Starting phenix.real_space_refine
on Fri May  9 19:54:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bzs_45074/05_2025/9bzs_45074.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bzs_45074/05_2025/9bzs_45074.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bzs_45074/05_2025/9bzs_45074.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bzs_45074/05_2025/9bzs_45074.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bzs_45074/05_2025/9bzs_45074.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bzs_45074/05_2025/9bzs_45074.cif"
  }
  resolution = 3.14
  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=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    2325      2.51       5
     N     590      2.21       5
     O     670      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3595
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 4, 'TRANS': 87}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 1.95, per 1000 atoms: 0.54
  Number of scatterers: 3595
  At special positions: 0
  Unit cell: (69.058, 87.032, 41.624, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      10     16.00
     O     670      8.00
     N     590      7.00
     C    2325      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.88
  Conformation dependent library (CDL) restraints added in 403.6 milliseconds
  

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  870

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 48.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 12 through 16
      removed outlier: 6.310A  pdb=" N   LEU B  12 " --> pdb=" O   MET D  13 " (cutoff:3.500A)
      removed outlier: 7.986A  pdb=" N   LYS D  15 " --> pdb=" O   LEU B  12 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL B  14 " --> pdb=" O   LYS D  15 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   LEU A  12 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   LYS B  15 " --> pdb=" O   LEU A  12 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   VAL A  14 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 19 through 21
      removed outlier: 6.324A  pdb=" N   ALA A  19 " --> pdb=" O   VAL C  20 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   ALA C  19 " --> pdb=" O   VAL E  20 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 26 through 34
      removed outlier: 6.324A  pdb=" N   ASN A  27 " --> pdb=" O   VAL C  28 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   MET C  30 " --> pdb=" O   ASN A  27 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ALA A  29 " --> pdb=" O   MET C  30 " (cutoff:3.500A)
      removed outlier: 8.152A  pdb=" N   VAL C  32 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   HIS A  31 " --> pdb=" O   VAL C  32 " (cutoff:3.500A)
      removed outlier: 8.076A  pdb=" N   ARG C  34 " --> pdb=" O   HIS A  31 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   PHE A  33 " --> pdb=" O   ARG C  34 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ASN C  27 " --> pdb=" O   VAL E  28 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   MET E  30 " --> pdb=" O   ASN C  27 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ALA C  29 " --> pdb=" O   MET E  30 " (cutoff:3.500A)
      removed outlier: 8.164A  pdb=" N   VAL E  32 " --> pdb=" O   ALA C  29 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   HIS C  31 " --> pdb=" O   VAL E  32 " (cutoff:3.500A)
      removed outlier: 8.090A  pdb=" N   ARG E  34 " --> pdb=" O   HIS C  31 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   PHE C  33 " --> pdb=" O   ARG E  34 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 66
      removed outlier: 7.121A  pdb=" N   THR B  60 " --> pdb=" O   THR D  59 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   GLU D  61 " --> pdb=" O   THR B  60 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   GLU B  62 " --> pdb=" O   GLU D  61 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   GLU D  63 " --> pdb=" O   GLU B  62 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   PHE B  64 " --> pdb=" O   GLU D  63 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   THR A  60 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   GLU B  61 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   GLU A  62 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   GLU B  63 " --> pdb=" O   GLU A  62 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE A  64 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 9.248A  pdb=" N   THR A  59 " --> pdb=" O   THR C  60 " (cutoff:3.500A)
      removed outlier: 10.568A  pdb=" N   GLU C  62 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 9.076A  pdb=" N   GLU A  61 " --> pdb=" O   GLU C  62 " (cutoff:3.500A)
      removed outlier: 9.329A  pdb=" N   PHE C  64 " --> pdb=" O   GLU A  61 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   GLU A  63 " --> pdb=" O   PHE C  64 " (cutoff:3.500A)
      removed outlier: 8.590A  pdb=" N   GLU C  66 " --> pdb=" O   GLU A  63 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   VAL A  65 " --> pdb=" O   GLU C  66 " (cutoff:3.500A)
      removed outlier: 9.268A  pdb=" N   THR C  59 " --> pdb=" O   THR E  60 " (cutoff:3.500A)
      removed outlier: 10.586A  pdb=" N   GLU E  62 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 9.099A  pdb=" N   GLU C  61 " --> pdb=" O   GLU E  62 " (cutoff:3.500A)
      removed outlier: 9.353A  pdb=" N   PHE E  64 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   GLU C  63 " --> pdb=" O   PHE E  64 " (cutoff:3.500A)
      removed outlier: 8.609A  pdb=" N   GLU E  66 " --> pdb=" O   GLU C  63 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   VAL C  65 " --> pdb=" O   GLU E  66 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 69 through 73
      removed outlier: 6.575A  pdb=" N   LYS B  70 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   ILE D  73 " --> pdb=" O   LYS B  70 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   GLU B  72 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LYS A  70 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 8.211A  pdb=" N   ILE B  73 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   GLU A  72 " --> pdb=" O   ILE B  73 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 79 through 80
      removed outlier: 6.541A  pdb=" N   TRP A  79 " --> pdb=" O   LYS C  80 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   TRP C  79 " --> pdb=" O   LYS E  80 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 99
      removed outlier: 6.492A  pdb=" N   GLU B  92 " --> pdb=" O   VAL D  93 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   PHE D  95 " --> pdb=" O   GLU B  92 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   VAL B  94 " --> pdb=" O   PHE D  95 " (cutoff:3.500A)
      removed outlier: 7.862A  pdb=" N   ALA D  97 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   THR B  96 " --> pdb=" O   ALA D  97 " (cutoff:3.500A)
      removed outlier: 8.208A  pdb=" N   ASP D  99 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   ASN B  98 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   GLU A  92 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 7.755A  pdb=" N   PHE B  95 " --> pdb=" O   GLU A  92 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   VAL A  94 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   ALA B  97 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 7.219A  pdb=" N   THR A  96 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 8.175A  pdb=" N   ASP B  99 " --> pdb=" O   THR A  96 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   ASN A  98 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 103 through 110
      removed outlier: 6.488A  pdb=" N   ARG B 104 " --> pdb=" O   TYR D 105 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   ILE D 107 " --> pdb=" O   ARG B 104 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   THR B 106 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   ALA D 109 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
      removed outlier: 7.975A  pdb=" N   ALA B 108 " --> pdb=" O   ALA D 109 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ARG A 104 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ILE B 107 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   THR A 106 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   ALA B 109 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   ALA A 108 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU C 110 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   LEU E 110 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 115
      removed outlier: 7.126A  pdb=" N   TYR B 114 " --> pdb=" O   SER D 115 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   TYR A 114 " --> pdb=" O   SER B 115 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 122
      removed outlier: 5.896A  pdb=" N   THR A 118 " --> pdb=" O   THR C 119 " (cutoff:3.500A)
      removed outlier: 7.869A  pdb=" N   VAL C 121 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   ALA A 120 " --> pdb=" O   VAL C 121 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   THR C 118 " --> pdb=" O   THR E 119 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   VAL E 121 " --> pdb=" O   THR C 118 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ALA C 120 " --> pdb=" O   VAL E 121 " (cutoff:3.500A)

    78 hydrogen bonds defined for protein.
    234 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.84

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1115
        1.34 -     1.46: 635
        1.46 -     1.57: 1910
        1.57 -     1.69: 0
        1.69 -     1.80: 20
  Bond restraints: 3680
  Sorted by residual:
  bond pdb=" C   SER D  23 "
       pdb=" N   PRO D  24 "
    ideal  model  delta    sigma   weight residual
    1.329  1.354 -0.025 1.20e-02 6.94e+03 4.47e+00
  bond pdb=" C   SER C  23 "
       pdb=" N   PRO C  24 "
    ideal  model  delta    sigma   weight residual
    1.329  1.353 -0.025 1.20e-02 6.94e+03 4.22e+00
  bond pdb=" C   SER A  23 "
       pdb=" N   PRO A  24 "
    ideal  model  delta    sigma   weight residual
    1.329  1.353 -0.025 1.20e-02 6.94e+03 4.19e+00
  bond pdb=" C   SER B  23 "
       pdb=" N   PRO B  24 "
    ideal  model  delta    sigma   weight residual
    1.329  1.353 -0.024 1.20e-02 6.94e+03 4.16e+00
  bond pdb=" C   SER E  23 "
       pdb=" N   PRO E  24 "
    ideal  model  delta    sigma   weight residual
    1.329  1.353 -0.024 1.20e-02 6.94e+03 4.10e+00
  ... (remaining 3675 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 4955
        2.57 -     5.14: 35
        5.14 -     7.71: 5
        7.71 -    10.28: 0
       10.28 -    12.85: 5
  Bond angle restraints: 5000
  Sorted by residual:
  angle pdb=" N   SER B  23 "
        pdb=" CA  SER B  23 "
        pdb=" C   SER B  23 "
      ideal   model   delta    sigma   weight residual
     109.81  122.66  -12.85 2.21e+00 2.05e-01 3.38e+01
  angle pdb=" N   SER D  23 "
        pdb=" CA  SER D  23 "
        pdb=" C   SER D  23 "
      ideal   model   delta    sigma   weight residual
     109.81  122.64  -12.83 2.21e+00 2.05e-01 3.37e+01
  angle pdb=" N   SER C  23 "
        pdb=" CA  SER C  23 "
        pdb=" C   SER C  23 "
      ideal   model   delta    sigma   weight residual
     109.81  122.62  -12.81 2.21e+00 2.05e-01 3.36e+01
  angle pdb=" N   SER A  23 "
        pdb=" CA  SER A  23 "
        pdb=" C   SER A  23 "
      ideal   model   delta    sigma   weight residual
     109.81  122.62  -12.81 2.21e+00 2.05e-01 3.36e+01
  angle pdb=" N   SER E  23 "
        pdb=" CA  SER E  23 "
        pdb=" C   SER E  23 "
      ideal   model   delta    sigma   weight residual
     109.81  122.59  -12.78 2.21e+00 2.05e-01 3.34e+01
  ... (remaining 4995 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.81: 1845
        9.81 -    19.61: 230
       19.61 -    29.42: 65
       29.42 -    39.22: 30
       39.22 -    49.03: 5
  Dihedral angle restraints: 2175
    sinusoidal: 830
      harmonic: 1345
  Sorted by residual:
  dihedral pdb=" CA  ILE D  26 "
           pdb=" C   ILE D  26 "
           pdb=" N   ASN D  27 "
           pdb=" CA  ASN D  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.15   16.85     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  ILE E  26 "
           pdb=" C   ILE E  26 "
           pdb=" N   ASN E  27 "
           pdb=" CA  ASN E  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.16   16.84     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  ILE A  26 "
           pdb=" C   ILE A  26 "
           pdb=" N   ASN A  27 "
           pdb=" CA  ASN A  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.19   16.81     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 2172 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 480
       0.063 -    0.125: 95
       0.125 -    0.188: 5
       0.188 -    0.250: 0
       0.250 -    0.313: 5
  Chirality restraints: 585
  Sorted by residual:
  chirality pdb=" CA  SER B  23 "
            pdb=" N   SER B  23 "
            pdb=" C   SER B  23 "
            pdb=" CB  SER B  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.45e+00
  chirality pdb=" CA  SER A  23 "
            pdb=" N   SER A  23 "
            pdb=" C   SER A  23 "
            pdb=" CB  SER A  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.45e+00
  chirality pdb=" CA  SER E  23 "
            pdb=" N   SER E  23 "
            pdb=" C   SER E  23 "
            pdb=" CB  SER E  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.44e+00
  ... (remaining 582 not shown)

  Planarity restraints: 615
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER E  23 "    0.011 2.00e-02 2.50e+03   2.16e-02 4.65e+00
        pdb=" C   SER E  23 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   SER E  23 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PRO E  24 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER D  23 "    0.011 2.00e-02 2.50e+03   2.16e-02 4.65e+00
        pdb=" C   SER D  23 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   SER D  23 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PRO D  24 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C  23 "    0.011 2.00e-02 2.50e+03   2.15e-02 4.61e+00
        pdb=" C   SER C  23 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   SER C  23 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PRO C  24 "    0.012 2.00e-02 2.50e+03
  ... (remaining 612 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1016
        2.83 -     3.35: 2818
        3.35 -     3.87: 5953
        3.87 -     4.38: 6471
        4.38 -     4.90: 11147
  Nonbonded interactions: 27405
  Sorted by model distance:
  nonbonded pdb=" O   SER C  85 "
            pdb=" OG  SER C  85 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O   SER E  85 "
            pdb=" OG  SER E  85 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   SER B  85 "
            pdb=" OG  SER B  85 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   SER A  85 "
            pdb=" OG  SER A  85 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   SER D  85 "
            pdb=" OG  SER D  85 "
     model   vdw
     2.315 3.040
  ... (remaining 27400 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.280
  Find NCS groups from input model:        0.080
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
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   0.025   3680  Z= 0.165
  Angle     :  0.762  12.855   5000  Z= 0.404
  Chirality :  0.057   0.313    585
  Planarity :  0.005   0.028    615
  Dihedral  : 10.691  49.028   1305
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  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: -2.40 (0.31), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.24), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B  79 
 HIS   0.001   0.000   HIS E  88 
 PHE   0.010   0.002   PHE C  33 
 TYR   0.012   0.002   TYR D 114 
 ARG   0.001   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20244 (   78)
  hydrogen bonds       : angle       8.22219 (  234)
  covalent geometry    : bond        0.00342 ( 3680)
  covalent geometry    : angle       0.76171 ( 5000)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A   72 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8214 (mt-10)
REVERT: A  104 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7870 (ttm-80)
REVERT: B  104 ARG cc_start: 0.8038 (ttm110) cc_final: 0.7205 (mtm-85)
REVERT: C   34 ARG cc_start: 0.8078 (ttt180) cc_final: 0.7663 (ttt90)
REVERT: C  104 ARG cc_start: 0.8008 (ttm110) cc_final: 0.7682 (ttm170)
REVERT: E  104 ARG cc_start: 0.7858 (ttm110) cc_final: 0.7626 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.2902
  time to fit residues: 19.6676
Evaluate side-chains
  51 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 18 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 40 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  88 HIS
A  98 ASN
B  88 HIS
B  98 ASN
C  88 HIS
C  98 ASN
D  88 HIS
D  98 ASN
E  88 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.096445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.082039 restraints weight = 4503.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 1.95
r_work: 0.3113 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.1116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3680  Z= 0.169
  Angle     :  0.627   5.770   5000  Z= 0.339
  Chirality :  0.052   0.164    585
  Planarity :  0.004   0.029    615
  Dihedral  :  5.786  17.780    495
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  5.13 %
    Favored  : 94.62 %
  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: -2.22 (0.33), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.25), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP E  79 
 HIS   0.007   0.002   HIS D  31 
 PHE   0.011   0.002   PHE B  64 
 TYR   0.018   0.002   TYR C 114 
 ARG   0.002   0.000   ARG E 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04365 (   78)
  hydrogen bonds       : angle       5.60721 (  234)
  covalent geometry    : bond        0.00423 ( 3680)
  covalent geometry    : angle       0.62679 ( 5000)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A   72 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8489 (mt-10)
REVERT: C   34 ARG cc_start: 0.8436 (ttt180) cc_final: 0.7939 (ttt90)
REVERT: C  104 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7716 (ttm170)
  outliers start: 1
  outliers final: 1
  residues processed: 53
  average time/residue: 0.3452
  time to fit residues: 20.4412
Evaluate side-chains
  50 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3409 r_free = 0.3409 target = 0.094744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.080211 restraints weight = 4458.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 2.02
r_work: 0.3067 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3680  Z= 0.194
  Angle     :  0.643   5.555   5000  Z= 0.347
  Chirality :  0.053   0.172    585
  Planarity :  0.004   0.023    615
  Dihedral  :  5.906  18.233    495
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  8.46 %
    Favored  : 90.77 %
  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: -2.25 (0.34), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.26), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  79 
 HIS   0.006   0.001   HIS A  31 
 PHE   0.012   0.002   PHE B  64 
 TYR   0.017   0.002   TYR C 114 
 ARG   0.004   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04240 (   78)
  hydrogen bonds       : angle       5.18040 (  234)
  covalent geometry    : bond        0.00494 ( 3680)
  covalent geometry    : angle       0.64257 ( 5000)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 50
  time to evaluate  : 0.413 
Fit side-chains
REVERT: A   72 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8482 (mt-10)
REVERT: B   13 MET cc_start: 0.8158 (tpp) cc_final: 0.7743 (tpp)
REVERT: C   34 ARG cc_start: 0.8448 (ttt180) cc_final: 0.8013 (ttt90)
REVERT: C  104 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7933 (ttm170)
REVERT: D   30 MET cc_start: 0.8413 (ttt) cc_final: 0.8158 (ttt)
REVERT: D  104 ARG cc_start: 0.8461 (ttm110) cc_final: 0.7754 (mtm-85)
  outliers start: 3
  outliers final: 3
  residues processed: 50
  average time/residue: 0.3386
  time to fit residues: 18.9912
Evaluate side-chains
  52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   30 MET
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
E  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.095097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.080656 restraints weight = 4412.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 1.98
r_work: 0.3089 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3680  Z= 0.164
  Angle     :  0.611   5.422   5000  Z= 0.330
  Chirality :  0.052   0.161    585
  Planarity :  0.003   0.022    615
  Dihedral  :  5.788  18.374    495
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 10.00 %
    Favored  : 89.49 %
  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: -2.32 (0.35), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.26), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C  79 
 HIS   0.006   0.001   HIS A  31 
 PHE   0.012   0.002   PHE B  64 
 TYR   0.016   0.002   TYR C 114 
 ARG   0.003   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03560 (   78)
  hydrogen bonds       : angle       4.92593 (  234)
  covalent geometry    : bond        0.00411 ( 3680)
  covalent geometry    : angle       0.61143 ( 5000)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.435 
Fit side-chains
REVERT: B   13 MET cc_start: 0.8096 (tpp) cc_final: 0.7662 (tpp)
REVERT: C   34 ARG cc_start: 0.8430 (ttt180) cc_final: 0.7982 (ttt90)
REVERT: C  104 ARG cc_start: 0.8107 (ttm110) cc_final: 0.7852 (ttm170)
REVERT: D   30 MET cc_start: 0.8399 (ttt) cc_final: 0.8169 (ttt)
  outliers start: 2
  outliers final: 2
  residues processed: 53
  average time/residue: 0.3307
  time to fit residues: 19.6279
Evaluate side-chains
  53 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 31 optimal weight:    0.3980
   chunk 6 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.3403 r_free = 0.3403 target = 0.094093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.079627 restraints weight = 4478.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.00
r_work: 0.3064 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3680  Z= 0.188
  Angle     :  0.624   5.473   5000  Z= 0.337
  Chirality :  0.052   0.160    585
  Planarity :  0.004   0.027    615
  Dihedral  :  5.866  18.101    495
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 10.77 %
    Favored  : 87.69 %
  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: -2.45 (0.34), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.86 (0.26), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  79 
 HIS   0.007   0.001   HIS A  31 
 PHE   0.012   0.002   PHE B  64 
 TYR   0.016   0.002   TYR C 114 
 ARG   0.002   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03715 (   78)
  hydrogen bonds       : angle       4.86553 (  234)
  covalent geometry    : bond        0.00479 ( 3680)
  covalent geometry    : angle       0.62420 ( 5000)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.428 
Fit side-chains
REVERT: B   13 MET cc_start: 0.8126 (tpp) cc_final: 0.7691 (tpp)
REVERT: C   34 ARG cc_start: 0.8416 (ttt180) cc_final: 0.7974 (ttt90)
REVERT: C  104 ARG cc_start: 0.8123 (ttm110) cc_final: 0.7874 (ttm170)
REVERT: D   30 MET cc_start: 0.8419 (ttt) cc_final: 0.8205 (ttt)
REVERT: D   34 ARG cc_start: 0.8507 (ttt180) cc_final: 0.8158 (ttt-90)
  outliers start: 6
  outliers final: 6
  residues processed: 51
  average time/residue: 0.3464
  time to fit residues: 19.7966
Evaluate side-chains
  55 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 MET
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0970
   chunk 23 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 42 optimal weight:    6.9990
   chunk 1 optimal weight:    0.3980
   chunk 40 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3466 r_free = 0.3466 target = 0.097497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.082866 restraints weight = 4490.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.03
r_work: 0.3139 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3680  Z= 0.108
  Angle     :  0.559   5.108   5000  Z= 0.300
  Chirality :  0.050   0.155    585
  Planarity :  0.004   0.031    615
  Dihedral  :  5.476  17.786    495
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.54 %
    Favored  : 87.18 %
  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: -2.47 (0.35), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP D  79 
 HIS   0.006   0.001   HIS A  31 
 PHE   0.011   0.001   PHE B  64 
 TYR   0.015   0.001   TYR C 114 
 ARG   0.006   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02720 (   78)
  hydrogen bonds       : angle       4.63282 (  234)
  covalent geometry    : bond        0.00257 ( 3680)
  covalent geometry    : angle       0.55944 ( 5000)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A   72 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8507 (mt-10)
REVERT: B   13 MET cc_start: 0.8113 (tpp) cc_final: 0.7710 (tpp)
REVERT: C   34 ARG cc_start: 0.8397 (ttt180) cc_final: 0.7976 (ttt90)
REVERT: C  104 ARG cc_start: 0.8117 (ttm110) cc_final: 0.7892 (ttm170)
REVERT: D   30 MET cc_start: 0.8377 (ttt) cc_final: 0.8155 (ttt)
REVERT: D   34 ARG cc_start: 0.8433 (ttt180) cc_final: 0.8127 (ttt-90)
  outliers start: 5
  outliers final: 5
  residues processed: 53
  average time/residue: 0.3058
  time to fit residues: 18.2520
Evaluate side-chains
  57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 MET
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 42 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.3498 r_free = 0.3498 target = 0.101253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.086943 restraints weight = 4348.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.87
r_work: 0.3056 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   3680  Z= 0.228
  Angle     :  0.645   5.564   5000  Z= 0.350
  Chirality :  0.053   0.157    585
  Planarity :  0.004   0.028    615
  Dihedral  :  5.922  18.280    495
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 11.28 %
    Favored  : 86.92 %
  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: -2.51 (0.35), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.26), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP D  79 
 HIS   0.007   0.001   HIS A  31 
 PHE   0.013   0.002   PHE B  64 
 TYR   0.017   0.002   TYR C 114 
 ARG   0.006   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03964 (   78)
  hydrogen bonds       : angle       4.82175 (  234)
  covalent geometry    : bond        0.00579 ( 3680)
  covalent geometry    : angle       0.64524 ( 5000)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.390 
Fit side-chains
REVERT: B   13 MET cc_start: 0.8139 (tpp) cc_final: 0.7714 (tpp)
REVERT: C   13 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7218 (tpt)
REVERT: C   34 ARG cc_start: 0.8401 (ttt180) cc_final: 0.7964 (ttt90)
REVERT: C  104 ARG cc_start: 0.8071 (ttm110) cc_final: 0.7806 (ttm170)
  outliers start: 7
  outliers final: 6
  residues processed: 50
  average time/residue: 0.3532
  time to fit residues: 19.7266
Evaluate side-chains
  54 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   13 MET
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 MET
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0040
   overall best weight:    0.6392

-------------------------------------------------------------------------------
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 = 0.3463 r_free = 0.3463 target = 0.097251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.082659 restraints weight = 4442.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.01
r_work: 0.3134 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3680  Z= 0.110
  Angle     :  0.560   5.142   5000  Z= 0.301
  Chirality :  0.050   0.152    585
  Planarity :  0.004   0.034    615
  Dihedral  :  5.521  17.886    495
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 11.54 %
    Favored  : 86.67 %
  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: -2.52 (0.35), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.91 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP E  79 
 HIS   0.006   0.001   HIS A  31 
 PHE   0.011   0.001   PHE B  64 
 TYR   0.015   0.001   TYR C 114 
 ARG   0.006   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02775 (   78)
  hydrogen bonds       : angle       4.60716 (  234)
  covalent geometry    : bond        0.00267 ( 3680)
  covalent geometry    : angle       0.56011 ( 5000)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A   72 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8483 (mt-10)
REVERT: B   13 MET cc_start: 0.8083 (tpp) cc_final: 0.7658 (tpp)
REVERT: C   13 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7240 (tpt)
REVERT: C   34 ARG cc_start: 0.8423 (ttt180) cc_final: 0.8000 (ttt90)
  outliers start: 7
  outliers final: 6
  residues processed: 53
  average time/residue: 0.3309
  time to fit residues: 19.6972
Evaluate side-chains
  59 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   13 MET
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 MET
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 13 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3553 r_free = 0.3553 target = 0.103859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.089494 restraints weight = 4245.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 1.91
r_work: 0.3116 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3680  Z= 0.145
  Angle     :  0.583   5.253   5000  Z= 0.314
  Chirality :  0.051   0.151    585
  Planarity :  0.004   0.030    615
  Dihedral  :  5.577  17.732    495
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 11.79 %
    Favored  : 86.67 %
  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: -2.47 (0.35), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP E  79 
 HIS   0.006   0.001   HIS A  31 
 PHE   0.011   0.002   PHE B  64 
 TYR   0.015   0.002   TYR C 114 
 ARG   0.003   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03167 (   78)
  hydrogen bonds       : angle       4.62784 (  234)
  covalent geometry    : bond        0.00363 ( 3680)
  covalent geometry    : angle       0.58344 ( 5000)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.418 
Fit side-chains
REVERT: A   72 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8460 (mt-10)
REVERT: B   13 MET cc_start: 0.8154 (tpp) cc_final: 0.7739 (tpp)
REVERT: C   13 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7232 (tpt)
REVERT: C   34 ARG cc_start: 0.8411 (ttt180) cc_final: 0.7988 (ttt90)
  outliers start: 6
  outliers final: 5
  residues processed: 54
  average time/residue: 0.3352
  time to fit residues: 20.3147
Evaluate side-chains
  59 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   13 MET
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 MET
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.095952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.081139 restraints weight = 4452.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.05
r_work: 0.3094 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3680  Z= 0.147
  Angle     :  0.584   5.296   5000  Z= 0.314
  Chirality :  0.051   0.151    585
  Planarity :  0.004   0.031    615
  Dihedral  :  5.609  17.876    495
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 11.28 %
    Favored  : 86.67 %
  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: -2.48 (0.35), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP E  79 
 HIS   0.006   0.001   HIS A  31 
 PHE   0.011   0.002   PHE B  64 
 TYR   0.016   0.002   TYR C 114 
 ARG   0.003   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03175 (   78)
  hydrogen bonds       : angle       4.62833 (  234)
  covalent geometry    : bond        0.00371 ( 3680)
  covalent geometry    : angle       0.58436 ( 5000)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A   72 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8494 (mt-10)
REVERT: C   13 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7296 (tpt)
REVERT: C   34 ARG cc_start: 0.8417 (ttt180) cc_final: 0.7991 (ttt90)
  outliers start: 8
  outliers final: 7
  residues processed: 53
  average time/residue: 0.3292
  time to fit residues: 19.7133
Evaluate side-chains
  60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   13 MET
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   30 MET
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 MET
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 30 optimal weight:    0.4980
   chunk 15 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0470
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.8480

-------------------------------------------------------------------------------
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 = 0.3564 r_free = 0.3564 target = 0.104332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.090113 restraints weight = 4331.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 1.89
r_work: 0.3133 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3680  Z= 0.126
  Angle     :  0.565   5.170   5000  Z= 0.303
  Chirality :  0.050   0.150    585
  Planarity :  0.004   0.031    615
  Dihedral  :  5.476  17.581    495
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 11.54 %
    Favored  : 86.67 %
  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: -2.44 (0.35), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP E  79 
 HIS   0.006   0.001   HIS A  31 
 PHE   0.010   0.002   PHE B  64 
 TYR   0.015   0.001   TYR C 114 
 ARG   0.003   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02922 (   78)
  hydrogen bonds       : angle       4.56875 (  234)
  covalent geometry    : bond        0.00312 ( 3680)
  covalent geometry    : angle       0.56452 ( 5000)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2122.12 seconds
wall clock time: 37 minutes 21.81 seconds (2241.81 seconds total)