Starting phenix.real_space_refine
on Fri Aug 22 19:57:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8faz_28961/08_2025/8faz_28961.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8faz_28961/08_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_28961/08_2025/8faz_28961.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8faz_28961/08_2025/8faz_28961.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8faz_28961/08_2025/8faz_28961.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8faz_28961/08_2025/8faz_28961.cif"
  }
  resolution = 2.3
  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=   0.015
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.44, per 1000 atoms: 0.20
  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: 0.38
  Conformation dependent library (CDL) restraints added in 266.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.28
  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: 1.00

  Time building geometry restraints manager: 0.52 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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.480
  Find NCS groups from input model:        0.030
  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:5.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.250
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (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
 ARG   0.002   0.000   ARG D 275 
 TYR   0.011   0.001   TYR C 210 
 PHE   0.007   0.001   PHE D 173 
 TRP   0.008   0.001   TRP X 231 
 HIS   0.002   0.001   HIS X  40 

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

*********************** 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  : 0.182 
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: 0.4878
  time to fit residues: 99.3981
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  : 0.246 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
B  65 GLN
C 263 ASN
C 267 GLN
D  60 GLN
D 301 GLN
X 252 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.128154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.116612 restraints weight = 12076.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3955 rms_B_bonded: 2.11
r_work: 0.3848 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3707 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   7443  Z= 0.272
  Angle     :  0.639   7.189  10057  Z= 0.317
  Chirality :  0.045   0.157   1177
  Planarity :  0.004   0.057   1258
  Dihedral  :  8.444 104.385   1067
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 11.19 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.27), residues: 904
  helix:  0.66 (0.24), residues: 433
  sheet: -0.38 (0.45), residues: 139
  loop : -0.25 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  18 
 TYR   0.015   0.002   TYR X 131 
 PHE   0.011   0.002   PHE C 346 
 TRP   0.009   0.002   TRP X 231 
 HIS   0.006   0.001   HIS X 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00586 ( 7443)
  covalent geometry    : angle       0.63883 (10057)
  hydrogen bonds       : bond        0.04735 (  365)
  hydrogen bonds       : angle       5.23619 ( 1056)

*********************** 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
  185 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 163
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  181 GLN cc_start: 0.7561 (tt0) cc_final: 0.7032 (tm-30)
REVERT: C  205 LEU cc_start: 0.7876 (mt) cc_final: 0.7632 (mp)
REVERT: D   36 LEU cc_start: 0.7442 (mt) cc_final: 0.7152 (mm)
REVERT: D  259 ARG cc_start: 0.7770 (pmm-80) cc_final: 0.7437 (pmm-80)
REVERT: X   26 GLU cc_start: 0.8009 (tt0) cc_final: 0.7376 (tp30)
REVERT: X  259 CYS cc_start: 0.7859 (t) cc_final: 0.7636 (t)
  outliers start: 22
  outliers final: 10
  residues processed: 176
  average time/residue: 0.5197
  time to fit residues: 96.1796
Evaluate side-chains
  155 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 145
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain C residue  200 THR
Chi-restraints excluded: chain D residue  277 LEU
Chi-restraints excluded: chain X residue   76 VAL
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  194 THR
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 8 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 87 optimal weight:    0.6980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4112 r_free = 0.4112 target = 0.129881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.118252 restraints weight = 11908.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3977 rms_B_bonded: 2.09
r_work: 0.3870 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3732 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2402

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= 0.153
  Angle     :  0.564   6.908  10057  Z= 0.277
  Chirality :  0.042   0.217   1177
  Planarity :  0.004   0.050   1258
  Dihedral  :  7.282  79.257   1065
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.18 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.28), residues: 904
  helix:  0.82 (0.24), residues: 438
  sheet: -0.40 (0.43), residues: 151
  loop : -0.30 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  18 
 TYR   0.013   0.001   TYR X 131 
 PHE   0.010   0.001   PHE X  32 
 TRP   0.007   0.001   TRP X 231 
 HIS   0.007   0.001   HIS X  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7443)
  covalent geometry    : angle       0.56375 (10057)
  hydrogen bonds       : bond        0.03605 (  365)
  hydrogen bonds       : angle       4.81427 ( 1056)

*********************** 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
  188 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 167
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   55 MET cc_start: 0.7698 (tpp) cc_final: 0.7446 (tpt)
REVERT: C  103 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7281 (t80)
REVERT: C  144 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8159 (mp)
REVERT: C  181 GLN cc_start: 0.7491 (tt0) cc_final: 0.6968 (tm-30)
REVERT: C  205 LEU cc_start: 0.7734 (mt) cc_final: 0.7527 (mp)
REVERT: D  259 ARG cc_start: 0.7806 (pmm-80) cc_final: 0.7534 (pmm-80)
REVERT: X   26 GLU cc_start: 0.7964 (tt0) cc_final: 0.7259 (tp30)
  outliers start: 21
  outliers final: 12
  residues processed: 178
  average time/residue: 0.5065
  time to fit residues: 95.1851
Evaluate side-chains
  163 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain C residue  103 PHE
Chi-restraints excluded: chain C residue  144 ILE
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  124 THR
Chi-restraints excluded: chain X residue  171 SER
Chi-restraints excluded: chain X residue  182 LYS
Chi-restraints excluded: chain X residue  194 THR
Chi-restraints excluded: chain X residue  236 LYS
Chi-restraints excluded: chain X residue  239 MET
Chi-restraints excluded: chain X residue  280 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 88 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 284 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 = 0.4111 r_free = 0.4111 target = 0.129697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.118121 restraints weight = 12086.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3977 rms_B_bonded: 2.10
r_work: 0.3869 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3732 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7443  Z= 0.154
  Angle     :  0.568   6.758  10057  Z= 0.276
  Chirality :  0.042   0.172   1177
  Planarity :  0.004   0.055   1258
  Dihedral  :  6.616  73.364   1065
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.17 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.28), residues: 904
  helix:  1.04 (0.25), residues: 426
  sheet: -0.40 (0.43), residues: 151
  loop : -0.09 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  18 
 TYR   0.014   0.001   TYR X 131 
 PHE   0.011   0.001   PHE C 148 
 TRP   0.008   0.001   TRP X 231 
 HIS   0.008   0.001   HIS X  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 7443)
  covalent geometry    : angle       0.56837 (10057)
  hydrogen bonds       : bond        0.03321 (  365)
  hydrogen bonds       : angle       4.65596 ( 1056)

*********************** 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
  183 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 160
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: B   33 LEU cc_start: 0.9287 (mt) cc_final: 0.8965 (mt)
REVERT: B   55 MET cc_start: 0.7804 (tpp) cc_final: 0.7510 (tpt)
REVERT: C  103 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7293 (t80)
REVERT: C  181 GLN cc_start: 0.7536 (tt0) cc_final: 0.7016 (tm-30)
REVERT: C  205 LEU cc_start: 0.7711 (mt) cc_final: 0.7491 (mp)
REVERT: C  301 LEU cc_start: 0.9117 (mm) cc_final: 0.8889 (mp)
REVERT: D  259 ARG cc_start: 0.7827 (pmm-80) cc_final: 0.7574 (pmm-80)
REVERT: X   26 GLU cc_start: 0.7957 (tt0) cc_final: 0.7226 (tp30)
REVERT: X   64 ARG cc_start: 0.8197 (mmm160) cc_final: 0.7917 (mmm160)
  outliers start: 23
  outliers final: 10
  residues processed: 172
  average time/residue: 0.4913
  time to fit residues: 89.1014
Evaluate side-chains
  151 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain C residue  103 PHE
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   27 ILE
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  280 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 64 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 58 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 133 GLN
** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 284 ASN
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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.128612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.116833 restraints weight = 12069.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3958 rms_B_bonded: 2.12
r_work: 0.3851 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3714 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7443  Z= 0.202
  Angle     :  0.613   6.926  10057  Z= 0.302
  Chirality :  0.043   0.208   1177
  Planarity :  0.004   0.062   1258
  Dihedral  :  6.539  71.186   1064
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 16.67 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.28), residues: 904
  helix:  1.03 (0.25), residues: 426
  sheet: -0.55 (0.43), residues: 152
  loop : -0.06 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  18 
 TYR   0.015   0.002   TYR C 210 
 PHE   0.012   0.002   PHE C 248 
 TRP   0.011   0.002   TRP D 314 
 HIS   0.009   0.001   HIS X  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 7443)
  covalent geometry    : angle       0.61279 (10057)
  hydrogen bonds       : bond        0.03501 (  365)
  hydrogen bonds       : angle       4.67334 ( 1056)

*********************** 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
  181 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 154
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
REVERT: B   55 MET cc_start: 0.7984 (tpp) cc_final: 0.7733 (tpt)
REVERT: C  103 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7416 (t80)
REVERT: C  144 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8236 (mp)
REVERT: C  181 GLN cc_start: 0.7550 (tt0) cc_final: 0.7064 (tm-30)
REVERT: C  205 LEU cc_start: 0.7769 (mt) cc_final: 0.7542 (mp)
REVERT: D  259 ARG cc_start: 0.7789 (pmm-80) cc_final: 0.7506 (pmm-80)
REVERT: X   26 GLU cc_start: 0.7994 (tt0) cc_final: 0.7279 (tp30)
REVERT: X   64 ARG cc_start: 0.8269 (mmm160) cc_final: 0.8042 (mmm160)
  outliers start: 27
  outliers final: 11
  residues processed: 167
  average time/residue: 0.5240
  time to fit residues: 92.4704
Evaluate side-chains
  152 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 139
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
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  103 PHE
Chi-restraints excluded: chain C residue  144 ILE
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   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  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 80 optimal weight:    0.4980
   chunk 13 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0670
   chunk 32 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.5718

-------------------------------------------------------------------------------
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 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.130457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.118919 restraints weight = 12004.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3989 rms_B_bonded: 2.11
r_work: 0.3883 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3745 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.3037

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= 0.132
  Angle     :  0.584   8.043  10057  Z= 0.286
  Chirality :  0.042   0.229   1177
  Planarity :  0.004   0.057   1258
  Dihedral  :  6.291  64.146   1064
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 17.66 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.28), residues: 904
  helix:  1.12 (0.25), residues: 426
  sheet: -0.46 (0.43), residues: 150
  loop : -0.01 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B  18 
 TYR   0.012   0.001   TYR X 131 
 PHE   0.012   0.001   PHE C 248 
 TRP   0.017   0.002   TRP D 314 
 HIS   0.009   0.001   HIS X  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7443)
  covalent geometry    : angle       0.58422 (10057)
  hydrogen bonds       : bond        0.03109 (  365)
  hydrogen bonds       : angle       4.55157 ( 1056)

*********************** 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
  177 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 152
  time to evaluate  : 0.188 
Fit side-chains
REVERT: B   55 MET cc_start: 0.7774 (tpp) cc_final: 0.7547 (tpt)
REVERT: C  103 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7240 (t80)
REVERT: C  144 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8206 (mp)
REVERT: C  181 GLN cc_start: 0.7503 (tt0) cc_final: 0.7036 (tm-30)
REVERT: C  260 ARG cc_start: 0.7561 (mtm110) cc_final: 0.7309 (ptt90)
REVERT: D  259 ARG cc_start: 0.7824 (pmm-80) cc_final: 0.7526 (pmm-80)
REVERT: X   26 GLU cc_start: 0.7983 (tt0) cc_final: 0.7195 (tp30)
REVERT: X   64 ARG cc_start: 0.8288 (mmm160) cc_final: 0.8079 (mmm160)
  outliers start: 25
  outliers final: 9
  residues processed: 165
  average time/residue: 0.4869
  time to fit residues: 84.8742
Evaluate side-chains
  146 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
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  103 PHE
Chi-restraints excluded: chain C residue  144 ILE
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain D residue  277 LEU
Chi-restraints excluded: chain X residue   83 THR
Chi-restraints excluded: chain X residue  124 THR
Chi-restraints excluded: chain X residue  194 THR
Chi-restraints excluded: chain X residue  266 LYS
Chi-restraints excluded: chain X residue  280 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    1.1786

-------------------------------------------------------------------------------
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 = 0.4100 r_free = 0.4100 target = 0.129070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.117253 restraints weight = 12103.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3960 rms_B_bonded: 2.14
r_work: 0.3853 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3714 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.3036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7443  Z= 0.191
  Angle     :  0.636   9.230  10057  Z= 0.308
  Chirality :  0.043   0.252   1177
  Planarity :  0.004   0.045   1258
  Dihedral  :  6.368  61.530   1064
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 18.16 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.28), residues: 904
  helix:  1.06 (0.25), residues: 426
  sheet: -0.53 (0.43), residues: 152
  loop :  0.04 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  18 
 TYR   0.015   0.002   TYR X 131 
 PHE   0.014   0.002   PHE C 248 
 TRP   0.027   0.002   TRP D 314 
 HIS   0.009   0.001   HIS X  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 7443)
  covalent geometry    : angle       0.63574 (10057)
  hydrogen bonds       : bond        0.03408 (  365)
  hydrogen bonds       : angle       4.62180 ( 1056)

*********************** 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
  163 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: B   55 MET cc_start: 0.7943 (tpp) cc_final: 0.7723 (tpt)
REVERT: C  103 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7313 (t80)
REVERT: C  144 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8209 (mp)
REVERT: C  181 GLN cc_start: 0.7546 (tt0) cc_final: 0.7089 (tm-30)
REVERT: D  259 ARG cc_start: 0.7776 (pmm-80) cc_final: 0.7457 (pmm-80)
REVERT: X   26 GLU cc_start: 0.8015 (tt0) cc_final: 0.7250 (tp30)
REVERT: X   64 ARG cc_start: 0.8354 (mmm160) cc_final: 0.8060 (mmm160)
  outliers start: 20
  outliers final: 14
  residues processed: 151
  average time/residue: 0.5294
  time to fit residues: 84.1959
Evaluate side-chains
  145 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
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  103 PHE
Chi-restraints excluded: chain C residue  144 ILE
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   83 THR
Chi-restraints excluded: chain X residue   90 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  199 MET
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 51 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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**
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 = 0.4114 r_free = 0.4114 target = 0.130131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.118581 restraints weight = 12020.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3981 rms_B_bonded: 2.12
r_work: 0.3875 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3736 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7443  Z= 0.150
  Angle     :  0.632   9.879  10057  Z= 0.307
  Chirality :  0.043   0.258   1177
  Planarity :  0.004   0.046   1258
  Dihedral  :  6.251  58.547   1064
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 19.65 %
    Favored  : 78.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.28), residues: 904
  helix:  1.08 (0.25), residues: 426
  sheet: -0.48 (0.43), residues: 152
  loop : -0.03 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  18 
 TYR   0.014   0.002   TYR X 131 
 PHE   0.012   0.001   PHE C 248 
 TRP   0.029   0.002   TRP D 314 
 HIS   0.009   0.001   HIS X  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 7443)
  covalent geometry    : angle       0.63195 (10057)
  hydrogen bonds       : bond        0.03154 (  365)
  hydrogen bonds       : angle       4.56896 ( 1056)

*********************** 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
  167 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 152
  time to evaluate  : 0.184 
Fit side-chains
REVERT: B   55 MET cc_start: 0.7926 (tpp) cc_final: 0.7662 (tpt)
REVERT: C  103 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7222 (t80)
REVERT: C  133 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7518 (mp10)
REVERT: C  144 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8212 (mp)
REVERT: C  181 GLN cc_start: 0.7504 (tt0) cc_final: 0.7013 (tm-30)
REVERT: C  260 ARG cc_start: 0.7617 (mtm110) cc_final: 0.7365 (ptt-90)
REVERT: D  259 ARG cc_start: 0.7803 (pmm-80) cc_final: 0.7475 (pmm-80)
REVERT: X   26 GLU cc_start: 0.8022 (tt0) cc_final: 0.7195 (tp30)
REVERT: X   64 ARG cc_start: 0.8337 (mmm160) cc_final: 0.8042 (mmm160)
  outliers start: 15
  outliers final: 10
  residues processed: 160
  average time/residue: 0.4838
  time to fit residues: 81.8777
Evaluate side-chains
  145 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
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  103 PHE
Chi-restraints excluded: chain C residue  133 GLN
Chi-restraints excluded: chain C residue  144 ILE
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  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 54 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0870
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.7760

-------------------------------------------------------------------------------
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  97 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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.130262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.118681 restraints weight = 11952.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3980 rms_B_bonded: 2.11
r_work: 0.3875 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3738 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7443  Z= 0.150
  Angle     :  0.642  11.099  10057  Z= 0.309
  Chirality :  0.043   0.214   1177
  Planarity :  0.004   0.052   1258
  Dihedral  :  6.233  59.167   1064
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 19.53 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.28), residues: 904
  helix:  1.09 (0.25), residues: 426
  sheet: -0.47 (0.43), residues: 152
  loop : -0.05 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  18 
 TYR   0.017   0.002   TYR X 131 
 PHE   0.011   0.001   PHE C 248 
 TRP   0.028   0.002   TRP D 314 
 HIS   0.009   0.001   HIS X  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 7443)
  covalent geometry    : angle       0.64163 (10057)
  hydrogen bonds       : bond        0.03168 (  365)
  hydrogen bonds       : angle       4.57204 ( 1056)

*********************** 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
  155 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 138
  time to evaluate  : 0.287 
Fit side-chains
REVERT: B   55 MET cc_start: 0.7896 (tpp) cc_final: 0.7635 (tpt)
REVERT: C  103 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.7185 (t80)
REVERT: C  133 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7582 (mp10)
REVERT: C  181 GLN cc_start: 0.7465 (tt0) cc_final: 0.6973 (tm-30)
REVERT: C  249 ARG cc_start: 0.7677 (mtp85) cc_final: 0.7432 (tpp80)
REVERT: C  260 ARG cc_start: 0.7484 (mtm110) cc_final: 0.7277 (ptt90)
REVERT: D  113 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7583 (mtmm)
REVERT: D  259 ARG cc_start: 0.7829 (pmm-80) cc_final: 0.7505 (pmm-80)
REVERT: X   26 GLU cc_start: 0.8036 (tt0) cc_final: 0.7218 (tp30)
REVERT: X   64 ARG cc_start: 0.8329 (mmm160) cc_final: 0.8035 (mmm160)
  outliers start: 17
  outliers final: 12
  residues processed: 145
  average time/residue: 0.5552
  time to fit residues: 84.6188
Evaluate side-chains
  144 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain C residue  103 PHE
Chi-restraints excluded: chain C residue  133 GLN
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 51 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0470
   chunk 73 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 9 optimal weight:    0.2980
   chunk 62 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 76 optimal weight:    0.4980
   overall best weight:    0.4878

-------------------------------------------------------------------------------
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**
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 = 0.4135 r_free = 0.4135 target = 0.131585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.120209 restraints weight = 12006.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.4003 rms_B_bonded: 2.10
r_work: 0.3898 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3763 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.3422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7443  Z= 0.131
  Angle     :  0.660  11.158  10057  Z= 0.320
  Chirality :  0.044   0.354   1177
  Planarity :  0.004   0.054   1258
  Dihedral  :  6.153  59.833   1064
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 20.52 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.28), residues: 904
  helix:  1.04 (0.25), residues: 433
  sheet: -0.41 (0.44), residues: 152
  loop : -0.12 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B  18 
 TYR   0.019   0.002   TYR X 131 
 PHE   0.010   0.001   PHE X  32 
 TRP   0.038   0.002   TRP D 314 
 HIS   0.008   0.001   HIS X  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7443)
  covalent geometry    : angle       0.66020 (10057)
  hydrogen bonds       : bond        0.03013 (  365)
  hydrogen bonds       : angle       4.51798 ( 1056)

********************** 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
  161 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 0.300 
Fit side-chains
REVERT: B   55 MET cc_start: 0.7879 (tpp) cc_final: 0.7626 (tpt)
REVERT: C  133 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7504 (mp10)
REVERT: C  181 GLN cc_start: 0.7424 (tt0) cc_final: 0.6918 (tm-30)
REVERT: C  260 ARG cc_start: 0.7427 (mtm110) cc_final: 0.7226 (ptt90)
REVERT: C  321 GLN cc_start: 0.7625 (tm-30) cc_final: 0.7368 (tm130)
REVERT: D  113 LYS cc_start: 0.8157 (mtmm) cc_final: 0.7533 (mtmm)
REVERT: D  259 ARG cc_start: 0.7833 (pmm-80) cc_final: 0.7514 (pmm-80)
REVERT: X   26 GLU cc_start: 0.7971 (tt0) cc_final: 0.7169 (tp30)
REVERT: X   64 ARG cc_start: 0.8316 (mmm160) cc_final: 0.8035 (mmm160)
  outliers start: 14
  outliers final: 12
  residues processed: 154
  average time/residue: 0.5473
  time to fit residues: 89.0648
Evaluate side-chains
  146 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
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  103 PHE
Chi-restraints excluded: chain C residue  133 GLN
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 1 optimal weight:    2.9990
   chunk 53 optimal weight:    0.4980
   chunk 13 optimal weight:    0.0770
   chunk 57 optimal weight:    7.9990
   chunk 52 optimal weight:    0.5980
   chunk 3 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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  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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.131711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.120233 restraints weight = 12028.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.4003 rms_B_bonded: 2.11
r_work: 0.3897 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3761 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7443  Z= 0.137
  Angle     :  0.674  11.010  10057  Z= 0.324
  Chirality :  0.043   0.324   1177
  Planarity :  0.004   0.055   1258
  Dihedral  :  6.141  59.506   1064
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 21.89 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.28), residues: 904
  helix:  1.08 (0.25), residues: 433
  sheet: -0.39 (0.44), residues: 152
  loop : -0.13 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  18 
 TYR   0.020   0.002   TYR X 131 
 PHE   0.013   0.001   PHE C  99 
 TRP   0.041   0.003   TRP D 314 
 HIS   0.008   0.001   HIS X  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 7443)
  covalent geometry    : angle       0.67366 (10057)
  hydrogen bonds       : bond        0.03069 (  365)
  hydrogen bonds       : angle       4.52312 ( 1056)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3170.02 seconds
wall clock time: 54 minutes 42.81 seconds (3282.81 seconds total)