Starting phenix.real_space_refine
on Wed Mar  5 16:27:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cgh_16643/03_2025/8cgh_16643.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cgh_16643/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cgh_16643/03_2025/8cgh_16643.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cgh_16643/03_2025/8cgh_16643.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cgh_16643/03_2025/8cgh_16643.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cgh_16643/03_2025/8cgh_16643.cif"
  }
  resolution = 2.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 2710
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      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:
    C, B, U, D
  Time building chain proxies: 1.43, per 1000 atoms: 0.53
  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: 0.60
  Conformation dependent library (CDL) restraints added in 351.3 milliseconds
  

  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: 0.45
  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: 0.60

  Time building geometry restraints manager: 0.72 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'U'
  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:             0.770
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     10.760
  Find NCS groups from input model:        0.060
  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:10.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.650
-------------------------------------------------------------------------------
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= 0.719
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.041   0.012   TRP C 334 
 PHE   0.014   0.005   PHE A 289 
 ARG   0.000   0.000   ARG C 293 

*********************** 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  : 0.309 
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: 1.1205
  time to fit residues: 64.6787
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  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 16 optimal weight:    9.9990
   chunk 10 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 12 optimal weight:   20.0000
   chunk 19 optimal weight:    4.9990
   chunk 23 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   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 = 0.3454 r_free = 0.3454 target = 0.103872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.082606 restraints weight = 2856.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 1.98
r_work: 0.3011 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9022
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   2745  Z= 0.306
  Angle     :  0.898   6.322   3650  Z= 0.478
  Chirality :  0.048   0.159    315
  Planarity :  0.003   0.015    545
  Dihedral  :  6.037  18.668    400
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 0.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  7.60 %
    Favored  : 91.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.17 (0.18), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.93 (0.14), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.004   TRP A 334 
 PHE   0.009   0.002   PHE D 289 
 ARG   0.000   0.000   ARG U 293 

*********************** 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
  49 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.295 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8577 (mtp) cc_final: 0.8217 (mtt)
  outliers start: 2
  outliers final: 0
  residues processed: 47
  average time/residue: 1.2836
  time to fit residues: 61.8200
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  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 26 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 24 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   overall best weight:    4.9788

-------------------------------------------------------------------------------
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 = 0.3453 r_free = 0.3453 target = 0.103556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.082504 restraints weight = 2848.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 1.99
r_work: 0.3004 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9029
moved from start:          0.1793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   2745  Z= 0.323
  Angle     :  0.901   7.612   3650  Z= 0.480
  Chirality :  0.047   0.149    315
  Planarity :  0.003   0.023    545
  Dihedral  :  5.831  18.918    400
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 0.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  8.00 %
    Favored  : 91.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.08 (0.18), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.86 (0.14), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.004   TRP B 334 
 PHE   0.018   0.002   PHE C 283 
 ARG   0.000   0.000   ARG U 293 

*********************** 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: 1
    poor density    : 49
  time to evaluate  : 0.289 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8627 (mtp) cc_final: 0.8235 (mtt)
  outliers start: 1
  outliers final: 0
  residues processed: 49
  average time/residue: 1.2774
  time to fit residues: 64.1010
Evaluate side-chains
  48 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 39 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 10 optimal weight:    0.1980
   chunk 5 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 1 optimal weight:   20.0000
   overall best weight:    4.8388

-------------------------------------------------------------------------------
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 = 0.3457 r_free = 0.3457 target = 0.103706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.082933 restraints weight = 2866.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 1.97
r_work: 0.3022 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9027
moved from start:          0.1894

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= 0.311
  Angle     :  0.885   8.281   3650  Z= 0.469
  Chirality :  0.046   0.142    315
  Planarity :  0.003   0.026    545
  Dihedral  :  5.733  18.719    400
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 0.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 11.20 %
    Favored  : 88.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.06 (0.18), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.85 (0.14), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP B 334 
 PHE   0.012   0.002   PHE B 289 
 ARG   0.000   0.000   ARG D 293 

*********************** 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
  52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.284 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8608 (mtp) cc_final: 0.8357 (mtm)
  outliers start: 1
  outliers final: 0
  residues processed: 51
  average time/residue: 1.2305
  time to fit residues: 64.2603
Evaluate side-chains
  49 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 18 optimal weight:   20.0000
   chunk 19 optimal weight:    9.9990
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 37 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    5.3788

-------------------------------------------------------------------------------
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 = 0.3444 r_free = 0.3444 target = 0.103111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.082731 restraints weight = 2839.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 1.96
r_work: 0.3003 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9034
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   2745  Z= 0.341
  Angle     :  0.914   8.680   3650  Z= 0.485
  Chirality :  0.046   0.146    315
  Planarity :  0.003   0.028    545
  Dihedral  :  5.818  19.089    400
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 0.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 12.80 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.02 (0.18), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.82 (0.14), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.004   TRP B 334 
 PHE   0.022   0.003   PHE C 283 
 ARG   0.000   0.000   ARG A 293 

*********************** 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
  52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.296 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8591 (mtp) cc_final: 0.8341 (mtm)
  outliers start: 1
  outliers final: 1
  residues processed: 51
  average time/residue: 1.2525
  time to fit residues: 65.4506
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  : 0.311 
-------------------------------------------------------------------------------
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 27 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 1 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 16 optimal weight:   20.0000
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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 = 0.3482 r_free = 0.3482 target = 0.104918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.084309 restraints weight = 2994.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 2.01
r_work: 0.3046 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9007
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2745  Z= 0.235
  Angle     :  0.793   8.407   3650  Z= 0.418
  Chirality :  0.044   0.127    315
  Planarity :  0.003   0.025    545
  Dihedral  :  5.452  17.349    400
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 0.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.97 (0.18), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.78 (0.14), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP B 334 
 PHE   0.021   0.002   PHE C 283 
 ARG   0.000   0.000   ARG C 293 

*********************** 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
  52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.323 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8610 (mtp) cc_final: 0.8181 (mtt)
  outliers start: 2
  outliers final: 2
  residues processed: 50
  average time/residue: 1.2084
  time to fit residues: 61.9714
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  : 0.294 
-------------------------------------------------------------------------------
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 6 optimal weight:   10.0000
   chunk 24 optimal weight:   20.0000
   chunk 10 optimal weight:    9.9990
   chunk 36 optimal weight:    6.9990
   chunk 8 optimal weight:   20.0000
   chunk 9 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 17 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    7.9990

-------------------------------------------------------------------------------
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 = 0.3420 r_free = 0.3420 target = 0.101533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.081038 restraints weight = 2950.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 1.99
r_work: 0.2987 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9054
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.036   2745  Z= 0.478
  Angle     :  1.024   9.595   3650  Z= 0.549
  Chirality :  0.049   0.157    315
  Planarity :  0.004   0.031    545
  Dihedral  :  6.057  20.190    400
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 0.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 13.60 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.05 (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
 TRP   0.018   0.004   TRP B 334 
 PHE   0.022   0.003   PHE C 283 
 ARG   0.001   0.000   ARG A 293 

*********************** 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
  56 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.262 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8626 (mtp) cc_final: 0.8387 (mtm)
  outliers start: 4
  outliers final: 2
  residues processed: 52
  average time/residue: 1.1742
  time to fit residues: 62.6192
Evaluate side-chains
  54 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
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 33 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 22 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 1 optimal weight:   10.0000
   chunk 3 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    2.3188

-------------------------------------------------------------------------------
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 = 0.3491 r_free = 0.3491 target = 0.105879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.085408 restraints weight = 2966.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 2.01
r_work: 0.3061 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8990
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2745  Z= 0.186
  Angle     :  0.737   8.233   3650  Z= 0.386
  Chirality :  0.042   0.121    315
  Planarity :  0.003   0.026    545
  Dihedral  :  5.278  16.517    400
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 0.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.012   0.002   TRP D 334 
 PHE   0.024   0.002   PHE C 283 
 ARG   0.001   0.000   ARG U 293 

*********************** 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
  53 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.374 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8590 (mtp) cc_final: 0.8180 (mtt)
  outliers start: 2
  outliers final: 1
  residues processed: 51
  average time/residue: 1.1745
  time to fit residues: 61.4569
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  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 15 optimal weight:    8.9990
   chunk 11 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 32 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 20 optimal weight:    7.9990
   chunk 34 optimal weight:    9.9990
   chunk 37 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    5.1988

-------------------------------------------------------------------------------
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 = 0.3438 r_free = 0.3438 target = 0.102654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.082346 restraints weight = 2854.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 1.96
r_work: 0.3016 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9030
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   2745  Z= 0.329
  Angle     :  0.889   9.147   3650  Z= 0.472
  Chirality :  0.045   0.139    315
  Planarity :  0.003   0.029    545
  Dihedral  :  5.687  19.049    400
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 0.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 15.60 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.95 (0.19), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.76 (0.14), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP B 334 
 PHE   0.027   0.003   PHE A 283 
 ARG   0.000   0.000   ARG U 293 

*********************** 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: 1
    poor density    : 52
  time to evaluate  : 0.291 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8586 (mtp) cc_final: 0.8201 (mtt)
  outliers start: 1
  outliers final: 1
  residues processed: 52
  average time/residue: 1.1439
  time to fit residues: 61.0454
Evaluate side-chains
  53 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 52
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 14 optimal weight:    0.9990
   chunk 17 optimal weight:   10.0000
   chunk 35 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 34 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 = 0.3443 r_free = 0.3443 target = 0.103043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.082685 restraints weight = 2884.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 1.97
r_work: 0.3017 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9030
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   2745  Z= 0.330
  Angle     :  0.897   9.315   3650  Z= 0.475
  Chirality :  0.046   0.142    315
  Planarity :  0.003   0.029    545
  Dihedral  :  5.699  18.864    400
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 0.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 16.00 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.95 (0.18), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.76 (0.14), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP B 334 
 PHE   0.024   0.003   PHE C 283 
 ARG   0.001   0.000   ARG U 293 

********************** 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
  54 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.259 
Fit side-chains
REVERT: B  337 MET cc_start: 0.8580 (mtp) cc_final: 0.8196 (mtt)
  outliers start: 1
  outliers final: 1
  residues processed: 53
  average time/residue: 1.1258
  time to fit residues: 61.1905
Evaluate side-chains
  54 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 2 optimal weight:    9.9990
   chunk 20 optimal weight:    2.9990
   chunk 39 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 10 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   chunk 1 optimal weight:   20.0000
   chunk 23 optimal weight:    6.9990
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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 = 0.3474 r_free = 0.3474 target = 0.104601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.084350 restraints weight = 2938.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.99
r_work: 0.3044 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9009
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2745  Z= 0.236
  Angle     :  0.796   8.824   3650  Z= 0.419
  Chirality :  0.043   0.127    315
  Planarity :  0.003   0.028    545
  Dihedral  :  5.421  17.323    400
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 0.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 15.60 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.90 (0.18), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.73 (0.14), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP D 334 
 PHE   0.028   0.003   PHE A 283 
 ARG   0.000   0.000   ARG C 293 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2181.48 seconds
wall clock time: 38 minutes 2.10 seconds (2282.10 seconds total)