Starting phenix.real_space_refine
on Wed Jun  4 17:21:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bzs_45074/06_2025/9bzs_45074.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bzs_45074/06_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_45074/06_2025/9bzs_45074.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bzs_45074/06_2025/9bzs_45074.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bzs_45074/06_2025/9bzs_45074.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bzs_45074/06_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-5710/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: 2.10, per 1000 atoms: 0.58
  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: 0.83
  Conformation dependent library (CDL) restraints added in 436.5 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: 0.56
  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: 0.93

  Time building geometry restraints manager: 1.00 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:             1.500
  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:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.010
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.680
-------------------------------------------------------------------------------
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  : 0.400 
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: 0.3140
  time to fit residues: 21.2500
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  : 0.417 
-------------------------------------------------------------------------------
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  : 0.361 
Fit side-chains
REVERT: A   72 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8490 (mt-10)
REVERT: C   34 ARG cc_start: 0.8436 (ttt180) cc_final: 0.7939 (ttt90)
REVERT: C  104 ARG cc_start: 0.8010 (ttm110) cc_final: 0.7716 (ttm170)
  outliers start: 1
  outliers final: 1
  residues processed: 53
  average time/residue: 0.3425
  time to fit residues: 20.3724
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  : 0.390 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   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 = 0.094733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.080196 restraints weight = 4457.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 2.01
r_work: 0.3070 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
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   5.581   5000  Z= 0.347
  Chirality :  0.053   0.171    585
  Planarity :  0.004   0.023    615
  Dihedral  :  5.908  18.181    495
  Min Nonbonded Distance : 2.467

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        0.04253 (   78)
  hydrogen bonds       : angle       5.18013 (  234)
  covalent geometry    : bond        0.00496 ( 3680)
  covalent geometry    : angle       0.64265 ( 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  : 0.378 
Fit side-chains
REVERT: A   72 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8480 (mt-10)
REVERT: B   13 MET cc_start: 0.8153 (tpp) cc_final: 0.7737 (tpp)
REVERT: C   34 ARG cc_start: 0.8443 (ttt180) cc_final: 0.8007 (ttt90)
REVERT: C  104 ARG cc_start: 0.8137 (ttm110) cc_final: 0.7922 (ttm170)
REVERT: D   30 MET cc_start: 0.8410 (ttt) cc_final: 0.8158 (ttt)
REVERT: D  104 ARG cc_start: 0.8459 (ttm110) cc_final: 0.7751 (mtm-85)
  outliers start: 3
  outliers final: 3
  residues processed: 50
  average time/residue: 0.3392
  time to fit residues: 19.0137
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:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 12 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3451 r_free = 0.3451 target = 0.096968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.082574 restraints weight = 4434.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 1.97
r_work: 0.3122 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.1643

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= 0.124
  Angle     :  0.577   5.119   5000  Z= 0.310
  Chirality :  0.051   0.162    585
  Planarity :  0.003   0.022    615
  Dihedral  :  5.554  18.069    495
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 10.51 %
    Favored  : 88.97 %
  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: -2.31 (0.35), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   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   0.002   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03095 (   78)
  hydrogen bonds       : angle       4.80538 (  234)
  covalent geometry    : bond        0.00302 ( 3680)
  covalent geometry    : angle       0.57744 ( 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  : 0.491 
Fit side-chains
REVERT: A   72 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8465 (mt-10)
REVERT: B   13 MET cc_start: 0.8111 (tpp) cc_final: 0.7696 (tpp)
REVERT: C   34 ARG cc_start: 0.8422 (ttt180) cc_final: 0.7989 (ttt90)
REVERT: C  104 ARG cc_start: 0.8124 (ttm110) cc_final: 0.7883 (ttm170)
REVERT: D   30 MET cc_start: 0.8345 (ttt) cc_final: 0.8121 (ttt)
  outliers start: 2
  outliers final: 2
  residues processed: 53
  average time/residue: 0.3807
  time to fit residues: 22.8418
Evaluate side-chains
  52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.9188

-------------------------------------------------------------------------------
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 = 0.3392 r_free = 0.3392 target = 0.093599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.079143 restraints weight = 4474.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 1.97
r_work: 0.3052 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.1767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   3680  Z= 0.230
  Angle     :  0.655   5.635   5000  Z= 0.354
  Chirality :  0.053   0.162    585
  Planarity :  0.004   0.025    615
  Dihedral  :  5.978  18.383    495
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 10.26 %
    Favored  : 88.21 %
  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 (0.35), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.26), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   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   0.002   0.000   ARG E 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04099 (   78)
  hydrogen bonds       : angle       4.93912 (  234)
  covalent geometry    : bond        0.00587 ( 3680)
  covalent geometry    : angle       0.65464 ( 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
  54 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.403 
Fit side-chains
REVERT: B   13 MET cc_start: 0.8131 (tpp) cc_final: 0.7704 (tpp)
REVERT: C   34 ARG cc_start: 0.8430 (ttt180) cc_final: 0.7996 (ttt90)
REVERT: C  104 ARG cc_start: 0.8156 (ttm110) cc_final: 0.7895 (ttm170)
REVERT: D   34 ARG cc_start: 0.8439 (ttt180) cc_final: 0.8169 (ttt-90)
  outliers start: 6
  outliers final: 6
  residues processed: 50
  average time/residue: 0.3364
  time to fit residues: 18.8937
Evaluate side-chains
  54 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 31 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 42 optimal weight:    6.9990
   chunk 1 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.9180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.096021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.081423 restraints weight = 4500.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.03
r_work: 0.3103 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3680  Z= 0.135
  Angle     :  0.585   5.316   5000  Z= 0.315
  Chirality :  0.051   0.153    585
  Planarity :  0.004   0.031    615
  Dihedral  :  5.662  18.235    495
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.79 %
    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: -2.46 (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   0.016   0.001   TYR C 114 
 ARG   0.006   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03131 (   78)
  hydrogen bonds       : angle       4.72628 (  234)
  covalent geometry    : bond        0.00335 ( 3680)
  covalent geometry    : angle       0.58460 ( 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  : 0.361 
Fit side-chains
REVERT: B   13 MET cc_start: 0.8111 (tpp) cc_final: 0.7707 (tpp)
REVERT: C   34 ARG cc_start: 0.8422 (ttt180) cc_final: 0.8001 (ttt90)
REVERT: C  104 ARG cc_start: 0.8124 (ttm110) cc_final: 0.7877 (ttm170)
REVERT: D   34 ARG cc_start: 0.8395 (ttt180) cc_final: 0.8148 (ttt-90)
  outliers start: 5
  outliers final: 5
  residues processed: 53
  average time/residue: 0.3211
  time to fit residues: 19.0863
Evaluate side-chains
  56 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
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:    3.9990
   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:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 12 optimal weight:    0.2980
   chunk 28 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.9984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.096052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.081154 restraints weight = 4449.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.11
r_work: 0.3093 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3680  Z= 0.140
  Angle     :  0.586   5.273   5000  Z= 0.315
  Chirality :  0.051   0.154    585
  Planarity :  0.004   0.030    615
  Dihedral  :  5.605  17.772    495
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 11.54 %
    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: -2.45 (0.35), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.86 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C  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   0.007   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03187 (   78)
  hydrogen bonds       : angle       4.68488 (  234)
  covalent geometry    : bond        0.00350 ( 3680)
  covalent geometry    : angle       0.58551 ( 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
  58 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.406 
Fit side-chains
REVERT: B   13 MET cc_start: 0.8163 (tpp) cc_final: 0.7752 (tpp)
REVERT: C   13 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7304 (tpt)
REVERT: C   34 ARG cc_start: 0.8458 (ttt180) cc_final: 0.8037 (ttt90)
REVERT: C  104 ARG cc_start: 0.8108 (ttm110) cc_final: 0.7870 (ttm170)
REVERT: D   34 ARG cc_start: 0.8403 (ttt180) cc_final: 0.8165 (ttt-90)
  outliers start: 6
  outliers final: 5
  residues processed: 53
  average time/residue: 0.3469
  time to fit residues: 20.6675
Evaluate side-chains
  58 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
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   30 MET
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:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 7 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3459 r_free = 0.3459 target = 0.096868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.082182 restraints weight = 4479.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 2.03
r_work: 0.3124 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1923

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= 0.122
  Angle     :  0.566   5.103   5000  Z= 0.304
  Chirality :  0.050   0.154    585
  Planarity :  0.004   0.030    615
  Dihedral  :  5.484  17.647    495
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  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: -2.43 (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   0.001   0.000   TRP E  79 
 HIS   0.006   0.001   HIS A  31 
 PHE   0.011   0.002   PHE B  64 
 TYR   0.015   0.001   TYR C 114 
 ARG   0.007   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02899 (   78)
  hydrogen bonds       : angle       4.57726 (  234)
  covalent geometry    : bond        0.00301 ( 3680)
  covalent geometry    : angle       0.56624 ( 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
  58 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.424 
Fit side-chains
REVERT: A   72 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8499 (mt-10)
REVERT: B   13 MET cc_start: 0.8096 (tpp) cc_final: 0.7678 (tpp)
REVERT: C   13 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7287 (tpt)
REVERT: C   34 ARG cc_start: 0.8432 (ttt180) cc_final: 0.8016 (ttt90)
REVERT: C  104 ARG cc_start: 0.8088 (ttm110) cc_final: 0.7791 (ttm170)
REVERT: D   34 ARG cc_start: 0.8379 (ttt180) cc_final: 0.8148 (ttt-90)
  outliers start: 7
  outliers final: 6
  residues processed: 52
  average time/residue: 0.3301
  time to fit residues: 19.2976
Evaluate side-chains
  58 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
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   26 ILE
Chi-restraints excluded: chain D residue   30 MET
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 13 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0010
   chunk 22 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   overall best weight:    0.6586

-------------------------------------------------------------------------------
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 = 0.3479 r_free = 0.3479 target = 0.098041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.083394 restraints weight = 4400.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.02
r_work: 0.3148 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3680  Z= 0.111
  Angle     :  0.552   4.921   5000  Z= 0.296
  Chirality :  0.050   0.151    585
  Planarity :  0.004   0.031    615
  Dihedral  :  5.339  17.272    495
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  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: -2.41 (0.36), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP E  79 
 HIS   0.005   0.001   HIS A  31 
 PHE   0.010   0.001   PHE B  64 
 TYR   0.014   0.001   TYR C 114 
 ARG   0.006   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02740 (   78)
  hydrogen bonds       : angle       4.53676 (  234)
  covalent geometry    : bond        0.00271 ( 3680)
  covalent geometry    : angle       0.55177 ( 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: 7
    poor density    : 52
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A   72 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8512 (mt-10)
REVERT: B   13 MET cc_start: 0.8060 (tpp) cc_final: 0.7658 (tpp)
REVERT: C   13 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7278 (tpt)
REVERT: C   34 ARG cc_start: 0.8408 (ttt180) cc_final: 0.7998 (ttt90)
REVERT: C  104 ARG cc_start: 0.8068 (ttm110) cc_final: 0.7759 (ttm170)
REVERT: D   34 ARG cc_start: 0.8378 (ttt180) cc_final: 0.8151 (ttt-90)
  outliers start: 7
  outliers final: 6
  residues processed: 52
  average time/residue: 0.3145
  time to fit residues: 18.4917
Evaluate side-chains
  58 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
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   26 ILE
Chi-restraints excluded: chain D residue   30 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 27 optimal weight:    0.4980
   chunk 15 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    1.2186

-------------------------------------------------------------------------------
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 = 0.3449 r_free = 0.3449 target = 0.096292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.081459 restraints weight = 4441.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.06
r_work: 0.3102 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3680  Z= 0.158
  Angle     :  0.587   5.376   5000  Z= 0.316
  Chirality :  0.051   0.151    585
  Planarity :  0.004   0.032    615
  Dihedral  :  5.560  17.716    495
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  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: -2.42 (0.35), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D  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   0.004   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03262 (   78)
  hydrogen bonds       : angle       4.62119 (  234)
  covalent geometry    : bond        0.00401 ( 3680)
  covalent geometry    : angle       0.58745 ( 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
  57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A   72 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8532 (mt-10)
REVERT: B   13 MET cc_start: 0.8116 (tpp) cc_final: 0.7720 (tpp)
REVERT: C   13 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7318 (tpt)
REVERT: C   34 ARG cc_start: 0.8436 (ttt180) cc_final: 0.8025 (ttt90)
REVERT: C  104 ARG cc_start: 0.8106 (ttm110) cc_final: 0.7807 (ttm170)
REVERT: D   34 ARG cc_start: 0.8430 (ttt180) cc_final: 0.8210 (ttt-90)
  outliers start: 7
  outliers final: 6
  residues processed: 52
  average time/residue: 0.3273
  time to fit residues: 19.1707
Evaluate side-chains
  57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
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   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:    4.9990
   chunk 30 optimal weight:    0.0030
   chunk 15 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.098217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.083473 restraints weight = 4461.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.03
r_work: 0.3151 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3680  Z= 0.106
  Angle     :  0.547   4.951   5000  Z= 0.294
  Chirality :  0.050   0.148    585
  Planarity :  0.004   0.035    615
  Dihedral  :  5.345  17.254    495
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  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: -2.40 (0.36), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP E  79 
 HIS   0.005   0.001   HIS A  31 
 PHE   0.010   0.001   PHE B  64 
 TYR   0.014   0.001   TYR C 114 
 ARG   0.003   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02682 (   78)
  hydrogen bonds       : angle       4.51501 (  234)
  covalent geometry    : bond        0.00261 ( 3680)
  covalent geometry    : angle       0.54680 ( 5000)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2155.75 seconds
wall clock time: 37 minutes 44.19 seconds (2264.19 seconds total)