: 455
  sheet: -0.64 (0.53), residues: 73
  loop : -0.48 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 181 
 TYR   0.012   0.001   TYR C 251 
 PHE   0.011   0.001   PHE A 231 
 TRP   0.011   0.001   TRP B 128 
 HIS   0.006   0.001   HIS A  10 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.14 ( 6630)
  covalent geometry    : angle       0.53297 /  0.27 ( 8994)
  hydrogen bonds       : bond        0.03540 /  2.45 (  348)
  hydrogen bonds       : angle       4.27573 /  3.12 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A  173 MET cc_start: 0.8938 (mtm) cc_final: 0.8699 (mtt)
REVERT: A  180 GLU cc_start: 0.8129 (tt0) cc_final: 0.7659 (tt0)
REVERT: A  184 ASP cc_start: 0.8225 (m-30) cc_final: 0.7894 (m-30)
REVERT: A  218 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8231 (m-30)
REVERT: A  264 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7033 (mt-10)
REVERT: B    4 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7937 (ttpt)
REVERT: B   82 ASP cc_start: 0.7564 (t0) cc_final: 0.7063 (m-30)
REVERT: B  118 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7166 (mp0)
REVERT: B  120 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7702 (mt-10)
REVERT: B  214 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7430 (t70)
REVERT: C  208 PHE cc_start: 0.6494 (OUTLIER) cc_final: 0.6077 (t80)
REVERT: C  231 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7281 (tm-30)
  outliers start: 21
  outliers final: 10
  residues processed: 103
  average time/residue: 0.4283
  time to fit residues: 46.4928
Evaluate side-chains
  109 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue    6 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  163 GLU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  214 ASP
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  208 PHE
Chi-restraints excluded: chain C residue  231 GLU
Chi-restraints excluded: chain C residue  260 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 20 optimal weight:    0.2980
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  10 HIS
B 243 HIS
C 189 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.160996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.122338 restraints weight = 6395.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.60
r_work: 0.3220 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   6630  Z= 0.164
  Angle     :  0.569  12.525   8994  Z= 0.283
  Chirality :  0.044   0.198   1034
  Planarity :  0.005   0.061   1127
  Dihedral  :  4.566  42.089    877
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 13.86 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.29), residues: 814
  helix:  1.74 (0.24), residues: 455
  sheet: -0.63 (0.53), residues: 73
  loop : -0.49 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 181 
 TYR   0.013   0.001   TYR C 251 
 PHE   0.013   0.001   PHE C  50 
 TRP   0.011   0.001   TRP B 128 
 HIS   0.006   0.001   HIS A  10 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00414 /  0.16 ( 6630)
  covalent geometry    : angle       0.56936 /  0.28 ( 8994)
  hydrogen bonds       : bond        0.03754 /  2.59 (  348)
  hydrogen bonds       : angle       4.36836 /  3.21 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A   62 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7862 (mm)
REVERT: A  173 MET cc_start: 0.8935 (mtm) cc_final: 0.8697 (mtt)
REVERT: A  180 GLU cc_start: 0.8147 (tt0) cc_final: 0.7698 (tt0)
REVERT: A  184 ASP cc_start: 0.8255 (m-30) cc_final: 0.7915 (m-30)
REVERT: A  218 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8244 (m-30)
REVERT: A  264 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7049 (mt-10)
REVERT: B    4 LYS cc_start: 0.8157 (ttpt) cc_final: 0.7942 (ttpt)
REVERT: B   82 ASP cc_start: 0.7578 (t0) cc_final: 0.7105 (m-30)
REVERT: B  118 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7183 (mp0)
REVERT: B  120 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7570 (mt-10)
REVERT: B  214 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7482 (t70)
REVERT: C  208 PHE cc_start: 0.6477 (OUTLIER) cc_final: 0.6041 (t80)
REVERT: C  231 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7267 (tm-30)
REVERT: C  257 ILE cc_start: 0.7176 (OUTLIER) cc_final: 0.6716 (mt)
  outliers start: 21
  outliers final: 12
  residues processed: 107
  average time/residue: 0.4360
  time to fit residues: 49.1983
Evaluate side-chains
  110 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue    6 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  163 GLU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  214 ASP
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  208 PHE
Chi-restraints excluded: chain C residue  231 GLU
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain C residue  260 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0570
   chunk 57 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.6698

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  10 HIS
B 243 HIS
C 189 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.160739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.122936 restraints weight = 6515.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 1.56
r_work: 0.3226 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   6630  Z= 0.146
  Angle     :  0.528   7.471   8994  Z= 0.267
  Chirality :  0.042   0.142   1034
  Planarity :  0.005   0.060   1127
  Dihedral  :  4.487  40.918    877
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.29 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.29), residues: 814
  helix:  1.82 (0.24), residues: 455
  sheet: -0.65 (0.53), residues: 73
  loop : -0.48 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 181 
 TYR   0.012   0.001   TYR C 251 
 PHE   0.012   0.001   PHE A 231 
 TRP   0.012   0.001   TRP B 128 
 HIS   0.006   0.001   HIS A  10 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.15 ( 6630)
  covalent geometry    : angle       0.52784 /  0.27 ( 8994)
  hydrogen bonds       : bond        0.03594 /  2.49 (  348)
  hydrogen bonds       : angle       4.29599 /  3.15 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A   62 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7826 (mm)
REVERT: A  173 MET cc_start: 0.8937 (mtm) cc_final: 0.8696 (mtt)
REVERT: A  180 GLU cc_start: 0.8142 (tt0) cc_final: 0.7672 (tt0)
REVERT: A  184 ASP cc_start: 0.8259 (m-30) cc_final: 0.7932 (m-30)
REVERT: A  218 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8226 (m-30)
REVERT: A  264 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6997 (mt-10)
REVERT: B    4 LYS cc_start: 0.8152 (ttpt) cc_final: 0.7934 (ttpt)
REVERT: B   82 ASP cc_start: 0.7557 (t0) cc_final: 0.7064 (m-30)
REVERT: B  118 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7129 (mp0)
REVERT: B  120 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7594 (mt-10)
REVERT: B  214 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7478 (t70)
REVERT: C  208 PHE cc_start: 0.6455 (OUTLIER) cc_final: 0.6028 (t80)
REVERT: C  231 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7249 (tm-30)
REVERT: C  257 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6735 (mt)
  outliers start: 19
  outliers final: 11
  residues processed: 103
  average time/residue: 0.4048
  time to fit residues: 44.0124
Evaluate side-chains
  113 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue    6 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  163 GLU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  214 ASP
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  208 PHE
Chi-restraints excluded: chain C residue  231 GLU
Chi-restraints excluded: chain C residue  257 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 55 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 69 optimal weight:    0.3980
   chunk 6 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  10 HIS
B 243 HIS
C 189 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.161740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.123653 restraints weight = 6319.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.60
r_work: 0.3241 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.1438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6630  Z= 0.136
  Angle     :  0.542  10.459   8994  Z= 0.268
  Chirality :  0.042   0.179   1034
  Planarity :  0.005   0.060   1127
  Dihedral  :  4.431  39.603    877
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 14.57 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.29), residues: 814
  helix:  1.84 (0.24), residues: 454
  sheet: -0.63 (0.53), residues: 73
  loop : -0.45 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 181 
 TYR   0.011   0.001   TYR C 251 
 PHE   0.011   0.001   PHE A 231 
 TRP   0.011   0.001   TRP B 128 
 HIS   0.007   0.001   HIS A  10 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.14 ( 6630)
  covalent geometry    : angle       0.54173 /  0.27 ( 8994)
  hydrogen bonds       : bond        0.03498 /  2.43 (  348)
  hydrogen bonds       : angle       4.30596 /  3.16 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A   62 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7877 (mm)
REVERT: A  173 MET cc_start: 0.8933 (mtm) cc_final: 0.8679 (mtt)
REVERT: A  180 GLU cc_start: 0.8136 (tt0) cc_final: 0.7667 (tt0)
REVERT: A  184 ASP cc_start: 0.8228 (m-30) cc_final: 0.7900 (m-30)
REVERT: A  218 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8215 (m-30)
REVERT: A  264 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7018 (mt-10)
REVERT: B    4 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7930 (ttpt)
REVERT: B   82 ASP cc_start: 0.7548 (t0) cc_final: 0.7061 (m-30)
REVERT: B  118 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7133 (mp0)
REVERT: B  120 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7512 (mt-10)
REVERT: B  214 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7439 (t70)
REVERT: C  208 PHE cc_start: 0.6546 (OUTLIER) cc_final: 0.6120 (t80)
REVERT: C  231 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7276 (tm-30)
REVERT: C  257 ILE cc_start: 0.7214 (OUTLIER) cc_final: 0.6748 (mt)
  outliers start: 18
  outliers final: 10
  residues processed: 101
  average time/residue: 0.4098
  time to fit residues: 43.7128
Evaluate side-chains
  108 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue    6 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  163 GLU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  214 ASP
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  208 PHE
Chi-restraints excluded: chain C residue  231 GLU
Chi-restraints excluded: chain C residue  257 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 64 optimal weight:    0.0070
   chunk 39 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.5998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  10 HIS
B 243 HIS
C 189 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.161796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.123794 restraints weight = 6401.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.56
r_work: 0.3238 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6630  Z= 0.138
  Angle     :  0.551  13.771   8994  Z= 0.270
  Chirality :  0.042   0.182   1034
  Planarity :  0.005   0.060   1127
  Dihedral  :  4.420  38.991    877
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.71 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.29), residues: 814
  helix:  1.82 (0.24), residues: 454
  sheet: -0.62 (0.53), residues: 73
  loop : -0.46 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 181 
 TYR   0.011   0.001   TYR C 251 
 PHE   0.011   0.001   PHE A 231 
 TRP   0.011   0.001   TRP B 128 
 HIS   0.007   0.001   HIS A  10 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.14 ( 6630)
  covalent geometry    : angle       0.55060 /  0.27 ( 8994)
  hydrogen bonds       : bond        0.03481 /  2.43 (  348)
  hydrogen bonds       : angle       4.31187 /  3.17 ( 1002)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2036.79 seconds
wall clock time: 35 minutes 26.21 seconds (2126.21 seconds total)