Starting phenix.real_space_refine
on Sat May  2 08:15:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9zld_74399/05_2026/9zld_74399.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9zld_74399/05_2026/9zld_74399.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9zld_74399/05_2026/9zld_74399.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9zld_74399/05_2026/9zld_74399.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9zld_74399/05_2026/9zld_74399.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9zld_74399/05_2026/9zld_74399.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       5      5.16       5
     C    2310      2.51       5
     N     590      2.21       5
     O     670      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3575
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 715
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 4, 'TRANS': 86}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 0.69, per 1000 atoms: 0.19
  Number of scatterers: 3575
  At special positions: 0
  Unit cell: (75.166, 78.47, 41.3, 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       5     16.00
     O     670      8.00
     N     590      7.00
     C    2310      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: 0.26
  Conformation dependent library (CDL) restraints added in 141.4 milliseconds
  

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 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, 48.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 12 through 16
      removed outlier: 6.637A  pdb=" N   MET B  13 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 8.165A  pdb=" N   VAL D  16 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   LYS B  15 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   MET A  13 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   VAL B  16 " --> pdb=" O   MET A  13 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   LYS A  15 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 19 through 20
      removed outlier: 6.354A  pdb=" N   ALA B  19 " --> pdb=" O   VAL D  20 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   ALA A  19 " --> pdb=" O   VAL B  20 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 25 through 34
      removed outlier: 6.460A  pdb=" N   ALA B  25 " --> pdb=" O   ILE D  26 " (cutoff:3.500A)
      removed outlier: 8.172A  pdb=" N   VAL D  28 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   ASN B  27 " --> pdb=" O   VAL D  28 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   VAL D  30 " --> pdb=" O   ASN B  27 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ALA B  29 " --> pdb=" O   VAL D  30 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   VAL D  32 " --> pdb=" O   ALA B  29 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   HIS B  31 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 8.070A  pdb=" N   ARG D  34 " --> pdb=" O   HIS B  31 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   PHE B  33 " --> pdb=" O   ARG D  34 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ALA A  25 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
      removed outlier: 8.160A  pdb=" N   VAL B  28 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   ASN A  27 " --> pdb=" O   VAL B  28 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   VAL B  30 " --> pdb=" O   ASN A  27 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ALA A  29 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   VAL B  32 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   HIS A  31 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 8.057A  pdb=" N   ARG B  34 " --> pdb=" O   HIS A  31 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   PHE A  33 " --> pdb=" O   ARG B  34 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 62
      removed outlier: 6.303A  pdb=" N   THR A  59 " --> pdb=" O   THR C  60 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   GLU C  62 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   GLU A  61 " --> pdb=" O   GLU C  62 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   THR C  59 " --> pdb=" O   THR E  60 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   GLU E  62 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   GLU C  61 " --> pdb=" O   GLU E  62 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 68 through 73
      removed outlier: 8.211A  pdb=" N   ILE B  68 " --> pdb=" O   TYR D  69 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   VAL D  71 " --> pdb=" O   ILE B  68 " (cutoff:3.500A)
      removed outlier: 9.203A  pdb=" N   LYS B  70 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 10.205A  pdb=" N   ILE D  73 " --> pdb=" O   LYS B  70 " (cutoff:3.500A)
      removed outlier: 9.161A  pdb=" N   GLU B  72 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
      removed outlier: 8.167A  pdb=" N   ILE A  68 " --> pdb=" O   TYR B  69 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   VAL B  71 " --> pdb=" O   ILE A  68 " (cutoff:3.500A)
      removed outlier: 9.165A  pdb=" N   LYS A  70 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 10.173A  pdb=" N   ILE B  73 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 9.126A  pdb=" N   GLU A  72 " --> pdb=" O   ILE B  73 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   LYS C  70 " --> pdb=" O   TYR A  69 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   VAL A  71 " --> pdb=" O   LYS C  70 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   GLU C  72 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   ILE A  73 " --> pdb=" O   GLU C  72 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   LYS E  70 " --> pdb=" O   TYR C  69 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   VAL C  71 " --> pdb=" O   LYS E  70 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   GLU E  72 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   ILE C  73 " --> pdb=" O   GLU E  72 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 76 through 80
      removed outlier: 6.895A  pdb=" N   LYS B  80 " --> pdb=" O   TRP D  79 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   LYS A  80 " --> pdb=" O   TRP B  79 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   SER A  77 " --> pdb=" O   TYR C  78 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   LYS C  80 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   TRP A  79 " --> pdb=" O   LYS C  80 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   SER C  77 " --> pdb=" O   TYR E  78 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   LYS E  80 " --> pdb=" O   SER C  77 " (cutoff:3.500A)
      removed outlier: 8.237A  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: 6.849A  pdb=" N   VAL B  93 " --> pdb=" O   VAL D  94 " (cutoff:3.500A)
      removed outlier: 7.973A  pdb=" N   THR D  96 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   PHE B  95 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   ASN D  98 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   ALA B  97 " --> pdb=" O   ASN D  98 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   VAL A  93 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   THR B  96 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   PHE A  95 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   ASN B  98 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   ALA A  97 " --> pdb=" O   ASN B  98 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 104 through 110
      removed outlier: 6.922A  pdb=" N   LEU D 110 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   LEU B 110 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ARG A 104 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   ILE C 107 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   THR A 106 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   ALA C 109 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
      removed outlier: 7.885A  pdb=" N   ALA A 108 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ARG C 104 " --> pdb=" O   TYR E 105 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   ILE E 107 " --> pdb=" O   ARG C 104 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   THR C 106 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   ALA E 109 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   ALA C 108 " --> pdb=" O   ALA E 109 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 115
      removed outlier: 6.872A  pdb=" N   TYR A 114 " --> pdb=" O   SER C 115 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   TYR C 114 " --> pdb=" O   SER E 115 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 122
      removed outlier: 5.829A  pdb=" N   THR B 118 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   VAL D 121 " --> pdb=" O   THR B 118 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ALA B 120 " --> pdb=" O   VAL D 121 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   THR A 118 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   VAL B 121 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ALA A 120 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)

    76 hydrogen bonds defined for protein.
    228 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: 0.44

  Time building geometry restraints manager: 0.36 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: 1120
        1.34 -     1.46: 674
        1.46 -     1.57: 1856
        1.57 -     1.69: 0
        1.69 -     1.80: 10
  Bond restraints: 3660
  Sorted by residual:
  bond pdb=" CG  ARG C 104 "
       pdb=" CD  ARG C 104 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.00e+00
  bond pdb=" CG  ARG A 104 "
       pdb=" CD  ARG A 104 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.00e+00
  bond pdb=" CG  ARG D 104 "
       pdb=" CD  ARG D 104 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.84e-01
  bond pdb=" CG  ARG E 104 "
       pdb=" CD  ARG E 104 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.74e-01
  bond pdb=" CG  ARG B 104 "
       pdb=" CD  ARG B 104 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.71e-01
  ... (remaining 3655 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.00: 4581
        1.00 -     2.00: 291
        2.00 -     3.01: 58
        3.01 -     4.01: 25
        4.01 -     5.01: 25
  Bond angle restraints: 4980
  Sorted by residual:
  angle pdb=" N   GLU C  63 "
        pdb=" CA  GLU C  63 "
        pdb=" C   GLU C  63 "
      ideal   model   delta    sigma   weight residual
     111.17  116.07   -4.90 1.41e+00 5.03e-01 1.21e+01
  angle pdb=" N   GLU E  63 "
        pdb=" CA  GLU E  63 "
        pdb=" C   GLU E  63 "
      ideal   model   delta    sigma   weight residual
     111.17  116.06   -4.89 1.41e+00 5.03e-01 1.20e+01
  angle pdb=" N   GLU A  63 "
        pdb=" CA  GLU A  63 "
        pdb=" C   GLU A  63 "
      ideal   model   delta    sigma   weight residual
     111.17  116.05   -4.88 1.41e+00 5.03e-01 1.20e+01
  angle pdb=" N   GLU B  63 "
        pdb=" CA  GLU B  63 "
        pdb=" C   GLU B  63 "
      ideal   model   delta    sigma   weight residual
     111.17  116.05   -4.88 1.41e+00 5.03e-01 1.20e+01
  angle pdb=" N   GLU D  63 "
        pdb=" CA  GLU D  63 "
        pdb=" C   GLU D  63 "
      ideal   model   delta    sigma   weight residual
     111.17  116.04   -4.87 1.41e+00 5.03e-01 1.19e+01
  ... (remaining 4975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.97: 1855
       13.97 -    27.94: 195
       27.94 -    41.91: 85
       41.91 -    55.89: 25
       55.89 -    69.86: 5
  Dihedral angle restraints: 2165
    sinusoidal: 825
      harmonic: 1340
  Sorted by residual:
  dihedral pdb=" CA  ALA C  25 "
           pdb=" C   ALA C  25 "
           pdb=" N   ILE C  26 "
           pdb=" CA  ILE C  26 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.75  -17.25     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  ALA E  25 "
           pdb=" C   ALA E  25 "
           pdb=" N   ILE E  26 "
           pdb=" CA  ILE E  26 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.76  -17.24     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  ALA B  25 "
           pdb=" C   ALA B  25 "
           pdb=" N   ILE B  26 "
           pdb=" CA  ILE B  26 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.77  -17.23     0      5.00e+00 4.00e-02 1.19e+01
  ... (remaining 2162 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 461
       0.054 -    0.108: 84
       0.108 -    0.163: 35
       0.163 -    0.217: 0
       0.217 -    0.271: 5
  Chirality restraints: 585
  Sorted by residual:
  chirality pdb=" CA  GLU B  63 "
            pdb=" N   GLU B  63 "
            pdb=" C   GLU B  63 "
            pdb=" CB  GLU B  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" CA  GLU E  63 "
            pdb=" N   GLU E  63 "
            pdb=" C   GLU E  63 "
            pdb=" CB  GLU E  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  GLU C  63 "
            pdb=" N   GLU C  63 "
            pdb=" C   GLU C  63 "
            pdb=" CB  GLU C  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.79e+00
  ... (remaining 582 not shown)

  Planarity restraints: 615
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E 104 "    0.117 9.50e-02 1.11e+02   5.31e-02 2.29e+00
        pdb=" NE  ARG E 104 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG E 104 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG E 104 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG E 104 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 104 "    0.117 9.50e-02 1.11e+02   5.30e-02 2.28e+00
        pdb=" NE  ARG A 104 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 104 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 104 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 104 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 104 "    0.117 9.50e-02 1.11e+02   5.28e-02 2.26e+00
        pdb=" NE  ARG B 104 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 104 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 104 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 104 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 612 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 276
        2.76 -     3.29: 3391
        3.29 -     3.83: 6293
        3.83 -     4.36: 7129
        4.36 -     4.90: 13027
  Nonbonded interactions: 30116
  Sorted by model distance:
  nonbonded pdb=" O   SER B  85 "
            pdb=" OG  SER B  85 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   SER A  85 "
            pdb=" OG  SER A  85 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   SER C  85 "
            pdb=" OG  SER C  85 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   SER E  85 "
            pdb=" OG  SER E  85 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   SER D  85 "
            pdb=" OG  SER D  85 "
     model   vdw
     2.222 3.040
  ... (remaining 30111 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.780
  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:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.630
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  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:             0.010
  Load rotamer database and sin/cos tables:5.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
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   0.032   3660  Z= 0.136
  Angle     :  0.667   5.011   4980  Z= 0.369
  Chirality :  0.055   0.271    585
  Planarity :  0.006   0.053    615
  Dihedral  : 14.979  69.856   1295
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.38 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.41 (0.33), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.25), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG E 104 
 TYR   0.018   0.002   TYR E 114 
 PHE   0.016   0.002   PHE C  33 
 TRP   0.002   0.001   TRP A  79 
 HIS   0.002   0.001   HIS D  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3660)
  covalent geometry    : angle       0.66733 ( 4980)
  hydrogen bonds       : bond        0.16652 (   76)
  hydrogen bonds       : angle       8.22819 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.130 
Fit side-chains
REVERT: B   13 MET cc_start: 0.7718 (ttp) cc_final: 0.7336 (tmm)
REVERT: C   89 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7901 (mm-30)
REVERT: C   92 GLU cc_start: 0.7077 (mp0) cc_final: 0.6786 (tm-30)
REVERT: E   13 MET cc_start: 0.7647 (ttp) cc_final: 0.7428 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.6113
  time to fit residues: 41.4433
Evaluate side-chains
  52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A  88 HIS
A 123 ASN
B  88 HIS
B 123 ASN
C  88 HIS
C 123 ASN
D  88 HIS
E  88 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.143956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.124541 restraints weight = 3891.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.4029 rms_B_bonded: 2.34
r_work: 0.3920 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3803 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3660  Z= 0.192
  Angle     :  0.641   7.223   4980  Z= 0.347
  Chirality :  0.052   0.153    585
  Planarity :  0.005   0.052    615
  Dihedral  :  5.514  17.138    490
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.62 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.33 (0.34), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.002   ARG B 104 
 TYR   0.021   0.002   TYR B 114 
 PHE   0.014   0.002   PHE C  33 
 TRP   0.005   0.001   TRP A  79 
 HIS   0.002   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 3660)
  covalent geometry    : angle       0.64093 ( 4980)
  hydrogen bonds       : bond        0.03254 (   76)
  hydrogen bonds       : angle       5.53350 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.151 
Fit side-chains
REVERT: B   15 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7802 (ttmm)
REVERT: B   26 ILE cc_start: 0.8437 (pt) cc_final: 0.8048 (mt)
REVERT: B   63 GLU cc_start: 0.7750 (pt0) cc_final: 0.7533 (pt0)
REVERT: C   72 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8217 (mt-10)
REVERT: C   89 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7455 (mt-10)
REVERT: C   92 GLU cc_start: 0.7074 (mp0) cc_final: 0.6557 (tm-30)
REVERT: E   13 MET cc_start: 0.7617 (ttp) cc_final: 0.7310 (tmm)
REVERT: E   26 ILE cc_start: 0.8519 (pt) cc_final: 0.8282 (mt)
  outliers start: 8
  outliers final: 3
  residues processed: 61
  average time/residue: 0.6588
  time to fit residues: 41.2387
Evaluate side-chains
  54 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain E residue   23 SER
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 30 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
B 123 ASN
C 123 ASN
E 123 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.136521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.117110 restraints weight = 3905.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3959 rms_B_bonded: 2.32
r_work: 0.3846 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3726 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   3660  Z= 0.240
  Angle     :  0.682   6.200   4980  Z= 0.373
  Chirality :  0.053   0.150    585
  Planarity :  0.005   0.055    615
  Dihedral  :  5.913  17.653    490
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 16.67 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.34), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 104 
 TYR   0.020   0.003   TYR B 114 
 PHE   0.013   0.002   PHE B  33 
 TRP   0.006   0.001   TRP A  79 
 HIS   0.002   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00590 ( 3660)
  covalent geometry    : angle       0.68209 ( 4980)
  hydrogen bonds       : bond        0.03500 (   76)
  hydrogen bonds       : angle       5.19385 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A   63 GLU cc_start: 0.7728 (pt0) cc_final: 0.7452 (pt0)
REVERT: A  104 ARG cc_start: 0.7624 (ttm110) cc_final: 0.7159 (ttm170)
REVERT: B   15 LYS cc_start: 0.8150 (ttmt) cc_final: 0.7917 (ttmm)
REVERT: B   63 GLU cc_start: 0.7730 (pt0) cc_final: 0.7444 (pt0)
REVERT: C   63 GLU cc_start: 0.7703 (pt0) cc_final: 0.7401 (pt0)
REVERT: C   72 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8267 (mt-10)
REVERT: C   89 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7413 (mt-10)
REVERT: C   92 GLU cc_start: 0.7211 (mp0) cc_final: 0.6653 (tm-30)
REVERT: C  117 SER cc_start: 0.9163 (OUTLIER) cc_final: 0.8564 (m)
REVERT: D   13 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7919 (tmt)
REVERT: D   15 LYS cc_start: 0.8587 (mtpm) cc_final: 0.8058 (mtpt)
REVERT: D   26 ILE cc_start: 0.8665 (pt) cc_final: 0.8345 (mt)
REVERT: E   13 MET cc_start: 0.7700 (ttp) cc_final: 0.7361 (tmm)
REVERT: E   92 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7454 (mt-10)
REVERT: E  123 ASN cc_start: 0.7416 (m-40) cc_final: 0.7059 (m-40)
  outliers start: 11
  outliers final: 4
  residues processed: 62
  average time/residue: 0.7197
  time to fit residues: 45.7425
Evaluate side-chains
  55 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   13 MET
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   92 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0030
   chunk 1 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0030
   chunk 31 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   overall best weight:    1.2006

-------------------------------------------------------------------------------
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 = 0.4157 r_free = 0.4157 target = 0.136828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.117020 restraints weight = 3883.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3977 rms_B_bonded: 2.35
r_work: 0.3862 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3739 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3660  Z= 0.179
  Angle     :  0.618   5.665   4980  Z= 0.337
  Chirality :  0.051   0.147    585
  Planarity :  0.005   0.059    615
  Dihedral  :  5.729  21.453    490
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.18 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.34), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG E 104 
 TYR   0.019   0.002   TYR B 114 
 PHE   0.012   0.002   PHE B  33 
 TRP   0.006   0.001   TRP D  79 
 HIS   0.002   0.000   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 3660)
  covalent geometry    : angle       0.61772 ( 4980)
  hydrogen bonds       : bond        0.02769 (   76)
  hydrogen bonds       : angle       5.01588 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A   63 GLU cc_start: 0.7749 (pt0) cc_final: 0.7474 (pt0)
REVERT: B   15 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7912 (ttmm)
REVERT: B   63 GLU cc_start: 0.7845 (pt0) cc_final: 0.7494 (pt0)
REVERT: C   63 GLU cc_start: 0.7724 (pt0) cc_final: 0.7423 (pt0)
REVERT: C   72 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8206 (mt-10)
REVERT: C   89 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7439 (mt-10)
REVERT: C   92 GLU cc_start: 0.7273 (mp0) cc_final: 0.6688 (tm-30)
REVERT: C  117 SER cc_start: 0.9139 (OUTLIER) cc_final: 0.8550 (m)
REVERT: D   13 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7976 (tmt)
REVERT: D   15 LYS cc_start: 0.8548 (mtpm) cc_final: 0.7917 (mttt)
REVERT: E   13 MET cc_start: 0.7712 (ttp) cc_final: 0.7369 (tmm)
REVERT: E   92 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7458 (mt-10)
REVERT: E  123 ASN cc_start: 0.7513 (m-40) cc_final: 0.7219 (m-40)
  outliers start: 11
  outliers final: 6
  residues processed: 63
  average time/residue: 0.6807
  time to fit residues: 43.9260
Evaluate side-chains
  61 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   13 MET
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   92 GLU
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 34 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 1 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.4168 r_free = 0.4168 target = 0.137287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.117641 restraints weight = 3891.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3981 rms_B_bonded: 2.34
r_work: 0.3864 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3742 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3660  Z= 0.179
  Angle     :  0.629   7.229   4980  Z= 0.340
  Chirality :  0.051   0.140    585
  Planarity :  0.005   0.066    615
  Dihedral  :  5.733  19.392    490
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.69 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.34), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG E 104 
 TYR   0.016   0.002   TYR B 114 
 PHE   0.016   0.002   PHE A  64 
 TRP   0.006   0.001   TRP D  79 
 HIS   0.002   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 3660)
  covalent geometry    : angle       0.62932 ( 4980)
  hydrogen bonds       : bond        0.02781 (   76)
  hydrogen bonds       : angle       4.92686 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   63 GLU cc_start: 0.7770 (pt0) cc_final: 0.7496 (pt0)
REVERT: A  104 ARG cc_start: 0.7626 (ttm110) cc_final: 0.7261 (ttm170)
REVERT: B   15 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7902 (ttmm)
REVERT: B   63 GLU cc_start: 0.7812 (pt0) cc_final: 0.7499 (pt0)
REVERT: C   63 GLU cc_start: 0.7654 (pt0) cc_final: 0.7316 (pt0)
REVERT: C   72 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8187 (mt-10)
REVERT: C   89 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7417 (mt-10)
REVERT: C   92 GLU cc_start: 0.7327 (mp0) cc_final: 0.6685 (tm-30)
REVERT: C  117 SER cc_start: 0.9141 (OUTLIER) cc_final: 0.8543 (m)
REVERT: D   15 LYS cc_start: 0.8539 (mtpm) cc_final: 0.8042 (mttt)
REVERT: D   26 ILE cc_start: 0.8572 (pt) cc_final: 0.8359 (mt)
REVERT: E   13 MET cc_start: 0.7712 (ttp) cc_final: 0.7346 (tmm)
REVERT: E  123 ASN cc_start: 0.7538 (m-40) cc_final: 0.7202 (m-40)
  outliers start: 11
  outliers final: 5
  residues processed: 61
  average time/residue: 0.6726
  time to fit residues: 42.0009
Evaluate side-chains
  57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue   23 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 20 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 4 optimal weight:    0.2980
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.4588

-------------------------------------------------------------------------------
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 = 0.4144 r_free = 0.4144 target = 0.135493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.115595 restraints weight = 3942.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3949 rms_B_bonded: 2.39
r_work: 0.3829 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3704 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   3660  Z= 0.210
  Angle     :  0.649   7.406   4980  Z= 0.350
  Chirality :  0.052   0.147    585
  Planarity :  0.005   0.070    615
  Dihedral  :  5.854  19.940    490
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 18.97 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.15 (0.34), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.63 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG E 104 
 TYR   0.016   0.002   TYR A  78 
 PHE   0.014   0.002   PHE A  64 
 TRP   0.006   0.001   TRP D  79 
 HIS   0.002   0.001   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 3660)
  covalent geometry    : angle       0.64890 ( 4980)
  hydrogen bonds       : bond        0.02912 (   76)
  hydrogen bonds       : angle       4.92448 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.7816 (pt0) cc_final: 0.7545 (pt0)
REVERT: B   15 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7887 (ttmm)
REVERT: B   63 GLU cc_start: 0.7803 (pt0) cc_final: 0.7492 (pt0)
REVERT: C   62 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7120 (mp0)
REVERT: C   63 GLU cc_start: 0.7655 (pt0) cc_final: 0.7323 (pt0)
REVERT: C   72 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8196 (mt-10)
REVERT: C   89 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7417 (mt-10)
REVERT: C   92 GLU cc_start: 0.7409 (mp0) cc_final: 0.6690 (tm-30)
REVERT: C  117 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8525 (m)
REVERT: D   13 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7516 (tmm)
REVERT: D   26 ILE cc_start: 0.8651 (pt) cc_final: 0.8356 (mt)
REVERT: E   13 MET cc_start: 0.7741 (ttp) cc_final: 0.7377 (tmm)
REVERT: E   18 ASP cc_start: 0.6976 (t0) cc_final: 0.6468 (t0)
REVERT: E   92 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7518 (mt-10)
REVERT: E  123 ASN cc_start: 0.7845 (m-40) cc_final: 0.7532 (m-40)
  outliers start: 8
  outliers final: 5
  residues processed: 58
  average time/residue: 0.6955
  time to fit residues: 41.2865
Evaluate side-chains
  62 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   13 MET
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   92 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 27 optimal weight:    0.1980
   chunk 0 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.4178 r_free = 0.4178 target = 0.138465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.118640 restraints weight = 3952.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.4000 rms_B_bonded: 2.40
r_work: 0.3881 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3754 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3660  Z= 0.140
  Angle     :  0.606   6.976   4980  Z= 0.326
  Chirality :  0.050   0.140    585
  Planarity :  0.006   0.070    615
  Dihedral  :  5.567  19.397    490
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 19.74 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.13 (0.34), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.62 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.002   ARG E 104 
 TYR   0.015   0.002   TYR B 114 
 PHE   0.015   0.002   PHE A  64 
 TRP   0.006   0.001   TRP D  79 
 HIS   0.002   0.001   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 3660)
  covalent geometry    : angle       0.60604 ( 4980)
  hydrogen bonds       : bond        0.02359 (   76)
  hydrogen bonds       : angle       4.79601 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 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: 7
    poor density    : 53
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.7755 (pt0) cc_final: 0.7475 (pt0)
REVERT: A  104 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7499 (ttm110)
REVERT: B   15 LYS cc_start: 0.8139 (ttmt) cc_final: 0.7879 (ttmm)
REVERT: B   63 GLU cc_start: 0.7775 (pt0) cc_final: 0.7465 (pt0)
REVERT: C   62 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7163 (mp0)
REVERT: C   63 GLU cc_start: 0.7721 (pt0) cc_final: 0.7365 (pt0)
REVERT: C   72 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8193 (mt-10)
REVERT: C   89 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7440 (mt-10)
REVERT: C   92 GLU cc_start: 0.7411 (mp0) cc_final: 0.6707 (tm-30)
REVERT: C  117 SER cc_start: 0.9129 (OUTLIER) cc_final: 0.8545 (m)
REVERT: D   13 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7561 (tmm)
REVERT: E   13 MET cc_start: 0.7730 (ttp) cc_final: 0.7385 (tmm)
REVERT: E   18 ASP cc_start: 0.6965 (t0) cc_final: 0.6512 (t0)
REVERT: E   92 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7423 (mt-10)
REVERT: E  123 ASN cc_start: 0.7917 (m-40) cc_final: 0.7628 (m-40)
  outliers start: 7
  outliers final: 4
  residues processed: 56
  average time/residue: 0.7165
  time to fit residues: 41.0728
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  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   13 MET
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   92 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0470
   overall best weight:    1.8084

-------------------------------------------------------------------------------
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 = 0.4123 r_free = 0.4123 target = 0.133293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.113387 restraints weight = 3987.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3926 rms_B_bonded: 2.39
r_work: 0.3806 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3682 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.2705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   3660  Z= 0.244
  Angle     :  0.688   7.383   4980  Z= 0.370
  Chirality :  0.053   0.146    585
  Planarity :  0.006   0.070    615
  Dihedral  :  5.943  19.116    490
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.23 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.08 (0.34), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.58 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.002   ARG E 104 
 TYR   0.016   0.003   TYR B  78 
 PHE   0.014   0.002   PHE A  64 
 TRP   0.008   0.002   TRP D  79 
 HIS   0.002   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 ( 3660)
  covalent geometry    : angle       0.68793 ( 4980)
  hydrogen bonds       : bond        0.03028 (   76)
  hydrogen bonds       : angle       4.93035 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.7812 (pt0) cc_final: 0.7405 (pt0)
REVERT: B   63 GLU cc_start: 0.7760 (pt0) cc_final: 0.7455 (pt0)
REVERT: C   62 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7154 (mp0)
REVERT: C   63 GLU cc_start: 0.7674 (pt0) cc_final: 0.7336 (pt0)
REVERT: C   72 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8207 (mt-10)
REVERT: C   89 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7448 (mt-10)
REVERT: C   92 GLU cc_start: 0.7518 (mp0) cc_final: 0.6780 (tm-30)
REVERT: D   13 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7524 (tmm)
REVERT: D   26 ILE cc_start: 0.8609 (pt) cc_final: 0.8359 (mt)
REVERT: E   13 MET cc_start: 0.7784 (ttp) cc_final: 0.7393 (tmm)
REVERT: E   18 ASP cc_start: 0.7006 (t0) cc_final: 0.6502 (t0)
  outliers start: 9
  outliers final: 6
  residues processed: 56
  average time/residue: 0.7197
  time to fit residues: 41.2070
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  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   13 MET
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue   23 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 29 optimal weight:    0.1980
   chunk 0 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 15 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   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 = 0.4156 r_free = 0.4156 target = 0.134939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.115309 restraints weight = 3949.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3979 rms_B_bonded: 2.43
r_work: 0.3856 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3728 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3660  Z= 0.162
  Angle     :  0.640   7.236   4980  Z= 0.341
  Chirality :  0.051   0.140    585
  Planarity :  0.006   0.078    615
  Dihedral  :  5.751  21.059    490
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 19.74 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.06 (0.35), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.56 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.002   ARG E 104 
 TYR   0.016   0.002   TYR B 114 
 PHE   0.017   0.002   PHE A  64 
 TRP   0.006   0.001   TRP D  79 
 HIS   0.002   0.001   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 3660)
  covalent geometry    : angle       0.63992 ( 4980)
  hydrogen bonds       : bond        0.02397 (   76)
  hydrogen bonds       : angle       4.78749 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 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  : 0.142 
Fit side-chains
REVERT: A   63 GLU cc_start: 0.7829 (pt0) cc_final: 0.7447 (pt0)
REVERT: B   63 GLU cc_start: 0.7784 (pt0) cc_final: 0.7500 (pt0)
REVERT: C   62 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7136 (mp0)
REVERT: C   63 GLU cc_start: 0.7718 (pt0) cc_final: 0.7370 (pt0)
REVERT: C   89 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7469 (mt-10)
REVERT: C   92 GLU cc_start: 0.7455 (mp0) cc_final: 0.6813 (tm-30)
REVERT: C  117 SER cc_start: 0.9139 (OUTLIER) cc_final: 0.8522 (m)
REVERT: D   15 LYS cc_start: 0.8586 (mtpm) cc_final: 0.8051 (mttt)
REVERT: D   26 ILE cc_start: 0.8616 (pt) cc_final: 0.8368 (mt)
REVERT: E   13 MET cc_start: 0.7789 (ttp) cc_final: 0.7425 (tmm)
REVERT: E   18 ASP cc_start: 0.6963 (t0) cc_final: 0.6474 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 55
  average time/residue: 0.7247
  time to fit residues: 40.8503
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  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue   23 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 12 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 41 optimal weight:    0.2980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.4154 r_free = 0.4154 target = 0.135633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.115873 restraints weight = 3986.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3972 rms_B_bonded: 2.40
r_work: 0.3849 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3723 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   3660  Z= 0.194
  Angle     :  0.664   7.749   4980  Z= 0.353
  Chirality :  0.052   0.142    585
  Planarity :  0.007   0.081    615
  Dihedral  :  5.805  21.140    490
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 20.26 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.01 (0.35), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.52 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.002   ARG E 104 
 TYR   0.016   0.002   TYR B 114 
 PHE   0.015   0.002   PHE A  64 
 TRP   0.007   0.001   TRP D  79 
 HIS   0.002   0.001   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 3660)
  covalent geometry    : angle       0.66416 ( 4980)
  hydrogen bonds       : bond        0.02605 (   76)
  hydrogen bonds       : angle       4.80207 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 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  : 0.100 
Fit side-chains
REVERT: A   63 GLU cc_start: 0.7789 (pt0) cc_final: 0.7428 (pt0)
REVERT: B   63 GLU cc_start: 0.7777 (pt0) cc_final: 0.7494 (pt0)
REVERT: C   62 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7181 (mp0)
REVERT: C   63 GLU cc_start: 0.7705 (pt0) cc_final: 0.7351 (pt0)
REVERT: C   89 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7505 (mt-10)
REVERT: C   92 GLU cc_start: 0.7461 (mp0) cc_final: 0.6816 (tm-30)
REVERT: C  117 SER cc_start: 0.9142 (OUTLIER) cc_final: 0.8542 (m)
REVERT: D   15 LYS cc_start: 0.8589 (mtpm) cc_final: 0.8082 (mttt)
REVERT: D   26 ILE cc_start: 0.8611 (pt) cc_final: 0.8353 (mt)
REVERT: E   13 MET cc_start: 0.7778 (ttp) cc_final: 0.7405 (tmm)
REVERT: E   18 ASP cc_start: 0.6983 (t0) cc_final: 0.6488 (t0)
  outliers start: 5
  outliers final: 4
  residues processed: 55
  average time/residue: 0.7196
  time to fit residues: 40.5310
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  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue   23 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.4151 r_free = 0.4151 target = 0.135439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.115873 restraints weight = 3957.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3957 rms_B_bonded: 2.37
r_work: 0.3841 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3718 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   3660  Z= 0.178
  Angle     :  0.652   7.707   4980  Z= 0.347
  Chirality :  0.052   0.140    585
  Planarity :  0.007   0.082    615
  Dihedral  :  5.764  20.814    490
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 20.77 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.98 (0.35), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.50 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.002   ARG E 104 
 TYR   0.016   0.002   TYR B 114 
 PHE   0.016   0.002   PHE A  64 
 TRP   0.006   0.001   TRP D  79 
 HIS   0.002   0.001   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 3660)
  covalent geometry    : angle       0.65186 ( 4980)
  hydrogen bonds       : bond        0.02482 (   76)
  hydrogen bonds       : angle       4.74979 (  228)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1465.28 seconds
wall clock time: 25 minutes 45.27 seconds (1545.27 seconds total)