Starting phenix.real_space_refine
on Sun Jul 27 08:10:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pm3_13511/07_2025/7pm3_13511.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pm3_13511/07_2025/7pm3_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pm3_13511/07_2025/7pm3_13511.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pm3_13511/07_2025/7pm3_13511.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pm3_13511/07_2025/7pm3_13511.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pm3_13511/07_2025/7pm3_13511.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 10.43, per 1000 atoms: 1.17
  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: 2.34
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.15
  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: 3.49

  Time building geometry restraints manager: 2.72 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:             29.400
  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:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.140
  Process input model:                     33.570
  Find NCS groups from input model:        0.570
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:3.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   67.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (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
 TRP   0.020   0.003   TRP C  79 
 HIS   0.007   0.001   HIS C 101 
 PHE   0.021   0.002   PHE D 262 
 TYR   0.029   0.006   TYR C  53 
 ARG   0.085   0.019   ARG D 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18269 (  426)
  hydrogen bonds       : angle       6.80154 ( 1113)
  covalent geometry    : bond        0.00534 ( 9138)
  covalent geometry    : angle       0.98382 (12414)

*********************** 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  : 1.077 
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: 0.7655 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2292
  time to fit residues: 48.7415
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  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.5980
   chunk 84 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 87 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.093453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.080376 restraints weight = 14992.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 2.00
r_work: 0.3105 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   9138  Z= 0.172
  Angle     :  0.733   8.634  12414  Z= 0.355
  Chirality :  0.052   0.392   1371
  Planarity :  0.005   0.047   1578
  Dihedral  : 28.865 175.844   1389
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  3.83 %
    Favored  : 95.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.25), residues: 1098
  helix:  0.38 (0.24), residues: 447
  sheet:  0.25 (0.34), residues: 210
  loop :  1.41 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 356 
 HIS   0.007   0.001   HIS C 371 
 PHE   0.024   0.002   PHE C 352 
 TYR   0.013   0.002   TYR B 143 
 ARG   0.005   0.001   ARG C 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03821 (  426)
  hydrogen bonds       : angle       4.78984 ( 1113)
  covalent geometry    : bond        0.00392 ( 9138)
  covalent geometry    : angle       0.73334 (12414)

*********************** 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
  86 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 1.070 
Fit side-chains
REVERT: C   47 MET cc_start: 0.7204 (tmm) cc_final: 0.6559 (tmm)
REVERT: C  190 MET cc_start: 0.8602 (mtp) cc_final: 0.8379 (mtp)
REVERT: D   47 MET cc_start: 0.7475 (tmm) cc_final: 0.6552 (tmm)
REVERT: D  190 MET cc_start: 0.8668 (mtp) cc_final: 0.8349 (mtt)
  outliers start: 4
  outliers final: 1
  residues processed: 85
  average time/residue: 0.1707
  time to fit residues: 22.1830
Evaluate side-chains
  73 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  318 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 105 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 87 optimal weight:    0.5980
   chunk 74 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
B 162 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.089291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.076201 restraints weight = 15515.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 2.05
r_work: 0.3025 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.3287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9138  Z= 0.209
  Angle     :  0.703   8.645  12414  Z= 0.340
  Chirality :  0.053   0.371   1371
  Planarity :  0.005   0.044   1578
  Dihedral  : 27.359 177.651   1389
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  6.07 %
    Favored  : 93.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.26), residues: 1098
  helix:  0.89 (0.25), residues: 438
  sheet:  0.55 (0.34), residues: 225
  loop :  1.64 (0.32), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 356 
 HIS   0.005   0.002   HIS B 101 
 PHE   0.014   0.002   PHE D 262 
 TYR   0.012   0.001   TYR B  91 
 ARG   0.003   0.000   ARG C 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04357 (  426)
  hydrogen bonds       : angle       4.67203 ( 1113)
  covalent geometry    : bond        0.00491 ( 9138)
  covalent geometry    : angle       0.70343 (12414)

*********************** 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
  81 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.979 
Fit side-chains
REVERT: B  206 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7631 (ttt180)
REVERT: B  236 LEU cc_start: 0.7916 (tt) cc_final: 0.7659 (mm)
REVERT: B  313 MET cc_start: 0.9242 (mmm) cc_final: 0.9011 (mmm)
REVERT: B  354 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8010 (pm20)
REVERT: C   47 MET cc_start: 0.7204 (tmm) cc_final: 0.6739 (tmm)
REVERT: C  269 MET cc_start: 0.7873 (mtm) cc_final: 0.7487 (mtm)
REVERT: D   47 MET cc_start: 0.7562 (tmm) cc_final: 0.6623 (tmm)
REVERT: D  190 MET cc_start: 0.8715 (mtp) cc_final: 0.8403 (mtt)
REVERT: D  305 MET cc_start: 0.8583 (mtp) cc_final: 0.8206 (mtm)
  outliers start: 7
  outliers final: 2
  residues processed: 80
  average time/residue: 0.1895
  time to fit residues: 22.8574
Evaluate side-chains
  71 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  354 GLN
Chi-restraints excluded: chain C residue  318 THR
Chi-restraints excluded: chain D residue  267 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 102 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 104 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.089634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.076754 restraints weight = 15391.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 2.02
r_work: 0.3040 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.3628

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= 0.162
  Angle     :  0.641   9.218  12414  Z= 0.305
  Chirality :  0.049   0.359   1371
  Planarity :  0.005   0.046   1578
  Dihedral  : 26.565 178.573   1389
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  6.92 %
    Favored  : 92.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.26), residues: 1098
  helix:  0.95 (0.25), residues: 456
  sheet:  0.59 (0.34), residues: 225
  loop :  1.52 (0.32), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D 340 
 HIS   0.004   0.001   HIS B 101 
 PHE   0.013   0.001   PHE B 375 
 TYR   0.009   0.001   TYR B  91 
 ARG   0.002   0.000   ARG C 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03577 (  426)
  hydrogen bonds       : angle       4.40242 ( 1113)
  covalent geometry    : bond        0.00380 ( 9138)
  covalent geometry    : angle       0.64130 (12414)

*********************** 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
  76 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 1.137 
Fit side-chains
REVERT: B  206 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7552 (ttt180)
REVERT: B  236 LEU cc_start: 0.8025 (tt) cc_final: 0.7818 (mm)
REVERT: B  313 MET cc_start: 0.9168 (mmm) cc_final: 0.8907 (mmm)
REVERT: B  355 MET cc_start: 0.7568 (mtt) cc_final: 0.7171 (mmt)
REVERT: B  375 PHE cc_start: 0.6688 (m-10) cc_final: 0.6378 (m-10)
REVERT: C  355 MET cc_start: 0.7405 (mmt) cc_final: 0.6902 (mmm)
REVERT: D   47 MET cc_start: 0.7520 (tmm) cc_final: 0.6431 (tmm)
REVERT: D  157 ASP cc_start: 0.8218 (t0) cc_final: 0.7712 (t0)
REVERT: D  190 MET cc_start: 0.8691 (mtp) cc_final: 0.8373 (mtt)
REVERT: D  305 MET cc_start: 0.8641 (mtp) cc_final: 0.8088 (mtm)
  outliers start: 4
  outliers final: 4
  residues processed: 75
  average time/residue: 0.1757
  time to fit residues: 20.3340
Evaluate side-chains
  72 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
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  318 THR
Chi-restraints excluded: chain D residue   14 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 79 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.089046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.076197 restraints weight = 15319.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 2.02
r_work: 0.3031 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.3847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9138  Z= 0.168
  Angle     :  0.638   9.541  12414  Z= 0.302
  Chirality :  0.049   0.384   1371
  Planarity :  0.005   0.046   1578
  Dihedral  : 26.359 179.760   1389
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  7.24 %
    Favored  : 91.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.26), residues: 1098
  helix:  1.07 (0.26), residues: 444
  sheet:  0.88 (0.35), residues: 219
  loop :  1.59 (0.32), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D  79 
 HIS   0.004   0.001   HIS B 101 
 PHE   0.010   0.001   PHE B 375 
 TYR   0.009   0.001   TYR B  91 
 ARG   0.003   0.000   ARG D 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03659 (  426)
  hydrogen bonds       : angle       4.35504 ( 1113)
  covalent geometry    : bond        0.00397 ( 9138)
  covalent geometry    : angle       0.63779 (12414)

*********************** 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: 11
    poor density    : 68
  time to evaluate  : 1.022 
Fit side-chains
REVERT: B  111 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8374 (t0)
REVERT: B  206 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7576 (ttt180)
REVERT: B  313 MET cc_start: 0.9197 (mmm) cc_final: 0.8933 (mmm)
REVERT: B  334 GLU cc_start: 0.7930 (tp30) cc_final: 0.7730 (tp30)
REVERT: B  354 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7939 (pm20)
REVERT: B  355 MET cc_start: 0.7549 (mtt) cc_final: 0.7212 (mtt)
REVERT: C  355 MET cc_start: 0.7516 (mmt) cc_final: 0.6971 (mmm)
REVERT: D   47 MET cc_start: 0.7518 (tmm) cc_final: 0.6483 (tmm)
REVERT: D  157 ASP cc_start: 0.8171 (t0) cc_final: 0.7731 (t0)
REVERT: D  190 MET cc_start: 0.8721 (mtp) cc_final: 0.8408 (mtt)
REVERT: D  305 MET cc_start: 0.8703 (mtp) cc_final: 0.8151 (mtm)
  outliers start: 11
  outliers final: 8
  residues processed: 78
  average time/residue: 0.1786
  time to fit residues: 21.2706
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  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue  111 ASN
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  354 GLN
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  267 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 96 optimal weight:    0.6980
   chunk 104 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.089163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.076245 restraints weight = 15450.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 2.03
r_work: 0.3026 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.3997

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= 0.166
  Angle     :  0.626   9.273  12414  Z= 0.297
  Chirality :  0.048   0.356   1371
  Planarity :  0.005   0.045   1578
  Dihedral  : 25.994 173.072   1389
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  7.45 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.26), residues: 1098
  helix:  0.93 (0.25), residues: 462
  sheet:  0.86 (0.35), residues: 219
  loop :  1.46 (0.32), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D 340 
 HIS   0.003   0.001   HIS B  88 
 PHE   0.009   0.001   PHE B 255 
 TYR   0.008   0.001   TYR B  91 
 ARG   0.003   0.000   ARG C 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03557 (  426)
  hydrogen bonds       : angle       4.31080 ( 1113)
  covalent geometry    : bond        0.00393 ( 9138)
  covalent geometry    : angle       0.62574 (12414)

*********************** 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
  81 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 1.034 
Fit side-chains
REVERT: B  111 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8466 (t0)
REVERT: B  206 ARG cc_start: 0.8077 (ttm-80) cc_final: 0.7552 (ttt180)
REVERT: B  313 MET cc_start: 0.9188 (mmm) cc_final: 0.8912 (mmm)
REVERT: B  355 MET cc_start: 0.7614 (mtt) cc_final: 0.7346 (mtt)
REVERT: C  355 MET cc_start: 0.7485 (mmt) cc_final: 0.7031 (mmm)
REVERT: D   47 MET cc_start: 0.7452 (tmm) cc_final: 0.6632 (tmm)
REVERT: D  157 ASP cc_start: 0.8124 (t0) cc_final: 0.7644 (t0)
REVERT: D  190 MET cc_start: 0.8723 (mtp) cc_final: 0.8414 (mtt)
REVERT: D  305 MET cc_start: 0.8719 (mtp) cc_final: 0.8193 (mtm)
  outliers start: 16
  outliers final: 11
  residues processed: 79
  average time/residue: 0.1738
  time to fit residues: 20.9599
Evaluate side-chains
  73 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue  111 ASN
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  236 LEU
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   14 SER
Chi-restraints excluded: chain D residue  111 ASN
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 98 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 104 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 73 optimal weight:    0.8980
   chunk 91 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0970
   overall best weight:    0.6578

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.089785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.076842 restraints weight = 15614.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 2.05
r_work: 0.3039 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.4076

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     :  0.601   9.494  12414  Z= 0.285
  Chirality :  0.047   0.345   1371
  Planarity :  0.005   0.045   1578
  Dihedral  : 25.702 171.671   1389
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  8.95 %
    Favored  : 89.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.26), residues: 1098
  helix:  1.03 (0.25), residues: 462
  sheet:  0.82 (0.35), residues: 219
  loop :  1.42 (0.32), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D 340 
 HIS   0.003   0.001   HIS D 101 
 PHE   0.007   0.001   PHE B 255 
 TYR   0.007   0.001   TYR B  91 
 ARG   0.002   0.000   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03284 (  426)
  hydrogen bonds       : angle       4.21794 ( 1113)
  covalent geometry    : bond        0.00330 ( 9138)
  covalent geometry    : angle       0.60137 (12414)

*********************** 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
  79 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.953 
Fit side-chains
REVERT: B  111 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8459 (t0)
REVERT: B  206 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7532 (ttt180)
REVERT: B  313 MET cc_start: 0.9169 (mmm) cc_final: 0.8838 (mmm)
REVERT: B  355 MET cc_start: 0.7532 (mtt) cc_final: 0.7187 (mtt)
REVERT: B  375 PHE cc_start: 0.6825 (m-10) cc_final: 0.6606 (m-10)
REVERT: C  355 MET cc_start: 0.7477 (mmt) cc_final: 0.7029 (mmm)
REVERT: D   47 MET cc_start: 0.7508 (tmm) cc_final: 0.6605 (tmm)
REVERT: D  157 ASP cc_start: 0.8144 (t0) cc_final: 0.7640 (t0)
REVERT: D  190 MET cc_start: 0.8694 (mtp) cc_final: 0.8383 (mtt)
REVERT: D  305 MET cc_start: 0.8648 (mtp) cc_final: 0.8090 (mtm)
  outliers start: 14
  outliers final: 9
  residues processed: 76
  average time/residue: 0.1778
  time to fit residues: 20.5450
Evaluate side-chains
  73 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue  111 ASN
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  236 LEU
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   14 SER
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  226 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 2 optimal weight:    0.0040
   chunk 92 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 104 optimal weight:    0.1980
   chunk 5 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.4392

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

Flipped N/Q/H residues before XYZ refinement:
B 162 ASN
C 162 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.090774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.077833 restraints weight = 15552.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 2.03
r_work: 0.3064 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.4179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9138  Z= 0.109
  Angle     :  0.576   9.811  12414  Z= 0.269
  Chirality :  0.046   0.314   1371
  Planarity :  0.005   0.045   1578
  Dihedral  : 25.451 172.989   1389
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  8.95 %
    Favored  : 89.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.26), residues: 1098
  helix:  1.17 (0.25), residues: 462
  sheet:  0.64 (0.36), residues: 201
  loop :  1.49 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 340 
 HIS   0.002   0.001   HIS B 101 
 PHE   0.007   0.001   PHE B 255 
 TYR   0.006   0.001   TYR C 294 
 ARG   0.002   0.000   ARG C 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02869 (  426)
  hydrogen bonds       : angle       4.06825 ( 1113)
  covalent geometry    : bond        0.00253 ( 9138)
  covalent geometry    : angle       0.57598 (12414)

*********************** 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
  82 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 1.081 
Fit side-chains
REVERT: B  111 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8386 (t0)
REVERT: B  206 ARG cc_start: 0.8029 (ttm-80) cc_final: 0.7527 (ttt180)
REVERT: B  305 MET cc_start: 0.8975 (mtp) cc_final: 0.8672 (mtm)
REVERT: B  313 MET cc_start: 0.9130 (mmm) cc_final: 0.8784 (mmm)
REVERT: B  355 MET cc_start: 0.7453 (mtt) cc_final: 0.7181 (mtt)
REVERT: C   47 MET cc_start: 0.7407 (tmm) cc_final: 0.7099 (tmm)
REVERT: C  355 MET cc_start: 0.7462 (mmt) cc_final: 0.7004 (mmm)
REVERT: D   47 MET cc_start: 0.7495 (tmm) cc_final: 0.6647 (tmm)
REVERT: D  157 ASP cc_start: 0.8135 (t0) cc_final: 0.7627 (t0)
REVERT: D  190 MET cc_start: 0.8661 (mtp) cc_final: 0.8353 (mtt)
REVERT: D  305 MET cc_start: 0.8618 (mtp) cc_final: 0.8092 (mtm)
  outliers start: 14
  outliers final: 9
  residues processed: 79
  average time/residue: 0.1758
  time to fit residues: 21.3235
Evaluate side-chains
  72 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue  111 ASN
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain B residue  236 LEU
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 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
B 162 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.087092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.074203 restraints weight = 15314.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 2.00
r_work: 0.2986 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.4201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   9138  Z= 0.249
  Angle     :  0.685   9.455  12414  Z= 0.331
  Chirality :  0.052   0.397   1371
  Planarity :  0.005   0.047   1578
  Dihedral  : 25.864 172.675   1389
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  9.58 %
    Favored  : 88.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.26), residues: 1098
  helix:  1.09 (0.26), residues: 444
  sheet:  0.50 (0.37), residues: 201
  loop :  1.35 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  79 
 HIS   0.004   0.001   HIS B  88 
 PHE   0.011   0.002   PHE B 262 
 TYR   0.009   0.001   TYR B  91 
 ARG   0.003   0.001   ARG B 254 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04257 (  426)
  hydrogen bonds       : angle       4.44613 ( 1113)
  covalent geometry    : bond        0.00593 ( 9138)
  covalent geometry    : angle       0.68539 (12414)

*********************** 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
  77 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 1.158 
Fit side-chains
REVERT: B  111 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8386 (t0)
REVERT: B  206 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7607 (ttt180)
REVERT: B  313 MET cc_start: 0.9184 (mmm) cc_final: 0.8931 (mmm)
REVERT: B  355 MET cc_start: 0.7202 (mtt) cc_final: 0.6913 (mtt)
REVERT: C   47 MET cc_start: 0.7265 (tmm) cc_final: 0.6983 (tmm)
REVERT: C  227 MET cc_start: 0.8429 (tpt) cc_final: 0.8212 (tpt)
REVERT: C  355 MET cc_start: 0.7399 (mmt) cc_final: 0.6943 (mmm)
REVERT: D   47 MET cc_start: 0.7439 (tmm) cc_final: 0.6666 (tmm)
REVERT: D  157 ASP cc_start: 0.8211 (t0) cc_final: 0.7792 (t0)
REVERT: D  190 MET cc_start: 0.8741 (mtp) cc_final: 0.8421 (mtt)
  outliers start: 14
  outliers final: 12
  residues processed: 75
  average time/residue: 0.1886
  time to fit residues: 21.9981
Evaluate side-chains
  76 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue  111 ASN
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain B residue  236 LEU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0570
   chunk 106 optimal weight:    0.3980
   chunk 94 optimal weight:    0.5980
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
C  12 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.089366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.076418 restraints weight = 15423.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 2.04
r_work: 0.3038 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.4230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9138  Z= 0.120
  Angle     :  0.598   9.725  12414  Z= 0.282
  Chirality :  0.047   0.329   1371
  Planarity :  0.005   0.050   1578
  Dihedral  : 25.597 172.128   1389
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  9.80 %
    Favored  : 88.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.26), residues: 1098
  helix:  1.05 (0.25), residues: 462
  sheet:  0.48 (0.36), residues: 201
  loop :  1.32 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D 340 
 HIS   0.002   0.001   HIS C 371 
 PHE   0.007   0.001   PHE B 255 
 TYR   0.007   0.001   TYR C  69 
 ARG   0.003   0.000   ARG C 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03202 (  426)
  hydrogen bonds       : angle       4.19648 ( 1113)
  covalent geometry    : bond        0.00278 ( 9138)
  covalent geometry    : angle       0.59790 (12414)

********************** 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
  77 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.970 
Fit side-chains
REVERT: B  111 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8427 (t0)
REVERT: B  206 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7537 (ttt180)
REVERT: B  305 MET cc_start: 0.8976 (mtp) cc_final: 0.8712 (mtm)
REVERT: B  313 MET cc_start: 0.9140 (mmm) cc_final: 0.8804 (mmm)
REVERT: B  355 MET cc_start: 0.7194 (mtt) cc_final: 0.6830 (mtt)
REVERT: C   47 MET cc_start: 0.7398 (tmm) cc_final: 0.7135 (tmm)
REVERT: C  355 MET cc_start: 0.7347 (mmt) cc_final: 0.6886 (mmm)
REVERT: D   47 MET cc_start: 0.7336 (tmm) cc_final: 0.6506 (tmm)
REVERT: D  157 ASP cc_start: 0.8128 (t0) cc_final: 0.7626 (t0)
REVERT: D  190 MET cc_start: 0.8707 (mtp) cc_final: 0.8392 (mtt)
  outliers start: 13
  outliers final: 11
  residues processed: 75
  average time/residue: 0.1778
  time to fit residues: 20.6003
Evaluate side-chains
  73 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue  111 ASN
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain B residue  236 LEU
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  270 GLU
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 75 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 103 optimal weight:    3.9990
   chunk 41 optimal weight:    0.1980
   chunk 78 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 57 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.6784

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

Flipped N/Q/H residues before XYZ refinement:
B 162 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.089086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.076151 restraints weight = 15480.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.04
r_work: 0.3031 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.4280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9138  Z= 0.143
  Angle     :  0.610   9.807  12414  Z= 0.288
  Chirality :  0.047   0.341   1371
  Planarity :  0.005   0.047   1578
  Dihedral  : 25.448 173.246   1389
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 10.12 %
    Favored  : 88.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.26), residues: 1098
  helix:  1.08 (0.25), residues: 462
  sheet:  0.48 (0.36), residues: 201
  loop :  1.35 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D 340 
 HIS   0.003   0.001   HIS B 101 
 PHE   0.007   0.001   PHE B 255 
 TYR   0.006   0.001   TYR B  91 
 ARG   0.004   0.000   ARG C 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03330 (  426)
  hydrogen bonds       : angle       4.18304 ( 1113)
  covalent geometry    : bond        0.00338 ( 9138)
  covalent geometry    : angle       0.60967 (12414)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5132.52 seconds
wall clock time: 90 minutes 49.78 seconds (5449.78 seconds total)