Starting phenix.real_space_refine
on Fri Jun  6 09:03:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8faz_28961/06_2025/8faz_28961.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8faz_28961/06_2025/8faz_28961.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8faz_28961/06_2025/8faz_28961.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8faz_28961/06_2025/8faz_28961.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8faz_28961/06_2025/8faz_28961.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8faz_28961/06_2025/8faz_28961.cif"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.015
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       8      5.49       5
     Mg      2      5.21       5
     S      50      5.16       5
     C    4619      2.51       5
     N    1275      2.21       5
     O    1377      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7331
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 570
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 570
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 2, 'TRANS': 70}
    Chain: "C"
      Number of atoms: 2470
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2470
          Classifications: {'peptide': 314}
          Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 301}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2288
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2288
          Classifications: {'peptide': 303}
          Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 294}
          Chain breaks: 2
    Chain: "X"
      Number of atoms: 1912
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1912
          Classifications: {'peptide': 236}
          Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 229}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "X"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.64, per 1000 atoms: 0.63
  Number of scatterers: 7331
  At special positions: 0
  Unit cell: (68.73, 80.91, 111.36, 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      50     16.00
     P       8     15.00
     Mg      2     11.99
     O    1377      8.00
     N    1275      7.00
     C    4619      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: 1.88
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1728

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 5 sheets defined
      52.6% alpha, 18.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'B' and resid 12 through 21
    Processing helix  chain 'B' and resid 26 through 33
      removed outlier: 3.515A  pdb=" N   LEU B  33 " --> pdb=" O   ASP B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 42
      removed outlier: 4.061A  pdb=" N   LYS B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 58
    Processing helix  chain 'B' and resid 67 through 75
    Processing helix  chain 'C' and resid 13 through 17
    Processing helix  chain 'C' and resid 20 through 30
    Processing helix  chain 'C' and resid 34 through 40
      removed outlier: 3.857A  pdb=" N   LEU C  38 " --> pdb=" O   THR C  34 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   GLU C  40 " --> pdb=" O   GLU C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 51
    Processing helix  chain 'C' and resid 53 through 67
    Processing helix  chain 'C' and resid 87 through 97
    Processing helix  chain 'C' and resid 104 through 110
    Processing helix  chain 'C' and resid 130 through 143
      removed outlier: 3.536A  pdb=" N   VAL C 140 " --> pdb=" O   MET C 136 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   GLN C 143 " --> pdb=" O   ALA C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 149
      removed outlier: 6.100A  pdb=" N   CYS C 147 " --> pdb=" O   ILE C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 187
      removed outlier: 3.883A  pdb=" N   GLU C 185 " --> pdb=" O   GLN C 181 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   LYS C 186 " --> pdb=" O   LEU C 182 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   HIS C 187 " --> pdb=" O   ILE C 183 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 189 through 196
      removed outlier: 4.174A  pdb=" N   ARG C 193 " --> pdb=" O   GLY C 189 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   ALA C 195 " --> pdb=" O   GLU C 191 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 207
    Processing helix  chain 'C' and resid 215 through 225
    Processing helix  chain 'C' and resid 225 through 233
    Processing helix  chain 'C' and resid 246 through 250
      removed outlier: 3.749A  pdb=" N   HIS C 250 " --> pdb=" O   PRO C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 254 through 277
    Processing helix  chain 'C' and resid 303 through 308
    Processing helix  chain 'D' and resid 13 through 23
      removed outlier: 3.650A  pdb=" N   HIS D  23 " --> pdb=" O   LEU D  19 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 27 through 34
    Processing helix  chain 'D' and resid 35 through 44
    Processing helix  chain 'D' and resid 46 through 62
    Processing helix  chain 'D' and resid 68 through 77
      removed outlier: 3.536A  pdb=" N   THR D  77 " --> pdb=" O   GLU D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 86 through 91
      removed outlier: 3.510A  pdb=" N   LYS D  91 " --> pdb=" O   GLY D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 112 through 127
    Processing helix  chain 'D' and resid 142 through 154
    Processing helix  chain 'D' and resid 156 through 166
      removed outlier: 3.553A  pdb=" N   ALA D 161 " --> pdb=" O   GLU D 157 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 174 through 192
    Processing helix  chain 'D' and resid 207 through 216
      removed outlier: 3.864A  pdb=" N   VAL D 211 " --> pdb=" O   SER D 207 " (cutoff:3.500A)
      Proline residue:  D 214  - end of helix
    Processing helix  chain 'D' and resid 221 through 240
    Processing helix  chain 'D' and resid 267 through 271
      removed outlier: 3.639A  pdb=" N   PHE D 270 " --> pdb=" O   SER D 267 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 23 through 28
    Processing helix  chain 'X' and resid 53 through 67
    Processing helix  chain 'X' and resid 88 through 100
    Processing helix  chain 'X' and resid 104 through 114
      removed outlier: 3.683A  pdb=" N   ARG X 114 " --> pdb=" O   TYR X 110 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 122 through 140
      removed outlier: 3.694A  pdb=" N   GLU X 134 " --> pdb=" O   LEU X 130 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   SER X 135 " --> pdb=" O   TYR X 131 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   MET X 136 " --> pdb=" O   SER X 132 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 154 through 162
    Processing helix  chain 'X' and resid 165 through 170
    Processing helix  chain 'X' and resid 170 through 188
    Processing helix  chain 'X' and resid 228 through 233
    Processing sheet with id=AA1, first strand: chain 'B' and resid 65 through 66
      removed outlier: 5.307A  pdb=" N   GLU C 154 " --> pdb=" O   VAL C 236 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   THR C 120 " --> pdb=" O   ILE C 311 " (cutoff:3.500A)
      removed outlier: 7.823A  pdb=" N   LEU C 313 " --> pdb=" O   THR C 120 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   GLU C 122 " --> pdb=" O   LEU C 313 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   PHE C 315 " --> pdb=" O   GLU C 122 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   CYS C 124 " --> pdb=" O   PHE C 315 " (cutoff:3.500A)
      removed outlier: 8.599A  pdb=" N   TRP C 317 " --> pdb=" O   CYS C 124 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   ARG C 312 " --> pdb=" O   TYR C 327 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 85 through 86
      removed outlier: 6.404A  pdb=" N   VAL D 132 " --> pdb=" O   GLN D 168 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   VAL D 170 " --> pdb=" O   VAL D 132 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   TYR D 134 " --> pdb=" O   VAL D 170 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ASN D 131 " --> pdb=" O   VAL D 200 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL D 202 " --> pdb=" O   ASN D 131 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   LYS D 201 " --> pdb=" O   ALA D 244 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   VAL D 246 " --> pdb=" O   LYS D 201 " (cutoff:3.500A)
      removed outlier: 5.952A  pdb=" N   VAL D 203 " --> pdb=" O   VAL D 246 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   THR D 248 " --> pdb=" O   VAL D 203 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   VAL D 205 " --> pdb=" O   THR D 248 " (cutoff:3.500A)
      removed outlier: 8.774A  pdb=" N   HIS D 250 " --> pdb=" O   VAL D 205 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 85 through 86
      removed outlier: 6.404A  pdb=" N   VAL D 132 " --> pdb=" O   GLN D 168 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   VAL D 170 " --> pdb=" O   VAL D 132 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   TYR D 134 " --> pdb=" O   VAL D 170 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ASN D 131 " --> pdb=" O   VAL D 200 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL D 202 " --> pdb=" O   ASN D 131 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   LYS D 201 " --> pdb=" O   ALA D 244 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   VAL D 246 " --> pdb=" O   LYS D 201 " (cutoff:3.500A)
      removed outlier: 5.952A  pdb=" N   VAL D 203 " --> pdb=" O   VAL D 246 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   THR D 248 " --> pdb=" O   VAL D 203 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   VAL D 205 " --> pdb=" O   THR D 248 " (cutoff:3.500A)
      removed outlier: 8.774A  pdb=" N   HIS D 250 " --> pdb=" O   VAL D 205 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   THR D 103 " --> pdb=" O   VAL D 247 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   ASN D 249 " --> pdb=" O   THR D 103 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   ILE D 105 " --> pdb=" O   ASN D 249 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ILE D 251 " --> pdb=" O   ILE D 105 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   GLY D 107 " --> pdb=" O   ILE D 251 " (cutoff:3.500A)
      removed outlier: 9.726A  pdb=" N   ARG D 253 " --> pdb=" O   GLY D 107 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   VAL D 102 " --> pdb=" O   THR D 274 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   ILE D 276 " --> pdb=" O   VAL D 102 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   GLU D 104 " --> pdb=" O   ILE D 276 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   LEU D 278 " --> pdb=" O   GLU D 104 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   VAL D 106 " --> pdb=" O   LEU D 278 " (cutoff:3.500A)
      removed outlier: 8.511A  pdb=" N   THR D 280 " --> pdb=" O   VAL D 106 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ARG D 275 " --> pdb=" O   ALA D 296 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 340 through 342
    Processing sheet with id=AA5, first strand: chain 'D' and resid 66 through 67
      removed outlier: 6.768A  pdb=" N   GLU X  77 " --> pdb=" O   LEU X 145 " (cutoff:3.500A)
      removed outlier: 8.235A  pdb=" N   ILE X 147 " --> pdb=" O   GLU X  77 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   LEU X  79 " --> pdb=" O   ILE X 147 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   ASP X  42 " --> pdb=" O   LEU X 191 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   ALA X 193 " --> pdb=" O   ASP X  42 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   LEU X  44 " --> pdb=" O   ALA X 193 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   THR X 195 " --> pdb=" O   LEU X  44 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   PHE X  46 " --> pdb=" O   THR X 195 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   ILE X  43 " --> pdb=" O   HIS X 237 " (cutoff:3.500A)
      removed outlier: 8.524A  pdb=" N   MET X 239 " --> pdb=" O   ILE X  43 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   GLU X  45 " --> pdb=" O   MET X 239 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   PHE X 241 " --> pdb=" O   GLU X  45 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   HIS X  47 " --> pdb=" O   PHE X 241 " (cutoff:3.500A)
      removed outlier: 8.614A  pdb=" N   LYS X 243 " --> pdb=" O   HIS X  47 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   PHE X 269 " --> pdb=" O   CYS X 280 " (cutoff:3.500A)

    371 hydrogen bonds defined for protein.
    1056 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: 2.34

  Time building geometry restraints manager: 2.23 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: 2410
        1.34 -     1.46: 1539
        1.46 -     1.58: 3409
        1.58 -     1.69: 13
        1.69 -     1.81: 72
  Bond restraints: 7443
  Sorted by residual:
  bond pdb=" O3A ANP D 401 "
       pdb=" PB  ANP D 401 "
    ideal  model  delta    sigma   weight residual
    1.700  1.555  0.145 2.00e-02 2.50e+03 5.23e+01
  bond pdb=" O3A ANP X 301 "
       pdb=" PB  ANP X 301 "
    ideal  model  delta    sigma   weight residual
    1.700  1.557  0.143 2.00e-02 2.50e+03 5.10e+01
  bond pdb=" N3B ANP X 301 "
       pdb=" PG  ANP X 301 "
    ideal  model  delta    sigma   weight residual
    1.795  1.690  0.105 2.00e-02 2.50e+03 2.73e+01
  bond pdb=" N3B ANP D 401 "
       pdb=" PG  ANP D 401 "
    ideal  model  delta    sigma   weight residual
    1.795  1.691  0.104 2.00e-02 2.50e+03 2.73e+01
  bond pdb=" O5' ANP D 401 "
       pdb=" PA  ANP D 401 "
    ideal  model  delta    sigma   weight residual
    1.655  1.579  0.076 2.00e-02 2.50e+03 1.43e+01
  ... (remaining 7438 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.47: 10005
        3.47 -     6.95: 44
        6.95 -    10.42: 4
       10.42 -    13.89: 2
       13.89 -    17.36: 2
  Bond angle restraints: 10057
  Sorted by residual:
  angle pdb=" PB  ANP X 301 "
        pdb=" N3B ANP X 301 "
        pdb=" PG  ANP X 301 "
      ideal   model   delta    sigma   weight residual
     126.95  109.59   17.36 3.00e+00 1.11e-01 3.35e+01
  angle pdb=" PB  ANP D 401 "
        pdb=" N3B ANP D 401 "
        pdb=" PG  ANP D 401 "
      ideal   model   delta    sigma   weight residual
     126.95  109.85   17.10 3.00e+00 1.11e-01 3.25e+01
  angle pdb=" N   ILE C 183 "
        pdb=" CA  ILE C 183 "
        pdb=" C   ILE C 183 "
      ideal   model   delta    sigma   weight residual
     112.80  108.50    4.30 1.15e+00 7.56e-01 1.40e+01
  angle pdb=" O1B ANP D 401 "
        pdb=" PB  ANP D 401 "
        pdb=" O2B ANP D 401 "
      ideal   model   delta    sigma   weight residual
     120.08  109.22   10.86 3.00e+00 1.11e-01 1.31e+01
  angle pdb=" O1B ANP X 301 "
        pdb=" PB  ANP X 301 "
        pdb=" O2B ANP X 301 "
      ideal   model   delta    sigma   weight residual
     120.08  109.40   10.68 3.00e+00 1.11e-01 1.27e+01
  ... (remaining 10052 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.63: 4424
       26.63 -    53.26: 106
       53.26 -    79.90: 8
       79.90 -   106.53: 3
      106.53 -   133.16: 1
  Dihedral angle restraints: 4542
    sinusoidal: 1879
      harmonic: 2663
  Sorted by residual:
  dihedral pdb=" O1B ADP C 401 "
           pdb=" O3A ADP C 401 "
           pdb=" PB  ADP C 401 "
           pdb=" PA  ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   73.16 -133.16     1      2.00e+01 2.50e-03 4.04e+01
  dihedral pdb=" O2A ADP C 401 "
           pdb=" O3A ADP C 401 "
           pdb=" PA  ADP C 401 "
           pdb=" PB  ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -147.03   87.03     1      2.00e+01 2.50e-03 2.28e+01
  dihedral pdb=" C5' ADP C 401 "
           pdb=" O5' ADP C 401 "
           pdb=" PA  ADP C 401 "
           pdb=" O2A ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   -0.52  -59.48     1      2.00e+01 2.50e-03 1.18e+01
  ... (remaining 4539 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1038
       0.056 -    0.112: 129
       0.112 -    0.167: 8
       0.167 -    0.223: 0
       0.223 -    0.279: 2
  Chirality restraints: 1177
  Sorted by residual:
  chirality pdb=" C3' ANP X 301 "
            pdb=" C2' ANP X 301 "
            pdb=" C4' ANP X 301 "
            pdb=" O3' ANP X 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.64    0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" C3' ANP D 401 "
            pdb=" C2' ANP D 401 "
            pdb=" C4' ANP D 401 "
            pdb=" O3' ANP D 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.63    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  ILE C 144 "
            pdb=" N   ILE C 144 "
            pdb=" C   ILE C 144 "
            pdb=" CB  ILE C 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.86e-01
  ... (remaining 1174 not shown)

  Planarity restraints: 1258
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY X  48 "   -0.018 5.00e-02 4.00e+02   2.77e-02 1.23e+00
        pdb=" N   PRO X  49 "    0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO X  49 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO X  49 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 342 "    0.018 5.00e-02 4.00e+02   2.68e-02 1.15e+00
        pdb=" N   PRO C 343 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO C 343 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO C 343 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  42 "    0.017 5.00e-02 4.00e+02   2.50e-02 9.98e-01
        pdb=" N   PRO C  43 "   -0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO C  43 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO C  43 "    0.014 5.00e-02 4.00e+02
  ... (remaining 1255 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 82
        2.57 -     3.15: 5991
        3.15 -     3.73: 12089
        3.73 -     4.32: 17103
        4.32 -     4.90: 27967
  Nonbonded interactions: 63232
  Sorted by model distance:
  nonbonded pdb=" OG1 THR X  55 "
            pdb="MG    MG X 302 "
     model   vdw
     1.986 2.170
  nonbonded pdb=" O3G ANP D 401 "
            pdb="MG    MG D 402 "
     model   vdw
     1.992 2.170
  nonbonded pdb=" O1G ANP X 301 "
            pdb="MG    MG X 302 "
     model   vdw
     2.013 2.170
  nonbonded pdb=" OG1 THR D 114 "
            pdb="MG    MG D 402 "
     model   vdw
     2.013 2.170
  nonbonded pdb=" O1B ANP X 301 "
            pdb="MG    MG X 302 "
     model   vdw
     2.027 2.170
  ... (remaining 63227 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:             0.960
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.690
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.145   7443  Z= 0.218
  Angle     :  0.616  17.364  10057  Z= 0.269
  Chirality :  0.039   0.279   1177
  Planarity :  0.003   0.028   1258
  Dihedral  : 11.246 133.159   2814
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  2.74 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.28), residues: 904
  helix:  0.68 (0.25), residues: 417
  sheet:  0.30 (0.45), residues: 151
  loop : -0.19 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP X 231 
 HIS   0.002   0.001   HIS X  40 
 PHE   0.007   0.001   PHE D 173 
 TYR   0.011   0.001   TYR C 210 
 ARG   0.002   0.000   ARG D 275 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23531 (  365)
  hydrogen bonds       : angle       7.52025 ( 1056)
  covalent geometry    : bond        0.00448 ( 7443)
  covalent geometry    : angle       0.61589 (10057)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 190
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
REVERT: B   13 GLN cc_start: 0.7078 (mm-40) cc_final: 0.6856 (mm-40)
REVERT: B   46 TYR cc_start: 0.7941 (t80) cc_final: 0.7361 (t80)
REVERT: C  181 GLN cc_start: 0.7027 (tt0) cc_final: 0.6563 (tm-30)
REVERT: D   36 LEU cc_start: 0.7396 (mt) cc_final: 0.7161 (mm)
REVERT: D  174 ASP cc_start: 0.7860 (m-30) cc_final: 0.7649 (m-30)
REVERT: D  292 MET cc_start: 0.8468 (mmm) cc_final: 0.8043 (mmp)
REVERT: X   26 GLU cc_start: 0.7634 (tt0) cc_final: 0.6915 (tp30)
REVERT: X   64 ARG cc_start: 0.8202 (mtp85) cc_final: 0.7911 (mmm160)
REVERT: X  224 ARG cc_start: 0.8649 (ttt-90) cc_final: 0.8192 (ttt-90)
  outliers start: 4
  outliers final: 2
  residues processed: 193
  average time/residue: 1.1502
  time to fit residues: 234.7372
Evaluate side-chains
  149 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 147
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  200 THR
Chi-restraints excluded: chain C residue  208 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 68 optimal weight:    0.1980
   chunk 38 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0070
   chunk 46 optimal weight:    0.1980
   chunk 36 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.4400

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

Flipped N/Q/H residues before XYZ refinement:
B  65 GLN
C 267 GLN
D  60 GLN
D 301 GLN
X 252 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.131252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.119992 restraints weight = 11786.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.4002 rms_B_bonded: 2.08
r_work: 0.3899 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3763 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7443  Z= 0.134
  Angle     :  0.570   6.541  10057  Z= 0.280
  Chirality :  0.042   0.149   1177
  Planarity :  0.004   0.048   1258
  Dihedral  :  8.150 103.238   1067
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 11.07 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.28), residues: 904
  helix:  0.88 (0.24), residues: 439
  sheet:  0.04 (0.45), residues: 146
  loop : -0.24 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP X 231 
 HIS   0.004   0.001   HIS X  60 
 PHE   0.011   0.001   PHE C 164 
 TYR   0.014   0.001   TYR X 131 
 ARG   0.009   0.000   ARG B  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04237 (  365)
  hydrogen bonds       : angle       5.08805 ( 1056)
  covalent geometry    : bond        0.00295 ( 7443)
  covalent geometry    : angle       0.57047 (10057)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 177
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
REVERT: C  181 GLN cc_start: 0.7434 (tt0) cc_final: 0.6930 (tm-30)
REVERT: C  205 LEU cc_start: 0.7708 (mt) cc_final: 0.7497 (mp)
REVERT: D   36 LEU cc_start: 0.7403 (mt) cc_final: 0.7160 (mm)
REVERT: D  259 ARG cc_start: 0.7789 (pmm-80) cc_final: 0.7465 (pmm-80)
REVERT: X   25 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.6750 (pmmt)
REVERT: X   26 GLU cc_start: 0.7918 (tt0) cc_final: 0.7269 (tp30)
REVERT: X   88 ASP cc_start: 0.7831 (t70) cc_final: 0.7407 (t70)
REVERT: X  259 CYS cc_start: 0.7759 (t) cc_final: 0.7550 (t)
  outliers start: 18
  outliers final: 9
  residues processed: 188
  average time/residue: 1.2355
  time to fit residues: 246.7827
Evaluate side-chains
  165 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 155
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  200 THR
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain D residue  277 LEU
Chi-restraints excluded: chain X residue   25 LYS
Chi-restraints excluded: chain X residue   61 LEU
Chi-restraints excluded: chain X residue   83 THR
Chi-restraints excluded: chain X residue  124 THR
Chi-restraints excluded: chain X residue  171 SER
Chi-restraints excluded: chain X residue  182 LYS
Chi-restraints excluded: chain X residue  239 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0570
   chunk 67 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.8900

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

Flipped N/Q/H residues before XYZ refinement:
C  11 GLN
** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 301 GLN
** X  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X 169 GLN
X 252 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.130295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.118733 restraints weight = 11946.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3987 rms_B_bonded: 2.09
r_work: 0.3881 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3744 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7443  Z= 0.159
  Angle     :  0.566   6.747  10057  Z= 0.277
  Chirality :  0.042   0.148   1177
  Planarity :  0.004   0.052   1258
  Dihedral  :  7.291  77.891   1067
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.17 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.28), residues: 904
  helix:  0.83 (0.24), residues: 439
  sheet: -0.23 (0.43), residues: 151
  loop : -0.16 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D 314 
 HIS   0.006   0.001   HIS X  40 
 PHE   0.010   0.001   PHE C 346 
 TYR   0.015   0.002   TYR X 131 
 ARG   0.010   0.001   ARG B  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03653 (  365)
  hydrogen bonds       : angle       4.77677 ( 1056)
  covalent geometry    : bond        0.00356 ( 7443)
  covalent geometry    : angle       0.56611 (10057)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 164
  time to evaluate  : 0.929 
Fit side-chains
REVERT: C  103 PHE cc_start: 0.7611 (t80) cc_final: 0.7279 (t80)
REVERT: C  181 GLN cc_start: 0.7464 (tt0) cc_final: 0.6921 (tm-30)
REVERT: D  259 ARG cc_start: 0.7825 (pmm-80) cc_final: 0.7539 (pmm-80)
REVERT: X   26 GLU cc_start: 0.7972 (tt0) cc_final: 0.7340 (tp30)
REVERT: X  199 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7755 (mtp)
REVERT: X  259 CYS cc_start: 0.7788 (t) cc_final: 0.7587 (t)
  outliers start: 18
  outliers final: 9
  residues processed: 172
  average time/residue: 1.1355
  time to fit residues: 206.6055
Evaluate side-chains
  161 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 151
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  200 THR
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain D residue  277 LEU
Chi-restraints excluded: chain X residue   27 ILE
Chi-restraints excluded: chain X residue   83 THR
Chi-restraints excluded: chain X residue  124 THR
Chi-restraints excluded: chain X residue  182 LYS
Chi-restraints excluded: chain X residue  199 MET
Chi-restraints excluded: chain X residue  236 LYS
Chi-restraints excluded: chain X residue  239 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 69 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X 169 GLN
X 252 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.129312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.117890 restraints weight = 12126.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3978 rms_B_bonded: 2.08
r_work: 0.3871 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3734 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7443  Z= 0.182
  Angle     :  0.600   6.919  10057  Z= 0.291
  Chirality :  0.043   0.150   1177
  Planarity :  0.004   0.058   1258
  Dihedral  :  6.767  74.861   1067
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 15.67 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.28), residues: 904
  helix:  0.93 (0.25), residues: 427
  sheet: -0.39 (0.43), residues: 153
  loop :  0.03 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D 314 
 HIS   0.008   0.001   HIS X  40 
 PHE   0.017   0.002   PHE C 248 
 TYR   0.014   0.001   TYR X 131 
 ARG   0.011   0.001   ARG B  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03529 (  365)
  hydrogen bonds       : angle       4.70781 ( 1056)
  covalent geometry    : bond        0.00408 ( 7443)
  covalent geometry    : angle       0.59990 (10057)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 157
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  103 PHE cc_start: 0.7576 (t80) cc_final: 0.7287 (t80)
REVERT: C  181 GLN cc_start: 0.7468 (tt0) cc_final: 0.6949 (tm-30)
REVERT: D   16 MET cc_start: 0.6115 (ptp) cc_final: 0.5804 (ptm)
REVERT: D  259 ARG cc_start: 0.7827 (pmm-80) cc_final: 0.7522 (pmm-80)
REVERT: X   26 GLU cc_start: 0.8006 (tt0) cc_final: 0.7417 (tp30)
REVERT: X   45 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7164 (tp30)
  outliers start: 24
  outliers final: 11
  residues processed: 169
  average time/residue: 1.2596
  time to fit residues: 224.4279
Evaluate side-chains
  150 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain D residue  157 GLU
Chi-restraints excluded: chain D residue  277 LEU
Chi-restraints excluded: chain X residue   45 GLU
Chi-restraints excluded: chain X residue   61 LEU
Chi-restraints excluded: chain X residue   83 THR
Chi-restraints excluded: chain X residue  124 THR
Chi-restraints excluded: chain X residue  182 LYS
Chi-restraints excluded: chain X residue  194 THR
Chi-restraints excluded: chain X residue  239 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 86 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
C  11 GLN
** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 301 GLN
** X  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X 169 GLN
X 252 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.129256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.117623 restraints weight = 12010.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3971 rms_B_bonded: 2.10
r_work: 0.3864 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3725 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7443  Z= 0.183
  Angle     :  0.592   6.984  10057  Z= 0.290
  Chirality :  0.042   0.178   1177
  Planarity :  0.004   0.059   1258
  Dihedral  :  6.491  71.350   1066
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 16.92 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.28), residues: 904
  helix:  0.98 (0.25), residues: 426
  sheet: -0.48 (0.42), residues: 152
  loop :  0.05 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 314 
 HIS   0.008   0.001   HIS X  40 
 PHE   0.013   0.002   PHE C 248 
 TYR   0.014   0.002   TYR C 210 
 ARG   0.013   0.001   ARG B  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03423 (  365)
  hydrogen bonds       : angle       4.64105 ( 1056)
  covalent geometry    : bond        0.00410 ( 7443)
  covalent geometry    : angle       0.59216 (10057)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
REVERT: B   55 MET cc_start: 0.7830 (tpp) cc_final: 0.7592 (tpt)
REVERT: C  103 PHE cc_start: 0.7610 (t80) cc_final: 0.7322 (t80)
REVERT: C  181 GLN cc_start: 0.7505 (tt0) cc_final: 0.7016 (tm-30)
REVERT: D  259 ARG cc_start: 0.7783 (pmm-80) cc_final: 0.7504 (pmm-80)
REVERT: X   26 GLU cc_start: 0.8019 (tt0) cc_final: 0.7389 (tp30)
REVERT: X   45 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7177 (tp30)
  outliers start: 21
  outliers final: 11
  residues processed: 153
  average time/residue: 1.1259
  time to fit residues: 182.6584
Evaluate side-chains
  156 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain D residue  157 GLU
Chi-restraints excluded: chain D residue  277 LEU
Chi-restraints excluded: chain X residue   45 GLU
Chi-restraints excluded: chain X residue  124 THR
Chi-restraints excluded: chain X residue  182 LYS
Chi-restraints excluded: chain X residue  194 THR
Chi-restraints excluded: chain X residue  239 MET
Chi-restraints excluded: chain X residue  266 LYS
Chi-restraints excluded: chain X residue  280 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 39 optimal weight:    0.4980
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
C  97 GLN
C 133 GLN
** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X 169 GLN
X 252 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.130058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.118439 restraints weight = 12011.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3982 rms_B_bonded: 2.10
r_work: 0.3875 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3738 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7443  Z= 0.147
  Angle     :  0.590   7.873  10057  Z= 0.286
  Chirality :  0.042   0.222   1177
  Planarity :  0.004   0.061   1258
  Dihedral  :  6.336  65.991   1066
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 18.41 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.28), residues: 904
  helix:  1.05 (0.25), residues: 426
  sheet: -0.47 (0.42), residues: 152
  loop : -0.03 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D 314 
 HIS   0.008   0.001   HIS X  40 
 PHE   0.011   0.001   PHE C 248 
 TYR   0.013   0.002   TYR C 210 
 ARG   0.016   0.001   ARG B  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03176 (  365)
  hydrogen bonds       : angle       4.56665 ( 1056)
  covalent geometry    : bond        0.00335 ( 7443)
  covalent geometry    : angle       0.58961 (10057)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.944 
Fit side-chains
REVERT: B   55 MET cc_start: 0.7721 (tpp) cc_final: 0.7490 (tpt)
REVERT: C  103 PHE cc_start: 0.7507 (t80) cc_final: 0.7202 (t80)
REVERT: C  181 GLN cc_start: 0.7462 (tt0) cc_final: 0.7015 (tm-30)
REVERT: C  260 ARG cc_start: 0.7650 (mtm110) cc_final: 0.7413 (ptt90)
REVERT: D  259 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7529 (pmm-80)
REVERT: X   26 GLU cc_start: 0.7975 (tt0) cc_final: 0.7358 (tp30)
REVERT: X   45 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7123 (tp30)
  outliers start: 17
  outliers final: 10
  residues processed: 151
  average time/residue: 1.0523
  time to fit residues: 169.0266
Evaluate side-chains
  144 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain D residue  259 ARG
Chi-restraints excluded: chain D residue  277 LEU
Chi-restraints excluded: chain X residue   45 GLU
Chi-restraints excluded: chain X residue   61 LEU
Chi-restraints excluded: chain X residue  124 THR
Chi-restraints excluded: chain X residue  182 LYS
Chi-restraints excluded: chain X residue  194 THR
Chi-restraints excluded: chain X residue  239 MET
Chi-restraints excluded: chain X residue  266 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0370
   chunk 63 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 79 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.6260

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
C  11 GLN
** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 301 GLN
** X  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X 169 GLN
X 252 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.130802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.119341 restraints weight = 11839.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 2.08
r_work: 0.3888 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3753 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.3041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7443  Z= 0.135
  Angle     :  0.601   9.249  10057  Z= 0.288
  Chirality :  0.042   0.248   1177
  Planarity :  0.004   0.042   1258
  Dihedral  :  6.213  60.286   1066
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 18.66 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.28), residues: 904
  helix:  1.07 (0.25), residues: 432
  sheet: -0.47 (0.42), residues: 152
  loop : -0.09 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP D 314 
 HIS   0.008   0.001   HIS X  40 
 PHE   0.009   0.001   PHE C 248 
 TYR   0.014   0.001   TYR X 131 
 ARG   0.009   0.000   ARG B  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03058 (  365)
  hydrogen bonds       : angle       4.51628 ( 1056)
  covalent geometry    : bond        0.00312 ( 7443)
  covalent geometry    : angle       0.60076 (10057)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 0.900 
Fit side-chains
REVERT: B   55 MET cc_start: 0.7715 (tpp) cc_final: 0.7504 (tpt)
REVERT: C  103 PHE cc_start: 0.7440 (t80) cc_final: 0.7102 (t80)
REVERT: C  181 GLN cc_start: 0.7464 (tt0) cc_final: 0.7004 (tm-30)
REVERT: C  260 ARG cc_start: 0.7606 (mtm110) cc_final: 0.7372 (ptt90)
REVERT: D  259 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7534 (pmm-80)
REVERT: X   26 GLU cc_start: 0.7961 (tt0) cc_final: 0.7357 (tp30)
REVERT: X   45 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7080 (tp30)
  outliers start: 17
  outliers final: 11
  residues processed: 150
  average time/residue: 1.0703
  time to fit residues: 170.9581
Evaluate side-chains
  142 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain D residue  259 ARG
Chi-restraints excluded: chain D residue  277 LEU
Chi-restraints excluded: chain X residue   45 GLU
Chi-restraints excluded: chain X residue   61 LEU
Chi-restraints excluded: chain X residue  124 THR
Chi-restraints excluded: chain X residue  182 LYS
Chi-restraints excluded: chain X residue  194 THR
Chi-restraints excluded: chain X residue  239 MET
Chi-restraints excluded: chain X residue  266 LYS
Chi-restraints excluded: chain X residue  280 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 34 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 60 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   chunk 85 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 HIS
D 301 GLN
** X  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X 169 GLN
X 252 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.130694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.119085 restraints weight = 12010.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3992 rms_B_bonded: 2.13
r_work: 0.3886 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3749 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.3195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7443  Z= 0.142
  Angle     :  0.618   9.353  10057  Z= 0.298
  Chirality :  0.042   0.175   1177
  Planarity :  0.003   0.044   1258
  Dihedral  :  6.187  57.488   1066
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 19.53 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.28), residues: 904
  helix:  1.14 (0.25), residues: 426
  sheet: -0.43 (0.43), residues: 152
  loop : -0.04 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP D 314 
 HIS   0.008   0.001   HIS X  40 
 PHE   0.010   0.001   PHE X  80 
 TYR   0.015   0.001   TYR X 131 
 ARG   0.010   0.001   ARG B  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03049 (  365)
  hydrogen bonds       : angle       4.49334 ( 1056)
  covalent geometry    : bond        0.00332 ( 7443)
  covalent geometry    : angle       0.61759 (10057)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.805 
Fit side-chains
REVERT: B   55 MET cc_start: 0.7789 (tpp) cc_final: 0.7573 (tpt)
REVERT: C  103 PHE cc_start: 0.7467 (t80) cc_final: 0.7180 (OUTLIER)
REVERT: C  181 GLN cc_start: 0.7517 (tt0) cc_final: 0.7017 (tm-30)
REVERT: C  260 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7387 (ptt90)
REVERT: D  259 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7551 (pmm-80)
REVERT: X   26 GLU cc_start: 0.7993 (tt0) cc_final: 0.7375 (tp30)
REVERT: X   45 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7132 (tp30)
  outliers start: 15
  outliers final: 12
  residues processed: 148
  average time/residue: 1.0459
  time to fit residues: 164.5651
Evaluate side-chains
  142 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain D residue  259 ARG
Chi-restraints excluded: chain D residue  277 LEU
Chi-restraints excluded: chain X residue   45 GLU
Chi-restraints excluded: chain X residue   61 LEU
Chi-restraints excluded: chain X residue  124 THR
Chi-restraints excluded: chain X residue  182 LYS
Chi-restraints excluded: chain X residue  194 THR
Chi-restraints excluded: chain X residue  239 MET
Chi-restraints excluded: chain X residue  266 LYS
Chi-restraints excluded: chain X residue  280 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 28 optimal weight:    0.7980
   chunk 80 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
C  11 GLN
** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 301 GLN
** X  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X 252 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.130296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.118842 restraints weight = 12132.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3987 rms_B_bonded: 2.10
r_work: 0.3882 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3746 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.3217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7443  Z= 0.164
  Angle     :  0.654  11.704  10057  Z= 0.314
  Chirality :  0.043   0.170   1177
  Planarity :  0.004   0.052   1258
  Dihedral  :  6.225  57.863   1066
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 20.52 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.28), residues: 904
  helix:  1.11 (0.25), residues: 426
  sheet: -0.44 (0.43), residues: 152
  loop : -0.09 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP D 314 
 HIS   0.008   0.001   HIS X  40 
 PHE   0.010   0.001   PHE X  80 
 TYR   0.018   0.002   TYR X 131 
 ARG   0.012   0.001   ARG B  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03138 (  365)
  hydrogen bonds       : angle       4.51396 ( 1056)
  covalent geometry    : bond        0.00382 ( 7443)
  covalent geometry    : angle       0.65363 (10057)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.793 
Fit side-chains
REVERT: B   55 MET cc_start: 0.7839 (tpp) cc_final: 0.7622 (tpt)
REVERT: C  103 PHE cc_start: 0.7488 (t80) cc_final: 0.7198 (t80)
REVERT: C  181 GLN cc_start: 0.7541 (tt0) cc_final: 0.7050 (tm-30)
REVERT: D  259 ARG cc_start: 0.7811 (pmm-80) cc_final: 0.7527 (pmm-80)
REVERT: X   26 GLU cc_start: 0.7998 (tt0) cc_final: 0.7391 (tp30)
REVERT: X   45 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7140 (tp30)
  outliers start: 12
  outliers final: 11
  residues processed: 143
  average time/residue: 1.1068
  time to fit residues: 168.6407
Evaluate side-chains
  142 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain D residue  277 LEU
Chi-restraints excluded: chain X residue   45 GLU
Chi-restraints excluded: chain X residue   61 LEU
Chi-restraints excluded: chain X residue  124 THR
Chi-restraints excluded: chain X residue  182 LYS
Chi-restraints excluded: chain X residue  194 THR
Chi-restraints excluded: chain X residue  239 MET
Chi-restraints excluded: chain X residue  266 LYS
Chi-restraints excluded: chain X residue  280 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 86 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0770
   chunk 44 optimal weight:    0.0470
   chunk 37 optimal weight:    5.9990
   chunk 78 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0670
   chunk 43 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   overall best weight:    0.3174

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

Flipped N/Q/H residues before XYZ refinement:
C  97 GLN
** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 301 GLN
** X  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X 252 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.132877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.121234 restraints weight = 12157.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.4018 rms_B_bonded: 2.14
r_work: 0.3911 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3773 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
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   0.037   7443  Z= 0.122
  Angle     :  0.655  16.769  10057  Z= 0.310
  Chirality :  0.043   0.245   1177
  Planarity :  0.004   0.052   1258
  Dihedral  :  6.111  58.340   1066
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 21.64 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.28), residues: 904
  helix:  1.11 (0.25), residues: 434
  sheet: -0.41 (0.43), residues: 152
  loop : -0.11 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP D 314 
 HIS   0.008   0.001   HIS X  40 
 PHE   0.012   0.001   PHE X  80 
 TYR   0.018   0.001   TYR X 131 
 ARG   0.013   0.001   ARG B  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02920 (  365)
  hydrogen bonds       : angle       4.46876 ( 1056)
  covalent geometry    : bond        0.00289 ( 7443)
  covalent geometry    : angle       0.65459 (10057)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 132
  time to evaluate  : 0.862 
Fit side-chains
REVERT: C  103 PHE cc_start: 0.7441 (t80) cc_final: 0.7200 (OUTLIER)
REVERT: C  181 GLN cc_start: 0.7402 (tt0) cc_final: 0.6876 (tm-30)
REVERT: D  113 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7532 (mtmm)
REVERT: D  259 ARG cc_start: 0.7857 (pmm-80) cc_final: 0.7567 (pmm-80)
REVERT: X   26 GLU cc_start: 0.7982 (tt0) cc_final: 0.7337 (tp30)
  outliers start: 10
  outliers final: 12
  residues processed: 137
  average time/residue: 1.1164
  time to fit residues: 162.2395
Evaluate side-chains
  138 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain D residue  277 LEU
Chi-restraints excluded: chain X residue   61 LEU
Chi-restraints excluded: chain X residue  124 THR
Chi-restraints excluded: chain X residue  182 LYS
Chi-restraints excluded: chain X residue  194 THR
Chi-restraints excluded: chain X residue  239 MET
Chi-restraints excluded: chain X residue  266 LYS
Chi-restraints excluded: chain X residue  280 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 53 optimal weight:    8.9990
   chunk 88 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
C  11 GLN
** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 301 GLN
** X  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X 252 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.131018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.119319 restraints weight = 11900.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 2.11
r_work: 0.3888 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3754 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7443  Z= 0.166
  Angle     :  0.653  13.112  10057  Z= 0.314
  Chirality :  0.043   0.153   1177
  Planarity :  0.004   0.052   1258
  Dihedral  :  6.233  57.910   1066
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 21.27 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.28), residues: 904
  helix:  1.05 (0.25), residues: 434
  sheet: -0.48 (0.43), residues: 152
  loop : -0.14 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP D 314 
 HIS   0.008   0.001   HIS X  40 
 PHE   0.009   0.001   PHE C 211 
 TYR   0.022   0.002   TYR X 131 
 ARG   0.012   0.001   ARG B  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03136 (  365)
  hydrogen bonds       : angle       4.52500 ( 1056)
  covalent geometry    : bond        0.00379 ( 7443)
  covalent geometry    : angle       0.65321 (10057)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6978.84 seconds
wall clock time: 119 minutes 24.81 seconds (7164.81 seconds total)