Starting phenix.real_space_refine
on Wed Aug  5 08:57:45 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7pm3_13511/08_2026/7pm3_13511.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pm3_13511/08_2026/7pm3_13511.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7pm3_13511/08_2026/7pm3_13511.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7pm3_13511/08_2026/7pm3_13511.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pm3_13511/08_2026/7pm3_13511.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pm3_13511/08_2026/7pm3_13511.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pm3_13511/08_2026/7pm3_13511.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pm3_13511/08_2026/7pm3_13511.map"
  }
  resolution = 3.1
  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=   0.001
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: 7
    Type Number    sf(0)   Gaussians
     Br      3      7.06       5
     P       9      5.49       5
     Mg      3      5.21       5
     S      63      5.16       5
     C    5649      2.51       5
     N    1494      2.21       5
     O    1719      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8940
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2900
          Classifications: {'peptide': 371}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 351}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 2900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2900
          Classifications: {'peptide': 371}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 351}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "D"
      Number of atoms: 2900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2900
          Classifications: {'peptide': 371}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 351}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 80
          Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1, 'PO4': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "D"
      Number of atoms: 127
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 127
          Unusual residues: {' MG': 1, '9UE': 2, 'ADP': 1, 'PO4': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 2.78, per 1000 atoms: 0.31
  Number of scatterers: 8940
  At special positions: 0
  Unit cell: (89.1, 90.2, 136.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Br      3     34.99
     S      63     16.00
     P       9     15.00
     Mg      3     11.99
     O    1719      8.00
     N    1494      7.00
     C    5649      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: 0.94
  Conformation dependent library (CDL) restraints added in 317.8 milliseconds
  

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2058

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 18 sheets defined
      49.3% alpha, 16.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'B' and resid 55 through 61
    Processing helix  chain 'B' and resid 78 through 91
    Processing helix  chain 'B' and resid 112 through 126
      removed outlier: 3.770A  pdb=" N   ARG B 116 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   MET B 119 " --> pdb=" O   ASN B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 146
    Processing helix  chain 'B' and resid 181 through 195
      removed outlier: 3.671A  pdb=" N   TYR B 188 " --> pdb=" O   ASP B 184 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   GLU B 195 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 217
    Processing helix  chain 'B' and resid 222 through 233
      removed outlier: 3.509A  pdb=" N   SER B 232 " --> pdb=" O   ALA B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 237
    Processing helix  chain 'B' and resid 252 through 263
      Proline residue:  B 258  - end of helix
      removed outlier: 4.695A  pdb=" N   LEU B 261 " --> pdb=" O   CYS B 257 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   PHE B 262 " --> pdb=" O   PRO B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 284
    Processing helix  chain 'B' and resid 286 through 295
      removed outlier: 4.208A  pdb=" N   LYS B 291 " --> pdb=" O   ILE B 287 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   ASP B 292 " --> pdb=" O   ASP B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 306
      removed outlier: 4.026A  pdb=" N   TYR B 306 " --> pdb=" O   THR B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 321
      removed outlier: 3.577A  pdb=" N   ALA B 319 " --> pdb=" O   LYS B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 336
      No H-bonds generated for 'chain 'B' and resid 334 through 336'
    Processing helix  chain 'B' and resid 337 through 349
    Processing helix  chain 'B' and resid 350 through 355
      removed outlier: 4.340A  pdb=" N   GLN B 354 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 366
    Processing helix  chain 'B' and resid 367 through 372
    Processing helix  chain 'C' and resid 55 through 61
    Processing helix  chain 'C' and resid 78 through 91
      removed outlier: 3.500A  pdb=" N   LYS C  84 " --> pdb=" O   ASP C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 126
      removed outlier: 3.770A  pdb=" N   ARG C 116 " --> pdb=" O   PRO C 112 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   MET C 119 " --> pdb=" O   ASN C 115 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 146
    Processing helix  chain 'C' and resid 181 through 195
      removed outlier: 3.648A  pdb=" N   TYR C 188 " --> pdb=" O   ASP C 184 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS C 191 " --> pdb=" O   ASP C 187 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLU C 195 " --> pdb=" O   LYS C 191 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 217
    Processing helix  chain 'C' and resid 222 through 233
    Processing helix  chain 'C' and resid 234 through 237
    Processing helix  chain 'C' and resid 252 through 263
      Proline residue:  C 258  - end of helix
      removed outlier: 4.758A  pdb=" N   LEU C 261 " --> pdb=" O   CYS C 257 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   PHE C 262 " --> pdb=" O   PRO C 258 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 273 through 284
    Processing helix  chain 'C' and resid 286 through 295
      removed outlier: 4.175A  pdb=" N   LYS C 291 " --> pdb=" O   ILE C 287 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   ASP C 292 " --> pdb=" O   ASP C 288 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 306
      removed outlier: 4.065A  pdb=" N   TYR C 306 " --> pdb=" O   THR C 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 321
      removed outlier: 3.572A  pdb=" N   ALA C 319 " --> pdb=" O   LYS C 315 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 334 through 336
      No H-bonds generated for 'chain 'C' and resid 334 through 336'
    Processing helix  chain 'C' and resid 337 through 349
    Processing helix  chain 'C' and resid 350 through 355
      removed outlier: 4.372A  pdb=" N   GLN C 354 " --> pdb=" O   THR C 351 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 359 through 366
    Processing helix  chain 'C' and resid 367 through 372
    Processing helix  chain 'D' and resid 55 through 61
    Processing helix  chain 'D' and resid 78 through 91
    Processing helix  chain 'D' and resid 112 through 126
      removed outlier: 3.755A  pdb=" N   ARG D 116 " --> pdb=" O   PRO D 112 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   MET D 119 " --> pdb=" O   ASN D 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 137 through 146
    Processing helix  chain 'D' and resid 181 through 195
      removed outlier: 3.648A  pdb=" N   TYR D 188 " --> pdb=" O   ASP D 184 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LYS D 191 " --> pdb=" O   ASP D 187 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLU D 195 " --> pdb=" O   LYS D 191 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 217
    Processing helix  chain 'D' and resid 222 through 233
      removed outlier: 3.556A  pdb=" N   SER D 232 " --> pdb=" O   ALA D 228 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 234 through 237
    Processing helix  chain 'D' and resid 252 through 263
      Proline residue:  D 258  - end of helix
      removed outlier: 4.727A  pdb=" N   LEU D 261 " --> pdb=" O   CYS D 257 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   PHE D 262 " --> pdb=" O   PRO D 258 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 273 through 284
    Processing helix  chain 'D' and resid 286 through 295
      removed outlier: 4.270A  pdb=" N   LYS D 291 " --> pdb=" O   ILE D 287 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   ASP D 292 " --> pdb=" O   ASP D 288 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 301 through 306
      removed outlier: 4.072A  pdb=" N   TYR D 306 " --> pdb=" O   THR D 303 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 308 through 321
      removed outlier: 3.533A  pdb=" N   ALA D 319 " --> pdb=" O   LYS D 315 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 334 through 336
      No H-bonds generated for 'chain 'D' and resid 334 through 336'
    Processing helix  chain 'D' and resid 337 through 349
    Processing helix  chain 'D' and resid 350 through 355
      removed outlier: 4.355A  pdb=" N   GLN D 354 " --> pdb=" O   THR D 351 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 359 through 366
    Processing helix  chain 'D' and resid 367 through 372
    Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31
      removed outlier: 4.092A  pdb=" N   THR B 106 " --> pdb=" O   CYS B  10 " (cutoff:3.500A)
      removed outlier: 5.382A  pdb=" N   ASN B  12 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   THR B 103 " --> pdb=" O   TYR B 133 " (cutoff:3.500A)
      removed outlier: 8.255A  pdb=" N   ALA B 135 " --> pdb=" O   THR B 103 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU B 105 " --> pdb=" O   ALA B 135 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54
    Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72
    Processing sheet with id=AA4, first strand: chain 'B' and resid 169 through 170
    Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 170
      removed outlier: 6.446A  pdb=" N   ASN B 297 " --> pdb=" O   ILE B 330 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241
    Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 31
      removed outlier: 4.199A  pdb=" N   THR C 106 " --> pdb=" O   CYS C  10 " (cutoff:3.500A)
      removed outlier: 5.523A  pdb=" N   ASN C  12 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR C 103 " --> pdb=" O   TYR C 133 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   ALA C 135 " --> pdb=" O   THR C 103 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   LEU C 105 " --> pdb=" O   ALA C 135 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AB1, first strand: chain 'C' and resid 169 through 170
    Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170
      removed outlier: 6.576A  pdb=" N   ASN C 297 " --> pdb=" O   ILE C 330 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 238 through 241
    Processing sheet with id=AB4, first strand: chain 'D' and resid 29 through 31
      removed outlier: 4.126A  pdb=" N   THR D 106 " --> pdb=" O   CYS D  10 " (cutoff:3.500A)
      removed outlier: 5.452A  pdb=" N   ASN D  12 " --> pdb=" O   THR D 106 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 53 through 54
    Processing sheet with id=AB6, first strand: chain 'D' and resid 71 through 72
    Processing sheet with id=AB7, first strand: chain 'D' and resid 169 through 170
    Processing sheet with id=AB8, first strand: chain 'D' and resid 169 through 170
      removed outlier: 6.504A  pdb=" N   ASN D 297 " --> pdb=" O   ILE D 330 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 238 through 241

    432 hydrogen bonds defined for protein.
    1113 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: 1.39

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2371
        1.33 -     1.47: 2623
        1.47 -     1.60: 4021
        1.60 -     1.73: 9
        1.73 -     1.86: 114
  Bond restraints: 9138
  Sorted by residual:
  bond pdb=" O4  PO4 C 403 "
       pdb=" P   PO4 C 403 "
    ideal  model  delta    sigma   weight residual
    1.568  1.505  0.063 2.00e-02 2.50e+03 9.81e+00
  bond pdb=" O3  PO4 B 402 "
       pdb=" P   PO4 B 402 "
    ideal  model  delta    sigma   weight residual
    1.569  1.507  0.062 2.00e-02 2.50e+03 9.62e+00
  bond pdb=" O4  PO4 D 403 "
       pdb=" P   PO4 D 403 "
    ideal  model  delta    sigma   weight residual
    1.568  1.506  0.062 2.00e-02 2.50e+03 9.53e+00
  bond pdb=" O3  PO4 D 403 "
       pdb=" P   PO4 D 403 "
    ideal  model  delta    sigma   weight residual
    1.569  1.508  0.061 2.00e-02 2.50e+03 9.32e+00
  bond pdb=" O3  PO4 C 403 "
       pdb=" P   PO4 C 403 "
    ideal  model  delta    sigma   weight residual
    1.569  1.508  0.061 2.00e-02 2.50e+03 9.19e+00
  ... (remaining 9133 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 12013
        2.45 -     4.90: 331
        4.90 -     7.35: 51
        7.35 -     9.80: 13
        9.80 -    12.25: 6
  Bond angle restraints: 12414
  Sorted by residual:
  angle pdb=" CA  MET D  44 "
        pdb=" CB  MET D  44 "
        pdb=" CG  MET D  44 "
      ideal   model   delta    sigma   weight residual
     114.10  103.58   10.52 2.00e+00 2.50e-01 2.77e+01
  angle pdb=" CB  MET D  44 "
        pdb=" CG  MET D  44 "
        pdb=" SD  MET D  44 "
      ideal   model   delta    sigma   weight residual
     112.70  124.95  -12.25 3.00e+00 1.11e-01 1.67e+01
  angle pdb=" C20 9UE C 401 "
        pdb=" C8  9UE C 401 "
        pdb=" C7  9UE C 401 "
      ideal   model   delta    sigma   weight residual
     118.25  106.55   11.70 3.00e+00 1.11e-01 1.52e+01
  angle pdb=" C20 9UE D 405 "
        pdb=" C8  9UE D 405 "
        pdb=" C7  9UE D 405 "
      ideal   model   delta    sigma   weight residual
     118.25  106.97   11.28 3.00e+00 1.11e-01 1.41e+01
  angle pdb=" N   PHE B 127 "
        pdb=" CA  PHE B 127 "
        pdb=" C   PHE B 127 "
      ideal   model   delta    sigma   weight residual
     109.50  103.74    5.76 1.58e+00 4.01e-01 1.33e+01
  ... (remaining 12409 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.92: 5361
       35.92 -    71.84: 87
       71.84 -   107.76: 30
      107.76 -   143.68: 21
      143.68 -   179.61: 36
  Dihedral angle restraints: 5535
    sinusoidal: 2319
      harmonic: 3216
  Sorted by residual:
  dihedral pdb=" O1B ADP D 402 "
           pdb=" O3A ADP D 402 "
           pdb=" PB  ADP D 402 "
           pdb=" PA  ADP D 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  168.79  131.21     1      2.00e+01 2.50e-03 3.98e+01
  dihedral pdb=" O1B ADP C 402 "
           pdb=" O3A ADP C 402 "
           pdb=" PB  ADP C 402 "
           pdb=" PA  ADP C 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  168.84  131.16     1      2.00e+01 2.50e-03 3.98e+01
  dihedral pdb=" O1B ADP B 401 "
           pdb=" O3A ADP B 401 "
           pdb=" PB  ADP B 401 "
           pdb=" PA  ADP B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  168.95  131.05     1      2.00e+01 2.50e-03 3.98e+01
  ... (remaining 5532 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 1179
       0.083 -    0.166: 173
       0.166 -    0.250: 10
       0.250 -    0.333: 3
       0.333 -    0.416: 6
  Chirality restraints: 1371
  Sorted by residual:
  chirality pdb=" C3  9UE D 405 "
            pdb=" O   9UE D 405 "
            pdb=" C2  9UE D 405 "
            pdb=" C35 9UE D 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.21    2.62   -0.42 2.00e-01 2.50e+01 4.33e+00
  chirality pdb=" C3  9UE C 401 "
            pdb=" O   9UE C 401 "
            pdb=" C2  9UE C 401 "
            pdb=" C35 9UE C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.21    2.62   -0.41 2.00e-01 2.50e+01 4.28e+00
  chirality pdb=" C3  9UE D 401 "
            pdb=" O   9UE D 401 "
            pdb=" C2  9UE D 401 "
            pdb=" C35 9UE D 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.21    2.61   -0.40 2.00e-01 2.50e+01 4.07e+00
  ... (remaining 1368 not shown)

  Planarity restraints: 1578
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 335 "    0.134 9.50e-02 1.11e+02   7.45e-02 2.63e+01
        pdb=" NE  ARG C 335 "   -0.037 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 335 "    0.084 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 335 "   -0.030 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 335 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 335 "    0.133 9.50e-02 1.11e+02   7.40e-02 2.63e+01
        pdb=" NE  ARG D 335 "   -0.037 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 335 "    0.084 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 335 "   -0.030 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 335 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 335 "    0.133 9.50e-02 1.11e+02   7.39e-02 2.60e+01
        pdb=" NE  ARG B 335 "   -0.036 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 335 "    0.083 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 335 "   -0.030 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 335 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 1575 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 69
        2.60 -     3.17: 7471
        3.17 -     3.75: 13405
        3.75 -     4.32: 19423
        4.32 -     4.90: 32273
  Nonbonded interactions: 72641
  Sorted by model distance:
  nonbonded pdb=" O3B ADP D 402 "
            pdb="MG    MG D 404 "
     model   vdw
     2.019 2.170
  nonbonded pdb=" OH  TYR C 218 "
            pdb=" OE2 GLU C 226 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OH  TYR B 169 "
            pdb=" OH  TYR D  53 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" NZ  LYS B  18 "
            pdb=" O2B ADP B 401 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" OG  SER B 234 "
            pdb=" OE1 GLU B 237 "
     model   vdw
     2.321 3.040
  ... (remaining 72636 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
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 5 through 375)
  selection = (chain 'C' and resid 5 through 375)
  selection = (chain 'D' and resid 5 through 375)
}

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:             2.380
  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:             0.020
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.370
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   9138  Z= 0.252
  Angle     :  0.984  12.251  12414  Z= 0.518
  Chirality :  0.062   0.416   1371
  Planarity :  0.010   0.074   1578
  Dihedral  : 24.621 179.605   3477
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.22), residues: 1098
  helix: -1.68 (0.19), residues: 435
  sheet:  0.13 (0.31), residues: 207
  loop :  0.36 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.085   0.019   ARG D 335 
 TYR   0.029   0.006   TYR C  53 
 PHE   0.021   0.002   PHE D 262 
 TRP   0.020   0.003   TRP C  79 
 HIS   0.007   0.001   HIS C 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00534 /  0.25 ( 9138)
  covalent geometry    : angle       0.98382 /  0.52 (12414)
  hydrogen bonds       : bond        0.18269 / 12.83 (  426)
  hydrogen bonds       : angle       6.80154 /  4.75 ( 1113)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: C   47 MET cc_start: 0.6837 (tmm) cc_final: 0.6118 (tmm)
REVERT: C  190 MET cc_start: 0.7621 (mtp) cc_final: 0.7396 (mtp)
REVERT: C  269 MET cc_start: 0.7419 (mtt) cc_final: 0.7215 (mtm)
REVERT: D  190 MET cc_start: 0.7986 (mtp) cc_final: 0.7654 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0920
  time to fit residues: 19.8053
Evaluate side-chains
  73 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.2980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    0.0370
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.5258

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.094448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.081543 restraints weight = 14972.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 1.97
r_work: 0.3128 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9138  Z= 0.151
  Angle     :  0.716   9.046  12414  Z= 0.344
  Chirality :  0.051   0.374   1371
  Planarity :  0.005   0.046   1578
  Dihedral  : 29.146 175.036   1389
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.83 %
    Favored  : 95.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.25), residues: 1098
  helix:  0.42 (0.24), residues: 447
  sheet:  0.28 (0.33), residues: 210
  loop :  1.44 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 312 
 TYR   0.013   0.001   TYR B 143 
 PHE   0.024   0.002   PHE C 352 
 TRP   0.014   0.002   TRP D 356 
 HIS   0.007   0.001   HIS C 371 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.15 ( 9138)
  covalent geometry    : angle       0.71574 /  0.34 (12414)
  hydrogen bonds       : bond        0.03693 /  2.54 (  426)
  hydrogen bonds       : angle       4.80026 /  3.31 ( 1113)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.352 
Fit side-chains
REVERT: C   47 MET cc_start: 0.7298 (tmm) cc_final: 0.6586 (tmm)
REVERT: C  190 MET cc_start: 0.8584 (mtp) cc_final: 0.8359 (mtp)
REVERT: D   47 MET cc_start: 0.7532 (tmm) cc_final: 0.6585 (tmm)
REVERT: D  190 MET cc_start: 0.8626 (mtp) cc_final: 0.8305 (mtt)
  outliers start: 2
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0683
  time to fit residues: 9.0629
Evaluate side-chains
  70 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 90 optimal weight:    0.6980
   chunk 109 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 60 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 162 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.091441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.078375 restraints weight = 15157.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.02
r_work: 0.3068 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.3081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9138  Z= 0.164
  Angle     :  0.667   8.833  12414  Z= 0.317
  Chirality :  0.050   0.331   1371
  Planarity :  0.005   0.044   1578
  Dihedral  : 27.110 178.555   1389
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  5.96 %
    Favored  : 93.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.26), residues: 1098
  helix:  0.95 (0.25), residues: 447
  sheet:  0.39 (0.34), residues: 210
  loop :  1.53 (0.32), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 256 
 TYR   0.011   0.001   TYR B 143 
 PHE   0.013   0.002   PHE B 375 
 TRP   0.012   0.002   TRP D 356 
 HIS   0.004   0.001   HIS D 173 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00376 /  0.16 ( 9138)
  covalent geometry    : angle       0.66700 /  0.32 (12414)
  hydrogen bonds       : bond        0.03816 /  2.63 (  426)
  hydrogen bonds       : angle       4.52291 /  3.12 ( 1113)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.340 
Fit side-chains
REVERT: B  206 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7551 (ttt180)
REVERT: B  354 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8012 (pm20)
REVERT: C   47 MET cc_start: 0.7270 (tmm) cc_final: 0.6842 (tmm)
REVERT: C  269 MET cc_start: 0.7757 (mtm) cc_final: 0.7360 (mtm)
REVERT: D   47 MET cc_start: 0.7444 (tmm) cc_final: 0.6498 (tmm)
REVERT: D  190 MET cc_start: 0.8618 (mtp) cc_final: 0.8279 (mtt)
REVERT: D  269 MET cc_start: 0.8479 (mtp) cc_final: 0.8155 (mtp)
REVERT: D  305 MET cc_start: 0.8609 (mtp) cc_final: 0.8284 (mtm)
  outliers start: 3
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0818
  time to fit residues: 9.8220
Evaluate side-chains
  69 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  354 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 6 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.6859 > 50:)
   chunk 90 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 103 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 98 optimal weight:    0.6980
   overall best weight:    0.7982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.090225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.077218 restraints weight = 15486.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 2.04
r_work: 0.3044 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.3540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9138  Z= 0.164
  Angle     :  0.645   9.592  12414  Z= 0.305
  Chirality :  0.049   0.365   1371
  Planarity :  0.005   0.046   1578
  Dihedral  : 26.374 178.198   1389
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  6.07 %
    Favored  : 93.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.26), residues: 1098
  helix:  1.23 (0.26), residues: 438
  sheet:  0.60 (0.34), residues: 225
  loop :  1.68 (0.32), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 256 
 TYR   0.009   0.001   TYR B  91 
 PHE   0.026   0.002   PHE C 352 
 TRP   0.011   0.002   TRP D  79 
 HIS   0.004   0.001   HIS B 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00385 /  0.16 ( 9138)
  covalent geometry    : angle       0.64501 /  0.31 (12414)
  hydrogen bonds       : bond        0.03625 /  2.48 (  426)
  hydrogen bonds       : angle       4.42253 /  3.05 ( 1113)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.274 
Fit side-chains
REVERT: B  206 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7568 (ttt180)
REVERT: B  236 LEU cc_start: 0.7995 (tt) cc_final: 0.7680 (mm)
REVERT: D   47 MET cc_start: 0.7490 (tmm) cc_final: 0.6442 (tmm)
REVERT: D  157 ASP cc_start: 0.8156 (t0) cc_final: 0.7700 (t0)
REVERT: D  190 MET cc_start: 0.8689 (mtp) cc_final: 0.8367 (mtt)
REVERT: D  305 MET cc_start: 0.8632 (mtp) cc_final: 0.8091 (mtm)
  outliers start: 6
  outliers final: 4
  residues processed: 77
  average time/residue: 0.0727
  time to fit residues: 8.8029
Evaluate side-chains
  73 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  111 ASN
Chi-restraints excluded: chain C residue  318 THR
Chi-restraints excluded: chain D residue   14 SER
Chi-restraints excluded: chain D residue  267 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0270
   chunk 48 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0470
   overall best weight:    0.5738

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.090917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.077991 restraints weight = 15357.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 2.03
r_work: 0.3061 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.3727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9138  Z= 0.129
  Angle     :  0.613   9.791  12414  Z= 0.286
  Chirality :  0.047   0.350   1371
  Planarity :  0.005   0.047   1578
  Dihedral  : 25.946 179.271   1389
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  6.92 %
    Favored  : 92.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.26), residues: 1098
  helix:  1.03 (0.25), residues: 468
  sheet:  0.83 (0.33), residues: 219
  loop :  1.46 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  39 
 TYR   0.007   0.001   TYR B  91 
 PHE   0.009   0.001   PHE B 375 
 TRP   0.010   0.002   TRP D  79 
 HIS   0.003   0.001   HIS B 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 9138)
  covalent geometry    : angle       0.61288 /  0.29 (12414)
  hydrogen bonds       : bond        0.03221 /  2.21 (  426)
  hydrogen bonds       : angle       4.23143 /  2.92 ( 1113)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.329 
Fit side-chains
REVERT: B   47 MET cc_start: 0.7902 (tpt) cc_final: 0.7660 (tpt)
REVERT: B  111 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8303 (t0)
REVERT: B  206 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7538 (ttt180)
REVERT: B  236 LEU cc_start: 0.7946 (tt) cc_final: 0.7682 (mm)
REVERT: B  313 MET cc_start: 0.9191 (mmm) cc_final: 0.8923 (mmm)
REVERT: C  355 MET cc_start: 0.7603 (mmt) cc_final: 0.7050 (mmm)
REVERT: D   47 MET cc_start: 0.7484 (tmm) cc_final: 0.6525 (tmm)
REVERT: D  157 ASP cc_start: 0.8137 (t0) cc_final: 0.7906 (t70)
REVERT: D  190 MET cc_start: 0.8676 (mtp) cc_final: 0.8362 (mtt)
REVERT: D  305 MET cc_start: 0.8619 (mtp) cc_final: 0.8051 (mtm)
  outliers start: 6
  outliers final: 5
  residues processed: 78
  average time/residue: 0.0677
  time to fit residues: 8.3960
Evaluate side-chains
  74 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  111 ASN
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  318 THR
Chi-restraints excluded: chain D residue   14 SER
Chi-restraints excluded: chain D residue  267 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 110 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 162 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.088235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.075402 restraints weight = 15236.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 1.99
r_work: 0.3012 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2885 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.3932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9138  Z= 0.190
  Angle     :  0.652   9.724  12414  Z= 0.310
  Chirality :  0.050   0.383   1371
  Planarity :  0.005   0.046   1578
  Dihedral  : 25.845 173.865   1389
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  6.50 %
    Favored  : 92.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.26), residues: 1098
  helix:  1.17 (0.26), residues: 444
  sheet:  0.87 (0.35), residues: 219
  loop :  1.55 (0.32), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 147 
 TYR   0.010   0.001   TYR B  91 
 PHE   0.011   0.001   PHE D 262 
 TRP   0.013   0.002   TRP D  79 
 HIS   0.003   0.001   HIS B 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00451 /  0.19 ( 9138)
  covalent geometry    : angle       0.65194 /  0.31 (12414)
  hydrogen bonds       : bond        0.03864 /  2.63 (  426)
  hydrogen bonds       : angle       4.36921 /  3.03 ( 1113)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.352 
Fit side-chains
REVERT: B  206 ARG cc_start: 0.8107 (ttm-80) cc_final: 0.7601 (ttt180)
REVERT: B  236 LEU cc_start: 0.8031 (tt) cc_final: 0.7818 (mm)
REVERT: B  313 MET cc_start: 0.9180 (mmm) cc_final: 0.8911 (mmm)
REVERT: C  355 MET cc_start: 0.7489 (mmt) cc_final: 0.7008 (mmm)
REVERT: D   47 MET cc_start: 0.7443 (tmm) cc_final: 0.6546 (tmm)
REVERT: D  157 ASP cc_start: 0.8189 (t0) cc_final: 0.7755 (t0)
REVERT: D  190 MET cc_start: 0.8674 (mtp) cc_final: 0.8347 (mtt)
REVERT: D  305 MET cc_start: 0.8721 (mtp) cc_final: 0.8214 (mtm)
  outliers start: 13
  outliers final: 10
  residues processed: 77
  average time/residue: 0.0735
  time to fit residues: 8.7153
Evaluate side-chains
  74 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain C residue  111 ASN
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  192 ILE
Chi-restraints excluded: chain C residue  318 THR
Chi-restraints excluded: chain D residue   14 SER
Chi-restraints excluded: chain D residue  226 GLU
Chi-restraints excluded: chain D residue  267 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 105 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 48 optimal weight:    0.4980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 162 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.088706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.075862 restraints weight = 15395.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 2.01
r_work: 0.3022 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.4018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9138  Z= 0.163
  Angle     :  0.628   9.823  12414  Z= 0.297
  Chirality :  0.048   0.358   1371
  Planarity :  0.005   0.046   1578
  Dihedral  : 25.678 171.918   1389
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  6.82 %
    Favored  : 91.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.26), residues: 1098
  helix:  1.02 (0.25), residues: 462
  sheet:  0.84 (0.35), residues: 219
  loop :  1.42 (0.32), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 147 
 TYR   0.007   0.001   TYR B  91 
 PHE   0.009   0.001   PHE C 352 
 TRP   0.011   0.002   TRP D 340 
 HIS   0.003   0.001   HIS B 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00385 /  0.16 ( 9138)
  covalent geometry    : angle       0.62771 /  0.30 (12414)
  hydrogen bonds       : bond        0.03522 /  2.41 (  426)
  hydrogen bonds       : angle       4.27728 /  2.96 ( 1113)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.361 
Fit side-chains
REVERT: B  206 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7558 (ttt180)
REVERT: B  236 LEU cc_start: 0.7987 (tt) cc_final: 0.7762 (mm)
REVERT: B  313 MET cc_start: 0.9171 (mmm) cc_final: 0.8888 (mmm)
REVERT: C  355 MET cc_start: 0.7438 (mmt) cc_final: 0.6973 (mmm)
REVERT: D   47 MET cc_start: 0.7542 (tmm) cc_final: 0.6699 (tmm)
REVERT: D  157 ASP cc_start: 0.8143 (t0) cc_final: 0.7656 (t0)
REVERT: D  190 MET cc_start: 0.8654 (mtp) cc_final: 0.8329 (mtt)
REVERT: D  305 MET cc_start: 0.8701 (mtp) cc_final: 0.8178 (mtm)
  outliers start: 16
  outliers final: 11
  residues processed: 77
  average time/residue: 0.0700
  time to fit residues: 8.4100
Evaluate side-chains
  75 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain C residue  111 ASN
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  192 ILE
Chi-restraints excluded: chain C residue  318 THR
Chi-restraints excluded: chain D residue   14 SER
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  226 GLU
Chi-restraints excluded: chain D residue  267 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   chunk 110 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   chunk 85 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 96 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 162 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.089180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.076415 restraints weight = 15385.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 1.99
r_work: 0.3038 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.4082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9138  Z= 0.140
  Angle     :  0.608   9.944  12414  Z= 0.287
  Chirality :  0.047   0.344   1371
  Planarity :  0.005   0.046   1578
  Dihedral  : 25.604 171.753   1389
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  7.45 %
    Favored  : 91.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.26), residues: 1098
  helix:  1.09 (0.25), residues: 462
  sheet:  0.58 (0.36), residues: 201
  loop :  1.46 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  39 
 TYR   0.006   0.001   TYR B  91 
 PHE   0.010   0.001   PHE C 352 
 TRP   0.011   0.002   TRP D 340 
 HIS   0.003   0.001   HIS B 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.14 ( 9138)
  covalent geometry    : angle       0.60850 /  0.29 (12414)
  hydrogen bonds       : bond        0.03315 /  2.27 (  426)
  hydrogen bonds       : angle       4.19895 /  2.90 ( 1113)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.329 
Fit side-chains
REVERT: B  206 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7549 (ttt180)
REVERT: B  313 MET cc_start: 0.9161 (mmm) cc_final: 0.8877 (mmm)
REVERT: C  355 MET cc_start: 0.7381 (mmt) cc_final: 0.6908 (mmm)
REVERT: D   47 MET cc_start: 0.7374 (tmm) cc_final: 0.6550 (tmm)
REVERT: D  157 ASP cc_start: 0.8128 (t0) cc_final: 0.7641 (t0)
REVERT: D  190 MET cc_start: 0.8691 (mtp) cc_final: 0.8381 (mtt)
REVERT: D  305 MET cc_start: 0.8692 (mtp) cc_final: 0.8200 (mtm)
  outliers start: 13
  outliers final: 11
  residues processed: 74
  average time/residue: 0.0645
  time to fit residues: 7.5385
Evaluate side-chains
  73 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain C residue  111 ASN
Chi-restraints excluded: chain C residue  132 MET
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  192 ILE
Chi-restraints excluded: chain C residue  318 THR
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  226 GLU
Chi-restraints excluded: chain D residue  267 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 3 optimal weight:    0.5980
   chunk 97 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 63 optimal weight:    0.4980
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 162 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.088582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.075731 restraints weight = 15252.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 2.00
r_work: 0.3017 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2889 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.4118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9138  Z= 0.175
  Angle     :  0.630   9.948  12414  Z= 0.299
  Chirality :  0.049   0.362   1371
  Planarity :  0.005   0.045   1578
  Dihedral  : 25.634 172.206   1389
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  7.67 %
    Favored  : 90.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.26), residues: 1098
  helix:  1.04 (0.25), residues: 462
  sheet:  0.55 (0.36), residues: 201
  loop :  1.43 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 147 
 TYR   0.007   0.001   TYR B  91 
 PHE   0.012   0.001   PHE C 352 
 TRP   0.011   0.002   TRP D 340 
 HIS   0.006   0.001   HIS B 161 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00417 /  0.18 ( 9138)
  covalent geometry    : angle       0.62981 /  0.30 (12414)
  hydrogen bonds       : bond        0.03578 /  2.45 (  426)
  hydrogen bonds       : angle       4.24750 /  2.94 ( 1113)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.327 
Fit side-chains
REVERT: B  206 ARG cc_start: 0.8090 (ttm-80) cc_final: 0.7583 (ttt180)
REVERT: B  313 MET cc_start: 0.9154 (mmm) cc_final: 0.8878 (mmm)
REVERT: C  355 MET cc_start: 0.7354 (mmt) cc_final: 0.6914 (mmm)
REVERT: D   47 MET cc_start: 0.7397 (tmm) cc_final: 0.6581 (tmm)
REVERT: D  157 ASP cc_start: 0.8153 (t0) cc_final: 0.7659 (t0)
REVERT: D  190 MET cc_start: 0.8684 (mtp) cc_final: 0.8374 (mtt)
REVERT: D  305 MET cc_start: 0.8652 (mtp) cc_final: 0.8173 (mtm)
  outliers start: 13
  outliers final: 12
  residues processed: 72
  average time/residue: 0.0655
  time to fit residues: 7.3471
Evaluate side-chains
  74 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain C residue  111 ASN
Chi-restraints excluded: chain C residue  132 MET
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  192 ILE
Chi-restraints excluded: chain C residue  318 THR
Chi-restraints excluded: chain D residue  111 ASN
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  226 GLU
Chi-restraints excluded: chain D residue  267 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0870
   chunk 21 optimal weight:    0.0980
   chunk 23 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 84 optimal weight:    0.8980
   chunk 106 optimal weight:    1.9990
   chunk 98 optimal weight:    0.6980
   overall best weight:    0.4558

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.090011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.077128 restraints weight = 15275.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.02
r_work: 0.3044 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.4165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9138  Z= 0.116
  Angle     :  0.595  10.137  12414  Z= 0.279
  Chirality :  0.046   0.326   1371
  Planarity :  0.005   0.047   1578
  Dihedral  : 25.370 172.237   1389
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  8.41 %
    Favored  : 90.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.26), residues: 1098
  helix:  1.17 (0.25), residues: 462
  sheet:  0.55 (0.36), residues: 201
  loop :  1.52 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 177 
 TYR   0.006   0.001   TYR B 306 
 PHE   0.010   0.001   PHE B 352 
 TRP   0.010   0.002   TRP D 340 
 HIS   0.006   0.001   HIS B 161 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 9138)
  covalent geometry    : angle       0.59546 /  0.28 (12414)
  hydrogen bonds       : bond        0.03061 /  2.10 (  426)
  hydrogen bonds       : angle       4.11803 /  2.85 ( 1113)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.341 
Fit side-chains
REVERT: B  206 ARG cc_start: 0.8043 (ttm-80) cc_final: 0.7521 (ttt180)
REVERT: B  305 MET cc_start: 0.8975 (mtp) cc_final: 0.8720 (mtm)
REVERT: B  313 MET cc_start: 0.9135 (mmm) cc_final: 0.8788 (mmm)
REVERT: C   72 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6968 (mm-30)
REVERT: C  355 MET cc_start: 0.7310 (mmt) cc_final: 0.7003 (mtt)
REVERT: D   47 MET cc_start: 0.7350 (tmm) cc_final: 0.6522 (tmm)
REVERT: D  157 ASP cc_start: 0.8147 (t0) cc_final: 0.7595 (t0)
REVERT: D  190 MET cc_start: 0.8664 (mtp) cc_final: 0.8343 (mtt)
REVERT: D  305 MET cc_start: 0.8644 (mtp) cc_final: 0.8118 (mtm)
  outliers start: 7
  outliers final: 7
  residues processed: 72
  average time/residue: 0.0688
  time to fit residues: 7.7269
Evaluate side-chains
  70 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain C residue  111 ASN
Chi-restraints excluded: chain C residue  132 MET
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue  111 ASN
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  226 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 76 optimal weight:    0.4980
   chunk 93 optimal weight:    0.7980
   chunk 105 optimal weight:    1.9990
   chunk 22 optimal weight:    0.2980
   chunk 33 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 162 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.089111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.076256 restraints weight = 15148.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 2.00
r_work: 0.3027 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.4211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9138  Z= 0.148
  Angle     :  0.614  10.110  12414  Z= 0.289
  Chirality :  0.047   0.343   1371
  Planarity :  0.005   0.045   1578
  Dihedral  : 25.292 172.898   1389
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  8.31 %
    Favored  : 90.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.26), residues: 1098
  helix:  1.14 (0.25), residues: 462
  sheet:  0.55 (0.36), residues: 201
  loop :  1.47 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  39 
 TYR   0.006   0.001   TYR B  91 
 PHE   0.011   0.001   PHE C 352 
 TRP   0.011   0.002   TRP D 340 
 HIS   0.003   0.001   HIS B 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.15 ( 9138)
  covalent geometry    : angle       0.61440 /  0.29 (12414)
  hydrogen bonds       : bond        0.03349 /  2.28 (  426)
  hydrogen bonds       : angle       4.17950 /  2.89 ( 1113)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1927.56 seconds
wall clock time: 33 minutes 48.45 seconds (2028.45 seconds total)