Starting phenix.real_space_refine
on Fri Aug 22 12:58:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cgh_16643/08_2025/8cgh_16643.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cgh_16643/08_2025/8cgh_16643.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cgh_16643/08_2025/8cgh_16643.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cgh_16643/08_2025/8cgh_16643.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cgh_16643/08_2025/8cgh_16643.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cgh_16643/08_2025/8cgh_16643.map"
  }
  resolution = 2.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      40      5.16       5
     C    1590      2.51       5
     N     530      2.21       5
     O     550      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2710
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "U"
      Number of atoms: 542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 542
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 2, 'TRANS': 77}
  Restraints were copied for chains:
    A, B, C, D
  Time building chain proxies: 0.52, per 1000 atoms: 0.19
  Number of scatterers: 2710
  At special positions: 0
  Unit cell: (72.24, 69.66, 45.58, 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      40     16.00
     O     550      8.00
     N     530      7.00
     C    1590      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.12
  Conformation dependent library (CDL) restraints added in 71.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  590

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 38.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 297 through 303
      removed outlier: 9.185A  pdb=" N   GLY A 298 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
      removed outlier: 10.464A  pdb=" N   ASN B 301 " --> pdb=" O   GLY A 298 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   GLY A 300 " --> pdb=" O   ASN B 301 " (cutoff:3.500A)
      removed outlier: 8.690A  pdb=" N   GLN B 303 " --> pdb=" O   GLY A 300 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   ASN A 302 " --> pdb=" O   GLN B 303 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   GLY B 298 " --> pdb=" O   ALA U 297 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   LEU U 299 " --> pdb=" O   GLY B 298 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   GLY B 300 " --> pdb=" O   LEU U 299 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   ASN U 301 " --> pdb=" O   GLY B 300 " (cutoff:3.500A)
      removed outlier: 9.186A  pdb=" N   GLY U 298 " --> pdb=" O   LEU C 299 " (cutoff:3.500A)
      removed outlier: 10.464A  pdb=" N   ASN C 301 " --> pdb=" O   GLY U 298 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   GLY U 300 " --> pdb=" O   ASN C 301 " (cutoff:3.500A)
      removed outlier: 8.690A  pdb=" N   GLN C 303 " --> pdb=" O   GLY U 300 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   ASN U 302 " --> pdb=" O   GLN C 303 " (cutoff:3.500A)
      removed outlier: 9.186A  pdb=" N   GLY C 298 " --> pdb=" O   LEU D 299 " (cutoff:3.500A)
      removed outlier: 10.464A  pdb=" N   ASN D 301 " --> pdb=" O   GLY C 298 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   GLY C 300 " --> pdb=" O   ASN D 301 " (cutoff:3.500A)
      removed outlier: 8.690A  pdb=" N   GLN D 303 " --> pdb=" O   GLY C 300 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   ASN C 302 " --> pdb=" O   GLN D 303 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 308
      removed outlier: 6.660A  pdb=" N   ASN U 306 " --> pdb=" O   MET B 307 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 311 through 318
      removed outlier: 6.698A  pdb=" N   MET A 311 " --> pdb=" O   ASN B 312 " (cutoff:3.500A)
      removed outlier: 8.478A  pdb=" N   GLY B 314 " --> pdb=" O   MET A 311 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   PHE A 313 " --> pdb=" O   GLY B 314 " (cutoff:3.500A)
      removed outlier: 8.248A  pdb=" N   PHE B 316 " --> pdb=" O   PHE A 313 " (cutoff:3.500A)
      removed outlier: 8.629A  pdb=" N   ALA A 315 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   ILE B 318 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
      removed outlier: 9.233A  pdb=" N   SER A 317 " --> pdb=" O   ILE B 318 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   SER B 317 " --> pdb=" O   PHE U 316 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   ILE U 318 " --> pdb=" O   SER B 317 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   MET U 311 " --> pdb=" O   ASN C 312 " (cutoff:3.500A)
      removed outlier: 8.478A  pdb=" N   GLY C 314 " --> pdb=" O   MET U 311 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   PHE U 313 " --> pdb=" O   GLY C 314 " (cutoff:3.500A)
      removed outlier: 8.249A  pdb=" N   PHE C 316 " --> pdb=" O   PHE U 313 " (cutoff:3.500A)
      removed outlier: 8.629A  pdb=" N   ALA U 315 " --> pdb=" O   PHE C 316 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   ILE C 318 " --> pdb=" O   ALA U 315 " (cutoff:3.500A)
      removed outlier: 9.233A  pdb=" N   SER U 317 " --> pdb=" O   ILE C 318 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   MET C 311 " --> pdb=" O   ASN D 312 " (cutoff:3.500A)
      removed outlier: 8.478A  pdb=" N   GLY D 314 " --> pdb=" O   MET C 311 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   PHE C 313 " --> pdb=" O   GLY D 314 " (cutoff:3.500A)
      removed outlier: 8.248A  pdb=" N   PHE D 316 " --> pdb=" O   PHE C 313 " (cutoff:3.500A)
      removed outlier: 8.630A  pdb=" N   ALA C 315 " --> pdb=" O   PHE D 316 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   ILE D 318 " --> pdb=" O   ALA C 315 " (cutoff:3.500A)
      removed outlier: 9.233A  pdb=" N   SER C 317 " --> pdb=" O   ILE D 318 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 327
      removed outlier: 6.762A  pdb=" N   ALA A 321 " --> pdb=" O   MET B 322 " (cutoff:3.500A)
      removed outlier: 8.502A  pdb=" N   ALA B 324 " --> pdb=" O   ALA A 321 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   MET A 323 " --> pdb=" O   ALA B 324 " (cutoff:3.500A)
      removed outlier: 8.395A  pdb=" N   ALA B 326 " --> pdb=" O   MET A 323 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ALA A 325 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ALA U 321 " --> pdb=" O   MET C 322 " (cutoff:3.500A)
      removed outlier: 8.502A  pdb=" N   ALA C 324 " --> pdb=" O   ALA U 321 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   MET U 323 " --> pdb=" O   ALA C 324 " (cutoff:3.500A)
      removed outlier: 8.394A  pdb=" N   ALA C 326 " --> pdb=" O   MET U 323 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ALA U 325 " --> pdb=" O   ALA C 326 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ALA C 321 " --> pdb=" O   MET D 322 " (cutoff:3.500A)
      removed outlier: 8.503A  pdb=" N   ALA D 324 " --> pdb=" O   ALA C 321 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   MET C 323 " --> pdb=" O   ALA D 324 " (cutoff:3.500A)
      removed outlier: 8.395A  pdb=" N   ALA D 326 " --> pdb=" O   MET C 323 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   ALA C 325 " --> pdb=" O   ALA D 326 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 330 through 331
      removed outlier: 6.634A  pdb=" N   LEU U 330 " --> pdb=" O   GLN B 331 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 334 through 336
      removed outlier: 7.059A  pdb=" N   MET B 336 " --> pdb=" O   GLY A 335 " (cutoff:3.500A)
      removed outlier: 8.151A  pdb=" N   TRP U 334 " --> pdb=" O   GLY B 335 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   MET C 336 " --> pdb=" O   GLY U 335 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   MET D 336 " --> pdb=" O   GLY C 335 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 342 through 347
      removed outlier: 7.086A  pdb=" N   GLN B 343 " --> pdb=" O   SER A 342 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   GLN A 344 " --> pdb=" O   GLN B 343 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   GLN U 343 " --> pdb=" O   GLN B 344 " (cutoff:3.500A)
      removed outlier: 9.300A  pdb=" N   GLN B 346 " --> pdb=" O   GLN U 343 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ASN U 345 " --> pdb=" O   GLN B 346 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   GLN C 343 " --> pdb=" O   SER U 342 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   GLN U 344 " --> pdb=" O   GLN C 343 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   GLN D 343 " --> pdb=" O   SER C 342 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   GLN C 344 " --> pdb=" O   GLN D 343 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 353 through 355
      removed outlier: 6.839A  pdb=" N   ASN U 353 " --> pdb=" O   GLN B 354 " (cutoff:3.500A)

    40 hydrogen bonds defined for protein.
    120 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: 0.32

  Time building geometry restraints manager: 0.18 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1001
        1.35 -     1.48: 649
        1.48 -     1.61: 1015
        1.61 -     1.74: 0
        1.74 -     1.87: 80
  Bond restraints: 2745
  Sorted by residual:
  bond pdb=" CG  MET C 359 "
       pdb=" SD  MET C 359 "
    ideal  model  delta    sigma   weight residual
    1.803  1.866 -0.063 2.50e-02 1.60e+03 6.35e+00
  bond pdb=" CG  MET A 359 "
       pdb=" SD  MET A 359 "
    ideal  model  delta    sigma   weight residual
    1.803  1.866 -0.063 2.50e-02 1.60e+03 6.26e+00
  bond pdb=" CG  MET D 359 "
       pdb=" SD  MET D 359 "
    ideal  model  delta    sigma   weight residual
    1.803  1.866 -0.063 2.50e-02 1.60e+03 6.26e+00
  bond pdb=" CG  MET B 359 "
       pdb=" SD  MET B 359 "
    ideal  model  delta    sigma   weight residual
    1.803  1.865 -0.062 2.50e-02 1.60e+03 6.25e+00
  bond pdb=" CG  MET U 359 "
       pdb=" SD  MET U 359 "
    ideal  model  delta    sigma   weight residual
    1.803  1.865 -0.062 2.50e-02 1.60e+03 6.22e+00
  ... (remaining 2740 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 2325
        1.30 -     2.61: 1022
        2.61 -     3.91: 233
        3.91 -     5.21: 41
        5.21 -     6.52: 29
  Bond angle restraints: 3650
  Sorted by residual:
  angle pdb=" N   SER D 333 "
        pdb=" CA  SER D 333 "
        pdb=" C   SER D 333 "
      ideal   model   delta    sigma   weight residual
     108.52  114.81   -6.29 1.52e+00 4.33e-01 1.71e+01
  angle pdb=" N   SER U 333 "
        pdb=" CA  SER U 333 "
        pdb=" C   SER U 333 "
      ideal   model   delta    sigma   weight residual
     108.52  114.79   -6.27 1.52e+00 4.33e-01 1.70e+01
  angle pdb=" N   SER A 333 "
        pdb=" CA  SER A 333 "
        pdb=" C   SER A 333 "
      ideal   model   delta    sigma   weight residual
     108.52  114.78   -6.26 1.52e+00 4.33e-01 1.70e+01
  angle pdb=" N   SER B 333 "
        pdb=" CA  SER B 333 "
        pdb=" C   SER B 333 "
      ideal   model   delta    sigma   weight residual
     108.52  114.78   -6.26 1.52e+00 4.33e-01 1.70e+01
  angle pdb=" N   SER C 333 "
        pdb=" CA  SER C 333 "
        pdb=" C   SER C 333 "
      ideal   model   delta    sigma   weight residual
     108.52  114.77   -6.25 1.52e+00 4.33e-01 1.69e+01
  ... (remaining 3645 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.23: 1325
       14.23 -    28.47: 155
       28.47 -    42.70: 45
       42.70 -    56.93: 15
       56.93 -    71.16: 20
  Dihedral angle restraints: 1560
    sinusoidal: 575
      harmonic: 985
  Sorted by residual:
  dihedral pdb=" CA  GLN C 327 "
           pdb=" C   GLN C 327 "
           pdb=" N   ALA C 328 "
           pdb=" CA  ALA C 328 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.02  -23.98     0      5.00e+00 4.00e-02 2.30e+01
  dihedral pdb=" CA  GLN B 327 "
           pdb=" C   GLN B 327 "
           pdb=" N   ALA B 328 "
           pdb=" CA  ALA B 328 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.08  -23.92     0      5.00e+00 4.00e-02 2.29e+01
  dihedral pdb=" CA  GLN U 327 "
           pdb=" C   GLN U 327 "
           pdb=" N   ALA U 328 "
           pdb=" CA  ALA U 328 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.09  -23.91     0      5.00e+00 4.00e-02 2.29e+01
  ... (remaining 1557 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.042: 88
       0.042 -    0.083: 116
       0.083 -    0.124: 91
       0.124 -    0.165: 5
       0.165 -    0.206: 15
  Chirality restraints: 315
  Sorted by residual:
  chirality pdb=" CA  LEU D 299 "
            pdb=" N   LEU D 299 "
            pdb=" C   LEU D 299 "
            pdb=" CB  LEU D 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  LEU C 299 "
            pdb=" N   LEU C 299 "
            pdb=" C   LEU C 299 "
            pdb=" CB  LEU C 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  LEU B 299 "
            pdb=" N   LEU B 299 "
            pdb=" C   LEU B 299 "
            pdb=" CB  LEU B 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 312 not shown)

  Planarity restraints: 545
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 334 "   -0.024 2.00e-02 2.50e+03   1.66e-02 6.92e+00
        pdb=" CG  TRP D 334 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 334 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 334 "    0.013 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 334 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 334 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 334 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 334 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 334 "   -0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 334 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 334 "   -0.024 2.00e-02 2.50e+03   1.66e-02 6.89e+00
        pdb=" CG  TRP C 334 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 334 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 334 "    0.013 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 334 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 334 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 334 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 334 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 334 "   -0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 334 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 334 "   -0.024 2.00e-02 2.50e+03   1.66e-02 6.88e+00
        pdb=" CG  TRP B 334 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 334 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 334 "    0.013 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 334 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 334 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 334 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 334 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 334 "   -0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 334 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 542 not shown)

  Histogram of nonbonded interaction distances:
        2.63 -     3.08: 1695
        3.08 -     3.54: 2462
        3.54 -     3.99: 3975
        3.99 -     4.45: 4792
        4.45 -     4.90: 7592
  Nonbonded interactions: 20516
  Sorted by model distance:
  nonbonded pdb=" N   MET B 337 "
            pdb=" O   MET B 337 "
     model   vdw
     2.629 2.496
  nonbonded pdb=" N   MET U 337 "
            pdb=" O   MET U 337 "
     model   vdw
     2.629 2.496
  nonbonded pdb=" N   MET C 337 "
            pdb=" O   MET C 337 "
     model   vdw
     2.629 2.496
  nonbonded pdb=" N   MET A 337 "
            pdb=" O   MET A 337 "
     model   vdw
     2.629 2.496
  nonbonded pdb=" N   MET D 337 "
            pdb=" O   MET D 337 "
     model   vdw
     2.630 2.496
  ... (remaining 20511 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 'U'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             1.050
  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:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.840
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9106
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      :  0.011   0.063   2745  Z= 0.686
  Angle     :  1.540   6.517   3650  Z= 1.009
  Chirality :  0.082   0.206    315
  Planarity :  0.007   0.035    545
  Dihedral  : 16.669  71.159    970
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  2.56 %
    Allowed  :  5.13 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  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: -5.57 (0.17), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.24 (0.13), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG C 293 
 PHE   0.014   0.005   PHE A 289 
 TRP   0.041   0.012   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.01060 ( 2745)
  covalent geometry    : angle       1.54000 ( 3650)
  hydrogen bonds       : bond        0.30618 (   40)
  hydrogen bonds       : angle       7.13025 (  120)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.087 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8612 (mtp) cc_final: 0.8269 (mtt)
REVERT: D  359 MET cc_start: 0.9168 (ttm) cc_final: 0.8910 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.4591
  time to fit residues: 26.4288
Evaluate side-chains
  51 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:    0.4980
   chunk 31 optimal weight:   20.0000
   chunk 25 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    3.8988

-------------------------------------------------------------------------------
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 = 0.3464 r_free = 0.3464 target = 0.104454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.083105 restraints weight = 2893.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 2.00
r_work: 0.3023 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9012
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2745  Z= 0.196
  Angle     :  0.858   6.068   3650  Z= 0.456
  Chirality :  0.047   0.153    315
  Planarity :  0.003   0.014    545
  Dihedral  :  5.921  18.202    400
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 0.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  8.00 %
    Favored  : 91.20 %
  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: -5.15 (0.18), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.92 (0.14), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG U 293 
 PHE   0.009   0.002   PHE D 289 
 TRP   0.019   0.004   TRP U 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 2745)
  covalent geometry    : angle       0.85800 ( 3650)
  hydrogen bonds       : bond        0.05514 (   40)
  hydrogen bonds       : angle       4.84069 (  120)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.109 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8520 (mtp) cc_final: 0.8159 (mtt)
  outliers start: 2
  outliers final: 0
  residues processed: 46
  average time/residue: 0.6422
  time to fit residues: 30.2242
Evaluate side-chains
  46 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 2 optimal weight:    4.9990
   chunk 1 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 17 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.102997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.081218 restraints weight = 2924.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 2.02
r_work: 0.2990 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9012
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2745  Z= 0.187
  Angle     :  0.830   7.524   3650  Z= 0.441
  Chirality :  0.045   0.139    315
  Planarity :  0.003   0.019    545
  Dihedral  :  5.588  18.022    400
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 0.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  8.40 %
    Favored  : 90.80 %
  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: -5.04 (0.18), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.84 (0.14), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG U 293 
 PHE   0.017   0.002   PHE C 283 
 TRP   0.016   0.003   TRP B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 2745)
  covalent geometry    : angle       0.83010 ( 3650)
  hydrogen bonds       : bond        0.05166 (   40)
  hydrogen bonds       : angle       4.78888 (  120)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 48
  time to evaluate  : 0.093 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8631 (mtp) cc_final: 0.8322 (mtt)
REVERT: D  311 MET cc_start: 0.9027 (ttt) cc_final: 0.8733 (ttt)
  outliers start: 2
  outliers final: 0
  residues processed: 48
  average time/residue: 0.5941
  time to fit residues: 29.1828
Evaluate side-chains
  47 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 2 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 16 optimal weight:   20.0000
   chunk 32 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.105920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.084278 restraints weight = 2907.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.02
r_work: 0.3040 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2936 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8963
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   2745  Z= 0.114
  Angle     :  0.679   7.356   3650  Z= 0.354
  Chirality :  0.041   0.117    315
  Planarity :  0.002   0.017    545
  Dihedral  :  5.030  15.344    400
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 0.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.40 %
    Favored  : 89.60 %
  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: -4.97 (0.18), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.78 (0.13), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 293 
 PHE   0.009   0.001   PHE B 289 
 TRP   0.011   0.002   TRP B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 2745)
  covalent geometry    : angle       0.67880 ( 3650)
  hydrogen bonds       : bond        0.03251 (   40)
  hydrogen bonds       : angle       4.52156 (  120)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.099 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8576 (mtp) cc_final: 0.8143 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.5971
  time to fit residues: 28.7209
Evaluate side-chains
  47 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 19 optimal weight:   20.0000
   chunk 12 optimal weight:    0.8980
   chunk 32 optimal weight:   10.0000
   chunk 3 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 16 optimal weight:   20.0000
   chunk 18 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   chunk 5 optimal weight:   20.0000
   chunk 0 optimal weight:    5.9990
   overall best weight:    6.9788

-------------------------------------------------------------------------------
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 = 0.3439 r_free = 0.3439 target = 0.102305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.081361 restraints weight = 2847.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 1.97
r_work: 0.3000 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9041
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032   2745  Z= 0.294
  Angle     :  0.971   9.328   3650  Z= 0.520
  Chirality :  0.047   0.146    315
  Planarity :  0.004   0.029    545
  Dihedral  :  5.875  19.605    400
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 0.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 12.00 %
    Favored  : 87.20 %
  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: -5.04 (0.18), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.84 (0.14), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG U 293 
 PHE   0.021   0.003   PHE C 283 
 TRP   0.017   0.004   TRP B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00619 ( 2745)
  covalent geometry    : angle       0.97057 ( 3650)
  hydrogen bonds       : bond        0.06471 (   40)
  hydrogen bonds       : angle       5.11871 (  120)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.103 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8635 (mtp) cc_final: 0.8234 (mtt)
  outliers start: 2
  outliers final: 1
  residues processed: 51
  average time/residue: 0.5644
  time to fit residues: 29.4628
Evaluate side-chains
  52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  340 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 22 optimal weight:   10.0000
   chunk 11 optimal weight:    0.5980
   chunk 37 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 17 optimal weight:   10.0000
   overall best weight:    2.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.105006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.083498 restraints weight = 2914.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 2.02
r_work: 0.3032 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8976
moved from start:          0.2195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2745  Z= 0.125
  Angle     :  0.705   7.791   3650  Z= 0.369
  Chirality :  0.041   0.120    315
  Planarity :  0.002   0.023    545
  Dihedral  :  5.136  16.245    400
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 0.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 13.20 %
    Favored  : 86.00 %
  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: -4.92 (0.18), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.74 (0.14), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG U 293 
 PHE   0.023   0.002   PHE C 283 
 TRP   0.011   0.002   TRP B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 2745)
  covalent geometry    : angle       0.70534 ( 3650)
  hydrogen bonds       : bond        0.03526 (   40)
  hydrogen bonds       : angle       4.65444 (  120)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.099 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8587 (mtp) cc_final: 0.8140 (mtt)
  outliers start: 2
  outliers final: 2
  residues processed: 49
  average time/residue: 0.5655
  time to fit residues: 28.3567
Evaluate side-chains
  50 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 48
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain D residue  340 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 5 optimal weight:   20.0000
   chunk 15 optimal weight:    8.9990
   chunk 10 optimal weight:    9.9990
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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 = 0.3462 r_free = 0.3462 target = 0.104150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.083578 restraints weight = 2971.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.00
r_work: 0.3025 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9020
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2745  Z= 0.209
  Angle     :  0.844   8.758   3650  Z= 0.450
  Chirality :  0.045   0.133    315
  Planarity :  0.003   0.027    545
  Dihedral  :  5.563  18.758    400
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 0.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 13.60 %
    Favored  : 85.60 %
  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: -4.92 (0.18), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.74 (0.14), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG U 293 
 PHE   0.013   0.002   PHE B 289 
 TRP   0.014   0.003   TRP B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 2745)
  covalent geometry    : angle       0.84443 ( 3650)
  hydrogen bonds       : bond        0.05219 (   40)
  hydrogen bonds       : angle       4.98229 (  120)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.105 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8599 (mtp) cc_final: 0.8192 (mtt)
  outliers start: 2
  outliers final: 2
  residues processed: 50
  average time/residue: 0.5710
  time to fit residues: 29.2308
Evaluate side-chains
  52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain D residue  340 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 26 optimal weight:   20.0000
   chunk 17 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 3 optimal weight:    9.9990
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.3472 r_free = 0.3472 target = 0.104769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.084109 restraints weight = 3006.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.02
r_work: 0.3034 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9013
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   2745  Z= 0.187
  Angle     :  0.816   8.776   3650  Z= 0.431
  Chirality :  0.044   0.130    315
  Planarity :  0.003   0.025    545
  Dihedral  :  5.453  17.836    400
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 0.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 14.00 %
    Favored  : 84.80 %
  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: -4.89 (0.18), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.72 (0.14), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG U 293 
 PHE   0.023   0.002   PHE C 283 
 TRP   0.013   0.003   TRP B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 2745)
  covalent geometry    : angle       0.81597 ( 3650)
  hydrogen bonds       : bond        0.04930 (   40)
  hydrogen bonds       : angle       4.88508 (  120)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.098 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8613 (mtp) cc_final: 0.8203 (mtt)
  outliers start: 3
  outliers final: 2
  residues processed: 51
  average time/residue: 0.5075
  time to fit residues: 26.5378
Evaluate side-chains
  53 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain D residue  340 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 13 optimal weight:    7.9990
   chunk 9 optimal weight:    0.8980
   chunk 27 optimal weight:    7.9990
   chunk 29 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   overall best weight:    4.5788

-------------------------------------------------------------------------------
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 = 0.3461 r_free = 0.3461 target = 0.104023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.083599 restraints weight = 3018.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.00
r_work: 0.3023 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9023
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2745  Z= 0.209
  Angle     :  0.857   9.066   3650  Z= 0.454
  Chirality :  0.045   0.135    315
  Planarity :  0.003   0.026    545
  Dihedral  :  5.569  18.534    400
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 0.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 14.80 %
    Favored  : 84.40 %
  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: -4.89 (0.18), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.72 (0.14), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG U 293 
 PHE   0.028   0.003   PHE D 283 
 TRP   0.014   0.003   TRP B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 2745)
  covalent geometry    : angle       0.85652 ( 3650)
  hydrogen bonds       : bond        0.05275 (   40)
  hydrogen bonds       : angle       4.98908 (  120)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.111 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8633 (mtp) cc_final: 0.8218 (mtt)
  outliers start: 2
  outliers final: 2
  residues processed: 51
  average time/residue: 0.4914
  time to fit residues: 25.6732
Evaluate side-chains
  53 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain D residue  340 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 17 optimal weight:    9.9990
   chunk 8 optimal weight:   20.0000
   chunk 19 optimal weight:    8.9990
   chunk 34 optimal weight:    8.9990
   chunk 7 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 15 optimal weight:    7.9990
   chunk 30 optimal weight:    8.9990
   overall best weight:    5.3988

-------------------------------------------------------------------------------
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 = 0.3436 r_free = 0.3436 target = 0.102729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.082330 restraints weight = 2926.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 1.98
r_work: 0.3007 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9030
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   2745  Z= 0.238
  Angle     :  0.905   9.396   3650  Z= 0.482
  Chirality :  0.046   0.142    315
  Planarity :  0.003   0.026    545
  Dihedral  :  5.689  18.991    400
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 0.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 15.20 %
    Favored  : 84.00 %
  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: -4.91 (0.18), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.74 (0.14), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG U 293 
 PHE   0.024   0.003   PHE C 283 
 TRP   0.015   0.003   TRP B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 2745)
  covalent geometry    : angle       0.90536 ( 3650)
  hydrogen bonds       : bond        0.05760 (   40)
  hydrogen bonds       : angle       5.06986 (  120)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.058 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8573 (mtp) cc_final: 0.8168 (mtt)
  outliers start: 2
  outliers final: 2
  residues processed: 51
  average time/residue: 0.5287
  time to fit residues: 27.6145
Evaluate side-chains
  53 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain D residue  340 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 17 optimal weight:    8.9990
   chunk 37 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 23 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    3.7788

-------------------------------------------------------------------------------
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 = 0.3473 r_free = 0.3473 target = 0.104610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.084154 restraints weight = 2982.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.00
r_work: 0.3040 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9013
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   2745  Z= 0.182
  Angle     :  0.814   8.919   3650  Z= 0.430
  Chirality :  0.044   0.128    315
  Planarity :  0.003   0.024    545
  Dihedral  :  5.448  17.733    400
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 0.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 15.20 %
    Favored  : 84.00 %
  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: -4.88 (0.18), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.72 (0.14), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG U 293 
 PHE   0.029   0.003   PHE A 283 
 TRP   0.013   0.003   TRP B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 2745)
  covalent geometry    : angle       0.81399 ( 3650)
  hydrogen bonds       : bond        0.04802 (   40)
  hydrogen bonds       : angle       4.88226 (  120)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1079.71 seconds
wall clock time: 19 minutes 2.59 seconds (1142.59 seconds total)