Starting phenix.real_space_refine
on Sat Aug 23 02:45:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fel_29032/08_2025/8fel_29032.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fel_29032/08_2025/8fel_29032.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fel_29032/08_2025/8fel_29032.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fel_29032/08_2025/8fel_29032.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fel_29032/08_2025/8fel_29032.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fel_29032/08_2025/8fel_29032.cif"
  }
  resolution = 4.64
  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=   0.002 sd=   0.078
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: 4
    Type Number    sf(0)   Gaussians
     S      51      5.16       5
     C    5820      2.51       5
     N    1509      2.21       5
     O    1821      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9201
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3067
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 397, 3067
          Classifications: {'peptide': 397}
          Link IDs: {'PTRANS': 13, 'TRANS': 383}
          Chain breaks: 2
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.34, per 1000 atoms: 0.25
  Number of scatterers: 9201
  At special positions: 0
  Unit cell: (93.96, 91.8, 172.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      51     16.00
     O    1821      8.00
     N    1509      7.00
     C    5820      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  66 " - pdb=" SG  CYS A 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 326 " - pdb=" SG  CYS A 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 350 " - pdb=" SG  CYS A 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 389 " - pdb=" SG  CYS A 412 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  66 " - pdb=" SG  CYS B 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  66 " - pdb=" SG  CYS C 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 326 " - pdb=" SG  CYS B 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 326 " - pdb=" SG  CYS C 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 350 " - pdb=" SG  CYS B 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 350 " - pdb=" SG  CYS C 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 382 " - pdb=" SG  CYS B 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 382 " - pdb=" SG  CYS C 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 389 " - pdb=" SG  CYS B 412 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 389 " - pdb=" SG  CYS C 412 " distance=2.03

  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: 0.91
  Conformation dependent library (CDL) restraints added in 260.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2232

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 15 sheets defined
      41.8% alpha, 7.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 32
    Processing helix  chain 'A' and resid 67 through 82
    Processing helix  chain 'A' and resid 85 through 92
    Processing helix  chain 'A' and resid 142 through 177
      removed outlier: 3.854A  pdb=" N   GLN A 147 " --> pdb=" O   LYS A 143 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ARG A 171 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 210
      removed outlier: 3.554A  pdb=" N   PHE A 209 " --> pdb=" O   ILE A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 215
      removed outlier: 3.613A  pdb=" N   GLN A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 227
    Processing helix  chain 'A' and resid 233 through 241
      removed outlier: 4.046A  pdb=" N   MET A 241 " --> pdb=" O   LEU A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 255
      removed outlier: 3.633A  pdb=" N   LEU A 248 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 353
      removed outlier: 3.787A  pdb=" N   ILE A 348 " --> pdb=" O   SER A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 477
      removed outlier: 3.603A  pdb=" N   GLU A 466 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LYS A 471 " --> pdb=" O   ASP A 467 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   SER A 472 " --> pdb=" O   TYR A 468 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 476 " --> pdb=" O   SER A 472 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LYS A 477 " --> pdb=" O   GLU A 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 32
    Processing helix  chain 'B' and resid 67 through 82
    Processing helix  chain 'B' and resid 85 through 92
    Processing helix  chain 'B' and resid 142 through 177
      removed outlier: 3.855A  pdb=" N   GLN B 147 " --> pdb=" O   LYS B 143 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ARG B 171 " --> pdb=" O   ILE B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 210
      removed outlier: 3.554A  pdb=" N   PHE B 209 " --> pdb=" O   ILE B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 215
      removed outlier: 3.613A  pdb=" N   GLN B 214 " --> pdb=" O   GLY B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 227
    Processing helix  chain 'B' and resid 233 through 241
      removed outlier: 4.045A  pdb=" N   MET B 241 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 255
      removed outlier: 3.635A  pdb=" N   LEU B 248 " --> pdb=" O   THR B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 353
      removed outlier: 3.789A  pdb=" N   ILE B 348 " --> pdb=" O   SER B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 477
      removed outlier: 3.601A  pdb=" N   GLU B 466 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LYS B 471 " --> pdb=" O   ASP B 467 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   SER B 472 " --> pdb=" O   TYR B 468 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU B 476 " --> pdb=" O   SER B 472 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LYS B 477 " --> pdb=" O   GLU B 473 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 32
    Processing helix  chain 'C' and resid 67 through 82
    Processing helix  chain 'C' and resid 85 through 92
    Processing helix  chain 'C' and resid 142 through 177
      removed outlier: 3.855A  pdb=" N   GLN C 147 " --> pdb=" O   LYS C 143 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ARG C 171 " --> pdb=" O   ILE C 167 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 210
      removed outlier: 3.553A  pdb=" N   PHE C 209 " --> pdb=" O   ILE C 205 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 210 through 215
      removed outlier: 3.613A  pdb=" N   GLN C 214 " --> pdb=" O   GLY C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 227
    Processing helix  chain 'C' and resid 233 through 241
      removed outlier: 4.046A  pdb=" N   MET C 241 " --> pdb=" O   LEU C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 255
      removed outlier: 3.634A  pdb=" N   LEU C 248 " --> pdb=" O   THR C 244 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 344 through 353
      removed outlier: 3.789A  pdb=" N   ILE C 348 " --> pdb=" O   SER C 344 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 477
      removed outlier: 3.602A  pdb=" N   GLU C 466 " --> pdb=" O   LEU C 462 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LYS C 471 " --> pdb=" O   ASP C 467 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   SER C 472 " --> pdb=" O   TYR C 468 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU C 476 " --> pdb=" O   SER C 472 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LYS C 477 " --> pdb=" O   GLU C 473 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 281 through 282
      removed outlier: 5.940A  pdb=" N   ASN A  40 " --> pdb=" O   VAL A 333 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   CYS A 335 " --> pdb=" O   ASN A  40 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   LYS A  42 " --> pdb=" O   CYS A 335 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 264
      removed outlier: 7.107A  pdb=" N   ALA A 272 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 290
      removed outlier: 3.852A  pdb=" N   GLN A 289 " --> pdb=" O   VAL A 311 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   VAL A 311 " --> pdb=" O   GLN A 289 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 298
    Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 374
      removed outlier: 3.693A  pdb=" N   ALA A 372 " --> pdb=" O   TYR A 379 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 281 through 282
      removed outlier: 5.940A  pdb=" N   ASN B  40 " --> pdb=" O   VAL B 333 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   CYS B 335 " --> pdb=" O   ASN B  40 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   LYS B  42 " --> pdb=" O   CYS B 335 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 261 through 264
      removed outlier: 7.107A  pdb=" N   ALA B 272 " --> pdb=" O   ILE B 262 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 288 through 290
      removed outlier: 3.852A  pdb=" N   GLN B 289 " --> pdb=" O   VAL B 311 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   VAL B 311 " --> pdb=" O   GLN B 289 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 296 through 298
    Processing sheet with id=AB1, first strand: chain 'B' and resid 372 through 374
      removed outlier: 3.692A  pdb=" N   ALA B 372 " --> pdb=" O   TYR B 379 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 281 through 282
      removed outlier: 5.940A  pdb=" N   ASN C  40 " --> pdb=" O   VAL C 333 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   CYS C 335 " --> pdb=" O   ASN C  40 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   LYS C  42 " --> pdb=" O   CYS C 335 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 261 through 264
      removed outlier: 7.107A  pdb=" N   ALA C 272 " --> pdb=" O   ILE C 262 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 288 through 290
      removed outlier: 3.853A  pdb=" N   GLN C 289 " --> pdb=" O   VAL C 311 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   VAL C 311 " --> pdb=" O   GLN C 289 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'C' and resid 296 through 298
    Processing sheet with id=AB6, first strand: chain 'C' and resid 372 through 374
      removed outlier: 3.693A  pdb=" N   ALA C 372 " --> pdb=" O   TYR C 379 " (cutoff:3.500A)

    381 hydrogen bonds defined for protein.
    1071 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: 1.10

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3033
        1.34 -     1.46: 1803
        1.46 -     1.58: 4410
        1.58 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 9318
  Sorted by residual:
  bond pdb=" C   ILE A 179 "
       pdb=" N   PRO A 180 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 2.34e-02 1.83e+03 7.76e-01
  bond pdb=" C   ILE C 179 "
       pdb=" N   PRO C 180 "
    ideal  model  delta    sigma   weight residual
    1.334  1.354 -0.021 2.34e-02 1.83e+03 7.68e-01
  bond pdb=" C   ILE B 179 "
       pdb=" N   PRO B 180 "
    ideal  model  delta    sigma   weight residual
    1.334  1.354 -0.020 2.34e-02 1.83e+03 7.67e-01
  bond pdb=" N   GLY B  36 "
       pdb=" CA  GLY B  36 "
    ideal  model  delta    sigma   weight residual
    1.445  1.451 -0.007 8.30e-03 1.45e+04 6.90e-01
  bond pdb=" N   GLY C  36 "
       pdb=" CA  GLY C  36 "
    ideal  model  delta    sigma   weight residual
    1.445  1.451 -0.007 8.30e-03 1.45e+04 6.54e-01
  ... (remaining 9313 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.97: 12435
        0.97 -     1.94: 159
        1.94 -     2.91: 45
        2.91 -     3.88: 6
        3.88 -     4.85: 9
  Bond angle restraints: 12654
  Sorted by residual:
  angle pdb=" CA  TYR B 468 "
        pdb=" CB  TYR B 468 "
        pdb=" CG  TYR B 468 "
      ideal   model   delta    sigma   weight residual
     113.90  118.53   -4.63 1.80e+00 3.09e-01 6.63e+00
  angle pdb=" CA  TYR C 468 "
        pdb=" CB  TYR C 468 "
        pdb=" CG  TYR C 468 "
      ideal   model   delta    sigma   weight residual
     113.90  118.52   -4.62 1.80e+00 3.09e-01 6.59e+00
  angle pdb=" CA  TYR A 468 "
        pdb=" CB  TYR A 468 "
        pdb=" CG  TYR A 468 "
      ideal   model   delta    sigma   weight residual
     113.90  118.48   -4.58 1.80e+00 3.09e-01 6.48e+00
  angle pdb=" C   PRO C  84 "
        pdb=" N   VAL C  85 "
        pdb=" CA  VAL C  85 "
      ideal   model   delta    sigma   weight residual
     121.97  126.32   -4.35 1.80e+00 3.09e-01 5.84e+00
  angle pdb=" C   PRO A  84 "
        pdb=" N   VAL A  85 "
        pdb=" CA  VAL A  85 "
      ideal   model   delta    sigma   weight residual
     121.97  126.30   -4.33 1.80e+00 3.09e-01 5.79e+00
  ... (remaining 12649 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 5124
       17.77 -    35.54: 429
       35.54 -    53.31: 165
       53.31 -    71.08: 15
       71.08 -    88.85: 6
  Dihedral angle restraints: 5739
    sinusoidal: 2271
      harmonic: 3468
  Sorted by residual:
  dihedral pdb=" CB  CYS B 326 "
           pdb=" SG  CYS B 326 "
           pdb=" SG  CYS B 335 "
           pdb=" CB  CYS B 335 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  123.72  -30.72     1      1.00e+01 1.00e-02 1.35e+01
  dihedral pdb=" CB  CYS C 326 "
           pdb=" SG  CYS C 326 "
           pdb=" SG  CYS C 335 "
           pdb=" CB  CYS C 335 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  123.70  -30.70     1      1.00e+01 1.00e-02 1.35e+01
  dihedral pdb=" CB  CYS A 326 "
           pdb=" SG  CYS A 326 "
           pdb=" SG  CYS A 335 "
           pdb=" CB  CYS A 335 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  123.67  -30.67     1      1.00e+01 1.00e-02 1.34e+01
  ... (remaining 5736 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 968
       0.024 -    0.048: 307
       0.048 -    0.072: 123
       0.072 -    0.096: 66
       0.096 -    0.120: 78
  Chirality restraints: 1542
  Sorted by residual:
  chirality pdb=" CA  ILE C  57 "
            pdb=" N   ILE C  57 "
            pdb=" C   ILE C  57 "
            pdb=" CB  ILE C  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.62e-01
  chirality pdb=" CA  ILE B  57 "
            pdb=" N   ILE B  57 "
            pdb=" C   ILE B  57 "
            pdb=" CB  ILE B  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.57e-01
  chirality pdb=" CA  ILE C 321 "
            pdb=" N   ILE C 321 "
            pdb=" C   ILE C 321 "
            pdb=" CB  ILE C 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.51e-01
  ... (remaining 1539 not shown)

  Planarity restraints: 1617
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 468 "   -0.007 2.00e-02 2.50e+03   6.63e-03 8.78e-01
        pdb=" CG  TYR C 468 "    0.016 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 468 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 468 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 468 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 468 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 468 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 468 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 468 "   -0.007 2.00e-02 2.50e+03   6.61e-03 8.73e-01
        pdb=" CG  TYR A 468 "    0.016 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 468 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 468 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 468 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 468 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 468 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 468 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 468 "   -0.007 2.00e-02 2.50e+03   6.50e-03 8.46e-01
        pdb=" CG  TYR B 468 "    0.016 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 468 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 468 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 468 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 468 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 468 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 468 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1614 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 433
        2.73 -     3.27: 9487
        3.27 -     3.82: 14639
        3.82 -     4.36: 16541
        4.36 -     4.90: 26898
  Nonbonded interactions: 67998
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG B 388 "
            pdb=" O   THR B 392 "
     model   vdw
     2.191 3.120
  nonbonded pdb=" NH1 ARG C 388 "
            pdb=" O   THR C 392 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" NH1 ARG A 388 "
            pdb=" O   THR A 392 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" O   SER B 186 "
            pdb=" OG1 THR B 189 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   SER A 186 "
            pdb=" OG1 THR A 189 "
     model   vdw
     2.206 3.040
  ... (remaining 67993 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
Set refine NCS operators
  NCS operators will be refined.
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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.360
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.740
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.000
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3825
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      :  0.001   0.021   9333  Z= 0.072
  Angle     :  0.349   4.845  12684  Z= 0.194
  Chirality :  0.039   0.120   1542
  Planarity :  0.002   0.020   1617
  Dihedral  : 14.882  88.852   3462
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 17.28 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.24 (0.24), residues: 1173
  helix:  1.32 (0.24), residues: 414
  sheet: -0.98 (0.54), residues: 87
  loop : -1.02 (0.24), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 220 
 TYR   0.016   0.001   TYR C 468 
 PHE   0.002   0.000   PHE A 230 
 TRP   0.000   0.000   TRP A 303 
 HIS   0.000   0.000   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00127 ( 9318)
  covalent geometry    : angle       0.34932 (12654)
  SS BOND              : bond        0.00048 (   15)
  SS BOND              : angle       0.10459 (   30)
  hydrogen bonds       : bond        0.20319 (  381)
  hydrogen bonds       : angle       8.04656 ( 1071)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A  168 ASP cc_start: 0.8283 (t0) cc_final: 0.8004 (m-30)
REVERT: A  273 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.4952 (pt)
  outliers start: 7
  outliers final: 1
  residues processed: 30
  average time/residue: 0.0539
  time to fit residues: 2.1428
Evaluate side-chains
  14 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 12
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    0.6580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 218 ASN
A 260 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.088136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.083368 restraints weight = 24785.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.083163 restraints weight = 20716.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.083762 restraints weight = 15863.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.084250 restraints weight = 12725.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.084640 restraints weight = 10269.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4389
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9333  Z= 0.126
  Angle     :  0.592   6.826  12684  Z= 0.306
  Chirality :  0.043   0.180   1542
  Planarity :  0.003   0.018   1617
  Dihedral  :  3.637  14.996   1269
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  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 aren not related in a simple way.
  whole:  0.22 (0.25), residues: 1173
  helix:  1.96 (0.24), residues: 444
  sheet: -0.98 (0.52), residues: 87
  loop : -1.04 (0.25), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 325 
 TYR   0.007   0.001   TYR A 270 
 PHE   0.013   0.002   PHE B 230 
 TRP   0.003   0.001   TRP B 303 
 HIS   0.002   0.001   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 9318)
  covalent geometry    : angle       0.58860 (12654)
  SS BOND              : bond        0.00381 (   15)
  SS BOND              : angle       1.38982 (   30)
  hydrogen bonds       : bond        0.04150 (  381)
  hydrogen bonds       : angle       5.45593 ( 1071)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  142 MET cc_start: 0.1857 (mmp) cc_final: 0.1186 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.0421
  time to fit residues: 1.0490
Evaluate side-chains
  10 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 105 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 102 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 77 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 113 optimal weight:    0.5980
   overall best weight:    0.6780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.087579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.083143 restraints weight = 24621.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.083277 restraints weight = 22785.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.083587 restraints weight = 18629.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.083587 restraints weight = 15743.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.083587 restraints weight = 15742.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4538
moved from start:          0.3415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9333  Z= 0.104
  Angle     :  0.515   7.215  12684  Z= 0.269
  Chirality :  0.042   0.135   1542
  Planarity :  0.002   0.015   1617
  Dihedral  :  3.577  16.899   1269
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  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 aren not related in a simple way.
  whole:  0.18 (0.25), residues: 1173
  helix:  1.90 (0.23), residues: 459
  sheet: -1.25 (0.48), residues: 99
  loop : -1.06 (0.26), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  64 
 TYR   0.012   0.001   TYR C 468 
 PHE   0.012   0.001   PHE C 230 
 TRP   0.003   0.001   TRP B 303 
 HIS   0.003   0.002   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 9318)
  covalent geometry    : angle       0.51110 (12654)
  SS BOND              : bond        0.00282 (   15)
  SS BOND              : angle       1.37294 (   30)
  hydrogen bonds       : bond        0.03277 (  381)
  hydrogen bonds       : angle       4.86297 ( 1071)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.128 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0443
  time to fit residues: 0.8761
Evaluate side-chains
  9 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 9
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 43 optimal weight:    0.0000
   chunk 11 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 92 optimal weight:    0.2980
   chunk 96 optimal weight:    5.9990
   chunk 100 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 84 optimal weight:    7.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    1.2590
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C 218 ASN
C 384 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.081142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.076805 restraints weight = 24889.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.076730 restraints weight = 23480.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.076641 restraints weight = 24129.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.076727 restraints weight = 16070.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.076059 restraints weight = 19083.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5094
moved from start:          0.4697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9333  Z= 0.127
  Angle     :  0.550   9.209  12684  Z= 0.293
  Chirality :  0.043   0.156   1542
  Planarity :  0.002   0.017   1617
  Dihedral  :  3.897  17.155   1269
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  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 aren not related in a simple way.
  whole:  0.33 (0.25), residues: 1173
  helix:  2.08 (0.23), residues: 465
  sheet: -1.23 (0.48), residues: 99
  loop : -1.05 (0.26), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 314 
 TYR   0.009   0.001   TYR B 468 
 PHE   0.008   0.001   PHE A 230 
 TRP   0.006   0.001   TRP A 303 
 HIS   0.003   0.002   HIS A 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9318)
  covalent geometry    : angle       0.54755 (12654)
  SS BOND              : bond        0.00687 (   15)
  SS BOND              : angle       1.28151 (   30)
  hydrogen bonds       : bond        0.02905 (  381)
  hydrogen bonds       : angle       4.48889 ( 1071)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.137 
Fit side-chains
REVERT: C   92 MET cc_start: 0.6611 (mpp) cc_final: 0.6247 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0437
  time to fit residues: 0.8109
Evaluate side-chains
  9 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 9
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 82 optimal weight:    0.1980
   chunk 78 optimal weight:    8.9990
   chunk 54 optimal weight:    7.9990
   chunk 84 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 37 optimal weight:    0.0010
   chunk 26 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 52 optimal weight:    0.2980
   chunk 74 optimal weight:    0.4980
   chunk 64 optimal weight:    0.1980
   overall best weight:    0.2386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.081411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.078110 restraints weight = 24896.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.078409 restraints weight = 24207.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.078514 restraints weight = 15747.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.078819 restraints weight = 13431.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.078863 restraints weight = 11342.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4502
moved from start:          0.4671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   9333  Z= 0.089
  Angle     :  0.496   4.614  12684  Z= 0.257
  Chirality :  0.042   0.130   1542
  Planarity :  0.002   0.018   1617
  Dihedral  :  3.488  12.170   1269
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  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 aren not related in a simple way.
  whole:  0.19 (0.25), residues: 1173
  helix:  2.02 (0.24), residues: 429
  sheet: -1.10 (0.49), residues: 99
  loop : -1.03 (0.25), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 388 
 TYR   0.014   0.001   TYR C 468 
 PHE   0.009   0.001   PHE A 475 
 TRP   0.002   0.000   TRP B 303 
 HIS   0.001   0.001   HIS A 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00176 ( 9318)
  covalent geometry    : angle       0.49501 (12654)
  SS BOND              : bond        0.00334 (   15)
  SS BOND              : angle       0.89026 (   30)
  hydrogen bonds       : bond        0.02922 (  381)
  hydrogen bonds       : angle       4.34454 ( 1071)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.099 
Fit side-chains
REVERT: B  471 LYS cc_start: 0.6506 (tptp) cc_final: 0.6143 (mtmt)
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0580
  time to fit residues: 1.1488
Evaluate side-chains
  12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 36 optimal weight:    6.9990
   chunk 82 optimal weight:    5.9990
   chunk 40 optimal weight:    0.1980
   chunk 79 optimal weight:    0.1980
   chunk 2 optimal weight:    0.0030
   chunk 93 optimal weight:    8.9990
   chunk 84 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.6392
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.084158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.079942 restraints weight = 24805.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.079240 restraints weight = 24014.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.079233 restraints weight = 26284.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.079230 restraints weight = 25970.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.078937 restraints weight = 21859.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4902
moved from start:          0.4942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9333  Z= 0.088
  Angle     :  0.492   5.129  12684  Z= 0.255
  Chirality :  0.042   0.139   1542
  Planarity :  0.002   0.018   1617
  Dihedral  :  3.613  14.792   1269
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.88 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  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 aren not related in a simple way.
  whole: -0.35 (0.24), residues: 1173
  helix:  1.50 (0.23), residues: 444
  sheet: -1.14 (0.52), residues: 84
  loop : -1.41 (0.25), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 309 
 TYR   0.007   0.001   TYR A 270 
 PHE   0.009   0.001   PHE C 230 
 TRP   0.003   0.001   TRP A 303 
 HIS   0.000   0.000   HIS A 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00183 ( 9318)
  covalent geometry    : angle       0.49020 (12654)
  SS BOND              : bond        0.00107 (   15)
  SS BOND              : angle       0.88346 (   30)
  hydrogen bonds       : bond        0.02573 (  381)
  hydrogen bonds       : angle       4.32678 ( 1071)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  471 LYS cc_start: 0.6560 (tptp) cc_final: 0.5829 (mtmt)
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0549
  time to fit residues: 1.2038
Evaluate side-chains
  11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 116 optimal weight:    0.2980
   chunk 85 optimal weight:    0.3980
   chunk 26 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 95 optimal weight:    8.9990
   chunk 90 optimal weight:    0.9980
   chunk 7 optimal weight:    0.3980
   overall best weight:    0.6180
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.084769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.081238 restraints weight = 24592.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.080388 restraints weight = 26453.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.080479 restraints weight = 20534.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.080697 restraints weight = 18311.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.080904 restraints weight = 14918.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4663
moved from start:          0.5170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9333  Z= 0.084
  Angle     :  0.479   4.674  12684  Z= 0.248
  Chirality :  0.042   0.127   1542
  Planarity :  0.002   0.019   1617
  Dihedral  :  3.529  16.802   1269
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  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 aren not related in a simple way.
  whole: -0.53 (0.24), residues: 1173
  helix:  1.38 (0.24), residues: 429
  sheet: -1.32 (0.51), residues: 84
  loop : -1.45 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 388 
 TYR   0.007   0.001   TYR A 270 
 PHE   0.008   0.001   PHE B 230 
 TRP   0.002   0.000   TRP B 303 
 HIS   0.000   0.000   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00173 ( 9318)
  covalent geometry    : angle       0.47690 (12654)
  SS BOND              : bond        0.00084 (   15)
  SS BOND              : angle       1.11578 (   30)
  hydrogen bonds       : bond        0.02392 (  381)
  hydrogen bonds       : angle       4.19538 ( 1071)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.135 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0612
  time to fit residues: 1.2950
Evaluate side-chains
  10 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 103 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   chunk 67 optimal weight:    6.9990
   chunk 104 optimal weight:    7.9990
   chunk 82 optimal weight:    0.0970
   chunk 114 optimal weight:    7.9990
   chunk 69 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0970
   chunk 60 optimal weight:    0.3980
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.5178
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.084480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.080819 restraints weight = 25317.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.080432 restraints weight = 26162.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.080384 restraints weight = 18175.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.080719 restraints weight = 16905.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.080817 restraints weight = 13795.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4659
moved from start:          0.5313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9333  Z= 0.084
  Angle     :  0.506   7.052  12684  Z= 0.255
  Chirality :  0.042   0.127   1542
  Planarity :  0.002   0.019   1617
  Dihedral  :  3.466  15.397   1269
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  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 aren not related in a simple way.
  whole: -0.67 (0.24), residues: 1173
  helix:  1.37 (0.24), residues: 429
  sheet: -1.44 (0.51), residues: 84
  loop : -1.63 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 309 
 TYR   0.010   0.001   TYR C 468 
 PHE   0.008   0.001   PHE B 230 
 TRP   0.002   0.000   TRP B 303 
 HIS   0.000   0.000   HIS A 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00178 ( 9318)
  covalent geometry    : angle       0.50167 (12654)
  SS BOND              : bond        0.00236 (   15)
  SS BOND              : angle       1.38955 (   30)
  hydrogen bonds       : bond        0.02420 (  381)
  hydrogen bonds       : angle       4.02502 ( 1071)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A  390 MET cc_start: 0.7672 (ppp) cc_final: 0.7175 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0632
  time to fit residues: 1.4005
Evaluate side-chains
  11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 1 optimal weight:    5.9990
   chunk 85 optimal weight:    0.5980
   chunk 111 optimal weight:    0.0000
   chunk 80 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0970
   chunk 63 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   chunk 20 optimal weight:    0.7980
   chunk 59 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.4582
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.085122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.080243 restraints weight = 25313.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.080187 restraints weight = 26282.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.080443 restraints weight = 23349.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.080656 restraints weight = 19283.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.080794 restraints weight = 18695.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4702
moved from start:          0.5545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9333  Z= 0.080
  Angle     :  0.485   4.747  12684  Z= 0.244
  Chirality :  0.042   0.132   1542
  Planarity :  0.002   0.019   1617
  Dihedral  :  3.330  14.783   1269
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  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 aren not related in a simple way.
  whole: -0.69 (0.24), residues: 1173
  helix:  1.16 (0.24), residues: 447
  sheet: -1.27 (0.54), residues: 84
  loop : -1.58 (0.24), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 388 
 TYR   0.012   0.001   TYR A 468 
 PHE   0.016   0.001   PHE B 475 
 TRP   0.000   0.000   TRP B 303 
 HIS   0.000   0.000   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00168 ( 9318)
  covalent geometry    : angle       0.48106 (12654)
  SS BOND              : bond        0.00145 (   15)
  SS BOND              : angle       1.32391 (   30)
  hydrogen bonds       : bond        0.02375 (  381)
  hydrogen bonds       : angle       3.92806 ( 1071)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.118 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0563
  time to fit residues: 1.1419
Evaluate side-chains
  11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0770
   chunk 31 optimal weight:    0.0170
   chunk 109 optimal weight:    0.0170
   chunk 11 optimal weight:    0.8980
   chunk 75 optimal weight:    6.9990
   chunk 71 optimal weight:    0.7980
   chunk 107 optimal weight:    0.2980
   chunk 102 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    0.2414
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.084719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.079631 restraints weight = 25502.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 73)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.079165 restraints weight = 23032.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.079693 restraints weight = 17230.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.080295 restraints weight = 13701.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.080461 restraints weight = 11202.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4819
moved from start:          0.5572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   9333  Z= 0.079
  Angle     :  0.482   4.869  12684  Z= 0.241
  Chirality :  0.042   0.134   1542
  Planarity :  0.002   0.019   1617
  Dihedral  :  3.207  13.651   1269
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  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 aren not related in a simple way.
  whole: -0.78 (0.24), residues: 1173
  helix:  1.08 (0.23), residues: 447
  sheet: -1.23 (0.55), residues: 84
  loop : -1.65 (0.24), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 388 
 TYR   0.012   0.001   TYR B 468 
 PHE   0.014   0.001   PHE C 475 
 TRP   0.002   0.001   TRP B 303 
 HIS   0.000   0.000   HIS C 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00166 ( 9318)
  covalent geometry    : angle       0.48044 (12654)
  SS BOND              : bond        0.00061 (   15)
  SS BOND              : angle       0.88036 (   30)
  hydrogen bonds       : bond        0.02205 (  381)
  hydrogen bonds       : angle       3.79980 ( 1071)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.150 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0581
  time to fit residues: 1.1798
Evaluate side-chains
  12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 100 optimal weight:    0.0370
   chunk 76 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 79 optimal weight:    8.9990
   chunk 61 optimal weight:    0.0370
   chunk 26 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 113 optimal weight:    0.8980
   chunk 105 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.5336
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.083965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.078630 restraints weight = 25835.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.078634 restraints weight = 25170.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.078552 restraints weight = 25850.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.078637 restraints weight = 19728.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.078947 restraints weight = 15633.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4966
moved from start:          0.5768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9333  Z= 0.082
  Angle     :  0.496   4.799  12684  Z= 0.250
  Chirality :  0.042   0.146   1542
  Planarity :  0.002   0.019   1617
  Dihedral  :  3.258  13.766   1269
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  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 aren not related in a simple way.
  whole: -0.76 (0.24), residues: 1173
  helix:  1.14 (0.24), residues: 447
  sheet: -1.31 (0.53), residues: 84
  loop : -1.67 (0.24), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 388 
 TYR   0.012   0.001   TYR C 468 
 PHE   0.009   0.001   PHE A 230 
 TRP   0.001   0.000   TRP C 303 
 HIS   0.000   0.000   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00174 ( 9318)
  covalent geometry    : angle       0.49349 (12654)
  SS BOND              : bond        0.00139 (   15)
  SS BOND              : angle       1.15252 (   30)
  hydrogen bonds       : bond        0.02234 (  381)
  hydrogen bonds       : angle       3.90536 ( 1071)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1135.01 seconds
wall clock time: 20 minutes 32.27 seconds (1232.27 seconds total)