Starting phenix.real_space_refine
on Sat Jun  7 23:33:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wnz_32636/06_2025/7wnz_32636.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wnz_32636/06_2025/7wnz_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wnz_32636/06_2025/7wnz_32636.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wnz_32636/06_2025/7wnz_32636.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wnz_32636/06_2025/7wnz_32636.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wnz_32636/06_2025/7wnz_32636.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9300
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      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:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 2.79, per 1000 atoms: 0.30
  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: 2.12
  Conformation dependent library (CDL) restraints added in 810.4 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: 1.08
  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: 3.12

  Time building geometry restraints manager: 2.63 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  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:             1.210
  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:             0.160
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     21.130
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.930
-------------------------------------------------------------------------------
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 : 6.80
  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 (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: -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
 HIS   0.004   0.002   HIS I  50 
 PHE   0.007   0.002   PHE H  94 
 TYR   0.004   0.001   TYR A  39 

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

*********************** 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  : 0.692 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.2364
  time to fit residues: 12.4150
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  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.6984

-------------------------------------------------------------------------------
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 = 0.5042 r_free = 0.5042 target = 0.170168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4856 r_free = 0.4856 target = 0.146095 restraints weight = 17546.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.4744 rms_B_bonded: 3.06
r_work: 0.4619 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.4619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6478
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4540  Z= 0.206
  Angle     :  0.587   4.937   6140  Z= 0.333
  Chirality :  0.051   0.124    810
  Planarity :  0.003   0.009    760
  Dihedral  :  6.013  15.173    650
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  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: -4.15 (0.24), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.16 (0.19), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.004   HIS H  50 
 PHE   0.006   0.002   PHE J  94 
 TYR   0.007   0.002   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02046 (   81)
  hydrogen bonds       : angle       4.05969 (  243)
  covalent geometry    : bond        0.00421 ( 4540)
  covalent geometry    : angle       0.58703 ( 6140)

*********************** 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
  35 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.653 
Fit side-chains
REVERT: H   65 ASN cc_start: 0.7053 (t0) cc_final: 0.6824 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.2641
  time to fit residues: 13.3876
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  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
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 = 0.4980 r_free = 0.4980 target = 0.161812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4793 r_free = 0.4793 target = 0.137847 restraints weight = 18452.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.4792 rms_B_bonded: 3.24
r_work: 0.4655 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.4655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6403
moved from start:          0.1981

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     :  0.534   4.454   6140  Z= 0.309
  Chirality :  0.052   0.126    810
  Planarity :  0.003   0.008    760
  Dihedral  :  5.941  14.160    650
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  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 (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: -4.68 (0.23), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.56 (0.18), residues: 630

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02368 (   81)
  hydrogen bonds       : angle       4.00833 (  243)
  covalent geometry    : bond        0.00378 ( 4540)
  covalent geometry    : angle       0.53418 ( 6140)

*********************** 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
  35 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.2315
  time to fit residues: 12.2623
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  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 = 0.4969 r_free = 0.4969 target = 0.159722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4774 r_free = 0.4774 target = 0.135849 restraints weight = 18376.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.4763 rms_B_bonded: 3.25
r_work: 0.4634 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.4634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6506
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   4540  Z= 0.200
  Angle     :  0.557   4.321   6140  Z= 0.324
  Chirality :  0.052   0.135    810
  Planarity :  0.003   0.009    760
  Dihedral  :  6.077  14.196    650
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.48 %
    Favored  : 89.52 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  6.17 %
    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 (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 (0.22), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.86 (0.17), residues: 630

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02120 (   81)
  hydrogen bonds       : angle       4.17708 (  243)
  covalent geometry    : bond        0.00404 ( 4540)
  covalent geometry    : angle       0.55662 ( 6140)

*********************** 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
  40 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 40
  average time/residue: 0.1970
  time to fit residues: 12.4592
Evaluate side-chains
  34 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 33
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   87 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0060
   chunk 24 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    1.5202

-------------------------------------------------------------------------------
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 = 0.4966 r_free = 0.4966 target = 0.159377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4776 r_free = 0.4776 target = 0.135700 restraints weight = 18444.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.4773 rms_B_bonded: 3.25
r_work: 0.4637 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.4637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6514
moved from start:          0.2687

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= 0.176
  Angle     :  0.529   4.324   6140  Z= 0.309
  Chirality :  0.052   0.138    810
  Planarity :  0.003   0.008    760
  Dihedral  :  5.913  14.163    650
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  6.81 %
    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 (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: -5.31 (0.21), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.04 (0.16), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS G  50 
 PHE   0.006   0.002   PHE B  94 
 TYR   0.004   0.001   TYR J  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02019 (   81)
  hydrogen bonds       : angle       4.20138 (  243)
  covalent geometry    : bond        0.00356 ( 4540)
  covalent geometry    : angle       0.52942 ( 6140)

*********************** 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
  39 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
REVERT: E   39 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.5984 (m-80)
  outliers start: 3
  outliers final: 2
  residues processed: 39
  average time/residue: 0.2059
  time to fit residues: 12.6126
Evaluate side-chains
  38 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain E residue   39 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0370
   chunk 50 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.1462

-------------------------------------------------------------------------------
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 = 0.163971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4790 r_free = 0.4790 target = 0.139614 restraints weight = 18016.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.4786 rms_B_bonded: 3.29
r_work: 0.4653 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.4653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6485
moved from start:          0.2825

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= 0.136
  Angle     :  0.486   4.039   6140  Z= 0.282
  Chirality :  0.052   0.141    810
  Planarity :  0.002   0.006    760
  Dihedral  :  5.490  13.556    650
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  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 (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: -5.37 (0.21), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.08 (0.16), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS G  50 
 PHE   0.006   0.002   PHE G  94 
 TYR   0.003   0.001   TYR H  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01712 (   81)
  hydrogen bonds       : angle       3.91496 (  243)
  covalent geometry    : bond        0.00274 ( 4540)
  covalent geometry    : angle       0.48564 ( 6140)

*********************** 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
  34 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 34
  average time/residue: 0.2020
  time to fit residues: 10.9112
Evaluate side-chains
  34 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    2.3788

-------------------------------------------------------------------------------
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 = 0.4944 r_free = 0.4944 target = 0.158339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4754 r_free = 0.4754 target = 0.135265 restraints weight = 19164.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.4749 rms_B_bonded: 3.20
r_work: 0.4620 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.4620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6637
moved from start:          0.3198

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= 0.260
  Angle     :  0.629   5.024   6140  Z= 0.369
  Chirality :  0.053   0.146    810
  Planarity :  0.004   0.011    760
  Dihedral  :  6.479  15.087    650
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.51 %
    Favored  : 83.49 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  5.96 %
    Favored  : 92.34 %
  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: -5.75 (0.21), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.38 (0.16), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.005   HIS G  50 
 PHE   0.007   0.003   PHE D  94 
 TYR   0.006   0.002   TYR G  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02482 (   81)
  hydrogen bonds       : angle       4.63494 (  243)
  covalent geometry    : bond        0.00517 ( 4540)
  covalent geometry    : angle       0.62946 ( 6140)

*********************** 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
  58 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 1.763 
Fit side-chains
   revert: symmetry clash
REVERT: G   94 PHE cc_start: 0.7716 (t80) cc_final: 0.7496 (t80)
REVERT: B   39 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.6690 (m-80)
REVERT: E   39 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.6196 (m-80)
REVERT: F   99 GLN cc_start: 0.7956 (mt0) cc_final: 0.7553 (mp10)
REVERT: J   39 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6574 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 57
  average time/residue: 0.2662
  time to fit residues: 23.5454
Evaluate side-chains
  57 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
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 C residue   87 SER
Chi-restraints excluded: chain D 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   overall best weight:    2.1388

-------------------------------------------------------------------------------
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 = 0.4957 r_free = 0.4957 target = 0.159791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4765 r_free = 0.4765 target = 0.136478 restraints weight = 19240.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.4759 rms_B_bonded: 3.18
r_work: 0.4629 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.4629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6612
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.024   4540  Z= 0.233
  Angle     :  0.606   5.058   6140  Z= 0.355
  Chirality :  0.053   0.150    810
  Planarity :  0.003   0.010    760
  Dihedral  :  6.510  16.388    650
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.98 %
    Favored  : 83.02 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  :  7.02 %
    Favored  : 91.06 %
  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: -5.94 (0.21), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.52 (0.16), residues: 630

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02448 (   81)
  hydrogen bonds       : angle       4.79334 (  243)
  covalent geometry    : bond        0.00468 ( 4540)
  covalent geometry    : angle       0.60614 ( 6140)

*********************** 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
  58 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   94 PHE cc_start: 0.7717 (t80) cc_final: 0.7494 (t80)
REVERT: A   39 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.7402 (m-80)
REVERT: E   39 TYR cc_start: 0.6965 (OUTLIER) cc_final: 0.6014 (m-80)
REVERT: J   39 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.6567 (m-80)
  outliers start: 9
  outliers final: 5
  residues processed: 56
  average time/residue: 0.2220
  time to fit residues: 18.8473
Evaluate side-chains
  57 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain E residue   39 TYR
Chi-restraints excluded: chain F residue   39 TYR
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain J residue   39 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 38 optimal weight:    0.4980
   chunk 11 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4940 r_free = 0.4940 target = 0.157586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.133441 restraints weight = 18765.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.4717 rms_B_bonded: 3.30
r_work: 0.4592 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.4592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6519
moved from start:          0.3285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   4540  Z= 0.097
  Angle     :  0.467   4.085   6140  Z= 0.270
  Chirality :  0.054   0.147    810
  Planarity :  0.002   0.006    760
  Dihedral  :  5.414  14.368    650
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  8.09 %
    Favored  : 91.28 %
  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: -5.83 (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
 HIS   0.002   0.001   HIS H  50 
 PHE   0.014   0.003   PHE B  94 
 TYR   0.002   0.000   TYR H  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01585 (   81)
  hydrogen bonds       : angle       3.99988 (  243)
  covalent geometry    : bond        0.00201 ( 4540)
  covalent geometry    : angle       0.46742 ( 6140)

*********************** 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
  33 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 33
  average time/residue: 0.1989
  time to fit residues: 10.3399
Evaluate side-chains
  33 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain C 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 6 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   overall best weight:    2.1386

-------------------------------------------------------------------------------
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 = 0.4948 r_free = 0.4948 target = 0.159071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4753 r_free = 0.4753 target = 0.135586 restraints weight = 19414.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.4752 rms_B_bonded: 3.23
r_work: 0.4618 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.4618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6628
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   4540  Z= 0.237
  Angle     :  0.607   5.087   6140  Z= 0.355
  Chirality :  0.053   0.150    810
  Planarity :  0.003   0.010    760
  Dihedral  :  6.201  15.452    650
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.68 %
    Favored  : 80.32 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  8.09 %
    Favored  : 91.06 %
  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: -5.99 (0.20), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.56 (0.15), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.004   HIS G  50 
 PHE   0.016   0.003   PHE J  94 
 TYR   0.006   0.002   TYR J  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02298 (   81)
  hydrogen bonds       : angle       4.61300 (  243)
  covalent geometry    : bond        0.00471 ( 4540)
  covalent geometry    : angle       0.60725 ( 6140)

********************** 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
  52 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
REVERT: F   99 GLN cc_start: 0.7963 (mt0) cc_final: 0.7694 (mm-40)
  outliers start: 4
  outliers final: 4
  residues processed: 52
  average time/residue: 0.2026
  time to fit residues: 15.9648
Evaluate side-chains
  52 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C 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 58 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.4920 r_free = 0.4920 target = 0.156061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.132119 restraints weight = 19070.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.4688 rms_B_bonded: 3.29
r_work: 0.4564 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.4564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6587
moved from start:          0.3457

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= 0.136
  Angle     :  0.507   4.509   6140  Z= 0.295
  Chirality :  0.054   0.149    810
  Planarity :  0.002   0.006    760
  Dihedral  :  5.759  15.314    650
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  7.87 %
    Favored  : 91.06 %
  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: -5.97 (0.20), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.54 (0.15), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS G  50 
 PHE   0.014   0.003   PHE B  94 
 TYR   0.003   0.001   TYR H  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01758 (   81)
  hydrogen bonds       : angle       4.23878 (  243)
  covalent geometry    : bond        0.00274 ( 4540)
  covalent geometry    : angle       0.50748 ( 6140)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4418.94 seconds
wall clock time: 77 minutes 28.50 seconds (4648.50 seconds total)