Starting phenix.real_space_refine
on Tue Mar  3 22:44:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wnz_32636/03_2026/7wnz_32636.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wnz_32636/03_2026/7wnz_32636.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wnz_32636/03_2026/7wnz_32636.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wnz_32636/03_2026/7wnz_32636.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wnz_32636/03_2026/7wnz_32636.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wnz_32636/03_2026/7wnz_32636.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     C    2830      2.51       5
     N     780      2.21       5
     O     910      1.98       5
     H    4780      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9300
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "G"
      Number of atoms: 930
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 930
          Classifications: {'peptide': 65}
          Modifications used: {'NH3': 1}
          Link IDs: {'TRANS': 64}
  Restraints were copied for chains:
    A, B, C, D, E, F, H, I, J
  Time building chain proxies: 0.77, per 1000 atoms: 0.08
  Number of scatterers: 9300
  At special positions: 0
  Unit cell: (92.13, 95.45, 42.33, 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)
     O     910      8.00
     N     780      7.00
     C    2830      6.00
     H    4780      1.00
    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: 0.82
  Conformation dependent library (CDL) restraints added in 212.4 milliseconds
  

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1100

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 31.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'F' and resid 37 through 40
      removed outlier: 6.447A  pdb=" N   LEU F  38 " --> pdb=" O   TYR I  39 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   VAL G  37 " --> pdb=" O   LEU H  38 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   VAL H  40 " --> pdb=" O   VAL G  37 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   TYR G  39 " --> pdb=" O   VAL H  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 45 through 50
      removed outlier: 6.832A  pdb=" N   GLU F  46 " --> pdb=" O   LYS I  45 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   GLY I  47 " --> pdb=" O   GLU F  46 " (cutoff:3.500A)
      removed outlier: 8.867A  pdb=" N   LYS H  45 " --> pdb=" O   GLU I  46 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   VAL I  48 " --> pdb=" O   LYS H  45 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   GLY H  47 " --> pdb=" O   VAL I  48 " (cutoff:3.500A)
      removed outlier: 7.954A  pdb=" N   HIS I  50 " --> pdb=" O   GLY H  47 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL H  49 " --> pdb=" O   HIS I  50 " (cutoff:3.500A)
      removed outlier: 8.891A  pdb=" N   LYS G  45 " --> pdb=" O   GLU H  46 " (cutoff:3.500A)
      removed outlier: 8.121A  pdb=" N   VAL H  48 " --> pdb=" O   LYS G  45 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   GLY G  47 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   HIS H  50 " --> pdb=" O   GLY G  47 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   VAL G  49 " --> pdb=" O   HIS H  50 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLU G  46 " --> pdb=" O   LYS J  45 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   GLY J  47 " --> pdb=" O   GLU G  46 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'I' and resid 54 through 57
      removed outlier: 6.683A  pdb=" N   THR H  54 " --> pdb=" O   VAL I  55 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   GLU I  57 " --> pdb=" O   THR H  54 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   ALA H  56 " --> pdb=" O   GLU I  57 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   THR G  54 " --> pdb=" O   VAL H  55 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   GLU H  57 " --> pdb=" O   THR G  54 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   ALA G  56 " --> pdb=" O   GLU H  57 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 62 through 63
      removed outlier: 6.422A  pdb=" N   GLN F  62 " --> pdb=" O   VAL I  63 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   GLN G  62 " --> pdb=" O   VAL J  63 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 69 through 71
      removed outlier: 6.535A  pdb=" N   ALA F  69 " --> pdb=" O   VAL I  70 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   VAL H  70 " --> pdb=" O   VAL I  71 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   VAL G  70 " --> pdb=" O   VAL H  71 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 77 through 78
      removed outlier: 6.652A  pdb=" N   VAL F  77 " --> pdb=" O   ALA I  78 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   VAL G  77 " --> pdb=" O   ALA J  78 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 81 through 82
      removed outlier: 6.528A  pdb=" N   THR H  81 " --> pdb=" O   VAL I  82 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   THR G  81 " --> pdb=" O   VAL H  82 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 87 through 89
      removed outlier: 6.185A  pdb=" N   SER F  87 " --> pdb=" O   ILE I  88 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   SER G  87 " --> pdb=" O   ILE J  88 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 95 through 98
      removed outlier: 6.389A  pdb=" N   VAL G  95 " --> pdb=" O   LYS J  96 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   ASP J  98 " --> pdb=" O   VAL G  95 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   LYS G  97 " --> pdb=" O   ASP J  98 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 37 through 40
      removed outlier: 6.452A  pdb=" N   LEU A  38 " --> pdb=" O   TYR B  39 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 45 through 50
      removed outlier: 6.836A  pdb=" N   GLU A  46 " --> pdb=" O   LYS B  45 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   GLY B  47 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   GLU B  46 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   GLY C  47 " --> pdb=" O   GLU B  46 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   GLU C  46 " --> pdb=" O   LYS D  45 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   GLY D  47 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   GLU D  46 " --> pdb=" O   LYS E  45 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   GLY E  47 " --> pdb=" O   GLU D  46 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 54 through 57
    Processing sheet with id=AB4, first strand: chain 'A' and resid 62 through 63
      removed outlier: 6.353A  pdb=" N   GLN A  62 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   GLN B  62 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   GLN C  62 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   GLN D  62 " --> pdb=" O   VAL E  63 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'A' and resid 69 through 71
    Processing sheet with id=AB6, first strand: chain 'A' and resid 77 through 78
      removed outlier: 6.630A  pdb=" N   VAL A  77 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   VAL B  77 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   VAL C  77 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   VAL D  77 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'A' and resid 81 through 82
    Processing sheet with id=AB8, first strand: chain 'A' and resid 87 through 89
      removed outlier: 6.228A  pdb=" N   SER A  87 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   SER B  87 " --> pdb=" O   ILE C  88 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   SER C  87 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   SER D  87 " --> pdb=" O   ILE E  88 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'A' and resid 95 through 98
      removed outlier: 6.481A  pdb=" N   VAL A  95 " --> pdb=" O   LYS B  96 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   ASP B  98 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   LYS A  97 " --> pdb=" O   ASP B  98 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   VAL B  95 " --> pdb=" O   LYS C  96 " (cutoff:3.500A)
      removed outlier: 7.875A  pdb=" N   ASP C  98 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   LYS B  97 " --> pdb=" O   ASP C  98 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   VAL C  95 " --> pdb=" O   LYS D  96 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   ASP D  98 " --> pdb=" O   VAL C  95 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   LYS C  97 " --> pdb=" O   ASP D  98 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   VAL D  95 " --> pdb=" O   LYS E  96 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   ASP E  98 " --> pdb=" O   VAL D  95 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   LYS D  97 " --> pdb=" O   ASP E  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9

    81 hydrogen bonds defined for protein.
    243 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.63

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        0.84 -     0.98: 4780
        0.98 -     1.12: 0
        1.12 -     1.26: 790
        1.26 -     1.40: 860
        1.40 -     1.54: 2890
  Bond restraints: 9320
  Sorted by residual:
  bond pdb=" CB  LYS C  80 "
       pdb=" CG  LYS C  80 "
    ideal  model  delta    sigma   weight residual
    1.520  1.499  0.021 3.00e-02 1.11e+03 4.85e-01
  bond pdb=" CB  LYS F  80 "
       pdb=" CG  LYS F  80 "
    ideal  model  delta    sigma   weight residual
    1.520  1.500  0.020 3.00e-02 1.11e+03 4.60e-01
  bond pdb=" CB  LYS J  80 "
       pdb=" CG  LYS J  80 "
    ideal  model  delta    sigma   weight residual
    1.520  1.500  0.020 3.00e-02 1.11e+03 4.58e-01
  bond pdb=" CB  LYS I  80 "
       pdb=" CG  LYS I  80 "
    ideal  model  delta    sigma   weight residual
    1.520  1.500  0.020 3.00e-02 1.11e+03 4.48e-01
  bond pdb=" CB  LYS D  80 "
       pdb=" CG  LYS D  80 "
    ideal  model  delta    sigma   weight residual
    1.520  1.500  0.020 3.00e-02 1.11e+03 4.44e-01
  ... (remaining 9315 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.12: 16546
        1.12 -     2.24: 386
        2.24 -     3.35: 28
        3.35 -     4.47: 0
        4.47 -     5.59: 10
  Bond angle restraints: 16970
  Sorted by residual:
  angle pdb=" N   GLY C  51 "
        pdb=" CA  GLY C  51 "
        pdb=" C   GLY C  51 "
      ideal   model   delta    sigma   weight residual
     113.18  118.77   -5.59 2.37e+00 1.78e-01 5.56e+00
  angle pdb=" N   GLY F  51 "
        pdb=" CA  GLY F  51 "
        pdb=" C   GLY F  51 "
      ideal   model   delta    sigma   weight residual
     113.18  118.77   -5.59 2.37e+00 1.78e-01 5.56e+00
  angle pdb=" N   GLY H  51 "
        pdb=" CA  GLY H  51 "
        pdb=" C   GLY H  51 "
      ideal   model   delta    sigma   weight residual
     113.18  118.74   -5.56 2.37e+00 1.78e-01 5.51e+00
  angle pdb=" N   GLY D  51 "
        pdb=" CA  GLY D  51 "
        pdb=" C   GLY D  51 "
      ideal   model   delta    sigma   weight residual
     113.18  118.72   -5.54 2.37e+00 1.78e-01 5.47e+00
  angle pdb=" N   GLY I  51 "
        pdb=" CA  GLY I  51 "
        pdb=" C   GLY I  51 "
      ideal   model   delta    sigma   weight residual
     113.18  118.72   -5.54 2.37e+00 1.78e-01 5.47e+00
  ... (remaining 16965 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.57: 3590
       11.57 -    23.13: 400
       23.13 -    34.70: 130
       34.70 -    46.26: 50
       46.26 -    57.83: 80
  Dihedral angle restraints: 4250
    sinusoidal: 2380
      harmonic: 1870
  Sorted by residual:
  dihedral pdb=" CA  HIS E  50 "
           pdb=" C   HIS E  50 "
           pdb=" N   GLY E  51 "
           pdb=" CA  GLY E  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.67   15.33     0      5.00e+00 4.00e-02 9.39e+00
  dihedral pdb=" CA  HIS J  50 "
           pdb=" C   HIS J  50 "
           pdb=" N   GLY J  51 "
           pdb=" CA  GLY J  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.69   15.31     0      5.00e+00 4.00e-02 9.38e+00
  dihedral pdb=" CA  HIS B  50 "
           pdb=" C   HIS B  50 "
           pdb=" N   GLY B  51 "
           pdb=" CA  GLY B  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.70   15.30     0      5.00e+00 4.00e-02 9.36e+00
  ... (remaining 4247 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 430
       0.027 -    0.053: 174
       0.053 -    0.080: 66
       0.080 -    0.106: 67
       0.106 -    0.133: 73
  Chirality restraints: 810
  Sorted by residual:
  chirality pdb=" CA  VAL E  82 "
            pdb=" N   VAL E  82 "
            pdb=" C   VAL E  82 "
            pdb=" CB  VAL E  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.41e-01
  chirality pdb=" CA  VAL J  82 "
            pdb=" N   VAL J  82 "
            pdb=" C   VAL J  82 "
            pdb=" CB  VAL J  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.29e-01
  chirality pdb=" CA  VAL F  82 "
            pdb=" N   VAL F  82 "
            pdb=" C   VAL F  82 "
            pdb=" CB  VAL F  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.26e-01
  ... (remaining 807 not shown)

  Planarity restraints: 1400
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY D  51 "   -0.004 2.00e-02 2.50e+03   7.54e-03 5.69e-01
        pdb=" C   GLY D  51 "    0.013 2.00e-02 2.50e+03
        pdb=" O   GLY D  51 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   VAL D  52 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  51 "   -0.004 2.00e-02 2.50e+03   7.47e-03 5.58e-01
        pdb=" C   GLY A  51 "    0.013 2.00e-02 2.50e+03
        pdb=" O   GLY A  51 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   VAL A  52 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY I  51 "    0.004 2.00e-02 2.50e+03   7.41e-03 5.49e-01
        pdb=" C   GLY I  51 "   -0.013 2.00e-02 2.50e+03
        pdb=" O   GLY I  51 "    0.005 2.00e-02 2.50e+03
        pdb=" N   VAL I  52 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1397 not shown)

  Histogram of nonbonded interaction distances:
        1.38 -     2.00: 72
        2.00 -     2.63: 11506
        2.63 -     3.25: 24647
        3.25 -     3.88: 32082
        3.88 -     4.50: 46069
  Nonbonded interactions: 114376
  Sorted by model distance:
  nonbonded pdb=" HE2 HIS E  50 "
            pdb=" OE2 GLU J  57 "
     model   vdw
     1.376 2.450
  nonbonded pdb=" OE2 GLU D  57 "
            pdb=" HE2 HIS J  50 "
     model   vdw
     1.400 2.450
  nonbonded pdb=" HE2 HIS A  50 "
            pdb=" OE2 GLU F  57 "
     model   vdw
     1.431 2.450
  nonbonded pdb=" OE2 GLU G  57 "
            pdb=" HE2 HIS D  50 "
     model   vdw
     1.445 2.450
  nonbonded pdb=" HE2 HIS C  50 "
            pdb=" OE2 GLU H  57 "
     model   vdw
     1.490 2.450
  ... (remaining 114371 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 'G'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.030
  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:             0.070
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.220
  Find NCS groups from input model:        0.040
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6762
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      :  0.003   0.021   4540  Z= 0.148
  Angle     :  0.516   5.591   6140  Z= 0.286
  Chirality :  0.053   0.133    810
  Planarity :  0.002   0.008    760
  Dihedral  : 10.392  37.268   1550
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.33 (0.27), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.53 (0.21), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR A  39 
 PHE   0.007   0.002   PHE H  94 
 HIS   0.004   0.002   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4540)
  covalent geometry    : angle       0.51608 ( 6140)
  hydrogen bonds       : bond        0.15459 (   81)
  hydrogen bonds       : angle       7.63088 (  243)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.228 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1079
  time to fit residues: 5.4680
Evaluate side-chains
  34 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.4980
   chunk 25 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.5081 r_free = 0.5081 target = 0.173431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4884 r_free = 0.4884 target = 0.147935 restraints weight = 16853.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.4809 rms_B_bonded: 3.10
r_work: 0.4690 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.4690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6386
moved from start:          0.0970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   4540  Z= 0.137
  Angle     :  0.492   4.792   6140  Z= 0.277
  Chirality :  0.051   0.123    810
  Planarity :  0.002   0.007    760
  Dihedral  :  5.312  15.760    650
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.62 (0.26), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.75 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR C  39 
 PHE   0.004   0.001   PHE H  94 
 HIS   0.003   0.001   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4540)
  covalent geometry    : angle       0.49240 ( 6140)
  hydrogen bonds       : bond        0.02207 (   81)
  hydrogen bonds       : angle       4.06468 (  243)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.229 
Fit side-chains
REVERT: H   65 ASN cc_start: 0.6986 (t0) cc_final: 0.6717 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0957
  time to fit residues: 4.9714
Evaluate side-chains
  34 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.4992 r_free = 0.4992 target = 0.168726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4781 r_free = 0.4781 target = 0.140796 restraints weight = 17221.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.4692 rms_B_bonded: 3.36
r_work: 0.4556 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.4556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6378
moved from start:          0.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4540  Z= 0.162
  Angle     :  0.497   4.764   6140  Z= 0.284
  Chirality :  0.052   0.124    810
  Planarity :  0.002   0.008    760
  Dihedral  :  5.457  14.137    650
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.08 (0.25), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.19), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR C  39 
 PHE   0.005   0.002   PHE H  94 
 HIS   0.005   0.002   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 4540)
  covalent geometry    : angle       0.49659 ( 6140)
  hydrogen bonds       : bond        0.01902 (   81)
  hydrogen bonds       : angle       3.68404 (  243)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.239 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.1045
  time to fit residues: 5.1967
Evaluate side-chains
  31 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
** H  65 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 = 0.4962 r_free = 0.4962 target = 0.159134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4767 r_free = 0.4767 target = 0.134998 restraints weight = 18578.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.4763 rms_B_bonded: 3.25
r_work: 0.4630 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.4630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6528
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   4540  Z= 0.232
  Angle     :  0.587   4.764   6140  Z= 0.340
  Chirality :  0.052   0.127    810
  Planarity :  0.003   0.010    760
  Dihedral  :  6.189  14.670    650
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.16 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.78 (0.22), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.64 (0.17), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR B  39 
 PHE   0.006   0.002   PHE B  94 
 HIS   0.007   0.004   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 4540)
  covalent geometry    : angle       0.58707 ( 6140)
  hydrogen bonds       : bond        0.02242 (   81)
  hydrogen bonds       : angle       4.15129 (  243)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0684
  time to fit residues: 4.2404
Evaluate side-chains
  33 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 29 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    2.1188

-------------------------------------------------------------------------------
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 = 0.4964 r_free = 0.4964 target = 0.160034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4777 r_free = 0.4777 target = 0.136423 restraints weight = 18621.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.4777 rms_B_bonded: 3.17
r_work: 0.4645 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.4645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6606
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   4540  Z= 0.235
  Angle     :  0.595   4.812   6140  Z= 0.348
  Chirality :  0.052   0.137    810
  Planarity :  0.003   0.009    760
  Dihedral  :  6.430  15.039    650
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.11 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  4.89 %
    Favored  : 93.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.29 (0.21), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.02 (0.16), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR I  39 
 PHE   0.007   0.002   PHE H  94 
 HIS   0.007   0.004   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 4540)
  covalent geometry    : angle       0.59543 ( 6140)
  hydrogen bonds       : bond        0.02378 (   81)
  hydrogen bonds       : angle       4.43811 (  243)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A   80 LYS cc_start: 0.7034 (mtpt) cc_final: 0.6401 (mttt)
REVERT: B   39 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.6676 (m-80)
REVERT: E   39 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.6196 (m-80)
REVERT: F   99 GLN cc_start: 0.7984 (mt0) cc_final: 0.7577 (mp10)
REVERT: J   39 TYR cc_start: 0.6990 (OUTLIER) cc_final: 0.6772 (m-80)
  outliers start: 7
  outliers final: 3
  residues processed: 51
  average time/residue: 0.0829
  time to fit residues: 6.6152
Evaluate side-chains
  46 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   39 TYR
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain E residue   39 TYR
Chi-restraints excluded: chain J residue   39 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0970
   chunk 1 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.1580

-------------------------------------------------------------------------------
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 = 0.4981 r_free = 0.4981 target = 0.160916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4790 r_free = 0.4790 target = 0.136828 restraints weight = 18353.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.4793 rms_B_bonded: 3.25
r_work: 0.4659 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.4659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6497
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   4540  Z= 0.140
  Angle     :  0.498   4.163   6140  Z= 0.289
  Chirality :  0.052   0.141    810
  Planarity :  0.002   0.008    760
  Dihedral  :  5.715  13.917    650
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  6.81 %
    Favored  : 92.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.37 (0.21), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.09 (0.16), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR B  39 
 PHE   0.020   0.003   PHE G  94 
 HIS   0.004   0.002   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4540)
  covalent geometry    : angle       0.49846 ( 6140)
  hydrogen bonds       : bond        0.01799 (   81)
  hydrogen bonds       : angle       4.00536 (  243)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.248 
Fit side-chains
REVERT: F   99 GLN cc_start: 0.7939 (mt0) cc_final: 0.7532 (mp10)
  outliers start: 2
  outliers final: 2
  residues processed: 35
  average time/residue: 0.0725
  time to fit residues: 4.3722
Evaluate side-chains
  35 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain D residue   87 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0170
   chunk 22 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    1.0022

-------------------------------------------------------------------------------
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 = 0.5023 r_free = 0.5023 target = 0.164727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4805 r_free = 0.4805 target = 0.139675 restraints weight = 18088.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.4785 rms_B_bonded: 3.29
r_work: 0.4652 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.4652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6531
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   4540  Z= 0.126
  Angle     :  0.472   3.892   6140  Z= 0.273
  Chirality :  0.053   0.141    810
  Planarity :  0.002   0.008    760
  Dihedral  :  5.362  13.670    650
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.89 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  6.81 %
    Favored  : 92.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.39 (0.21), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.10 (0.16), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR B  39 
 PHE   0.017   0.003   PHE G  94 
 HIS   0.003   0.002   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 4540)
  covalent geometry    : angle       0.47171 ( 6140)
  hydrogen bonds       : bond        0.01640 (   81)
  hydrogen bonds       : angle       3.77977 (  243)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 29
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 31
  average time/residue: 0.0620
  time to fit residues: 3.4205
Evaluate side-chains
  30 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain D residue   87 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   overall best weight:    1.2382

-------------------------------------------------------------------------------
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 = 0.5016 r_free = 0.5016 target = 0.163884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4797 r_free = 0.4797 target = 0.139173 restraints weight = 18174.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.4773 rms_B_bonded: 3.29
r_work: 0.4638 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.4638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6510
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   4540  Z= 0.146
  Angle     :  0.492   4.129   6140  Z= 0.285
  Chirality :  0.052   0.142    810
  Planarity :  0.002   0.007    760
  Dihedral  :  5.478  13.737    650
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  7.02 %
    Favored  : 92.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.50 (0.21), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.19 (0.16), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR J  39 
 PHE   0.015   0.002   PHE G  94 
 HIS   0.005   0.002   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4540)
  covalent geometry    : angle       0.49189 ( 6140)
  hydrogen bonds       : bond        0.01708 (   81)
  hydrogen bonds       : angle       3.84637 (  243)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 0.242 
Fit side-chains
REVERT: F   99 GLN cc_start: 0.7889 (mt0) cc_final: 0.7479 (mp10)
  outliers start: 2
  outliers final: 2
  residues processed: 32
  average time/residue: 0.0699
  time to fit residues: 3.9335
Evaluate side-chains
  32 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain D residue   87 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    1.7188

-------------------------------------------------------------------------------
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 = 0.5004 r_free = 0.5004 target = 0.162079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4780 r_free = 0.4780 target = 0.137881 restraints weight = 18604.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.4777 rms_B_bonded: 3.31
r_work: 0.4644 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.4644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6472
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   4540  Z= 0.195
  Angle     :  0.548   4.589   6140  Z= 0.319
  Chirality :  0.052   0.144    810
  Planarity :  0.003   0.008    760
  Dihedral  :  5.923  14.397    650
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.54 %
    Favored  : 87.46 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  7.02 %
    Favored  : 92.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.69 (0.20), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.33 (0.15), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.002   TYR J  39 
 PHE   0.014   0.003   PHE J  94 
 HIS   0.007   0.004   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 4540)
  covalent geometry    : angle       0.54798 ( 6140)
  hydrogen bonds       : bond        0.02029 (   81)
  hydrogen bonds       : angle       4.19523 (  243)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A   80 LYS cc_start: 0.6755 (mtpt) cc_final: 0.6460 (mttt)
REVERT: F   99 GLN cc_start: 0.7929 (mt0) cc_final: 0.7517 (mp10)
  outliers start: 2
  outliers final: 2
  residues processed: 39
  average time/residue: 0.0878
  time to fit residues: 5.3243
Evaluate side-chains
  39 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain D residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 37 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 = 0.4995 r_free = 0.4995 target = 0.161667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.137288 restraints weight = 18708.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.4750 rms_B_bonded: 3.34
r_work: 0.4619 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.4619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6471
moved from start:          0.3334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   4540  Z= 0.187
  Angle     :  0.547   4.693   6140  Z= 0.319
  Chirality :  0.053   0.148    810
  Planarity :  0.003   0.008    760
  Dihedral  :  6.013  15.195    650
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.13 %
    Favored  : 85.87 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  7.02 %
    Favored  : 92.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.83 (0.20), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.44 (0.15), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.002   TYR B  39 
 PHE   0.019   0.003   PHE J  94 
 HIS   0.006   0.003   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 4540)
  covalent geometry    : angle       0.54743 ( 6140)
  hydrogen bonds       : bond        0.02045 (   81)
  hydrogen bonds       : angle       4.31238 (  243)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 41
  average time/residue: 0.0874
  time to fit residues: 5.5425
Evaluate side-chains
  41 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain D residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.4992 r_free = 0.4992 target = 0.162312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4776 r_free = 0.4776 target = 0.137574 restraints weight = 18354.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.4765 rms_B_bonded: 3.26
r_work: 0.4634 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.4634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6568
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   4540  Z= 0.147
  Angle     :  0.507   4.336   6140  Z= 0.294
  Chirality :  0.053   0.148    810
  Planarity :  0.002   0.007    760
  Dihedral  :  5.701  14.738    650
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.79 %
    Favored  : 89.21 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  7.45 %
    Favored  : 92.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.84 (0.20), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.45 (0.15), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR B  39 
 PHE   0.015   0.003   PHE J  94 
 HIS   0.005   0.003   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4540)
  covalent geometry    : angle       0.50744 ( 6140)
  hydrogen bonds       : bond        0.01825 (   81)
  hydrogen bonds       : angle       4.12208 (  243)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2215.54 seconds
wall clock time: 38 minutes 9.75 seconds (2289.75 seconds total)