Starting phenix.real_space_refine
on Tue Feb  3 14:24:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d24_46482/02_2026/9d24_46482.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d24_46482/02_2026/9d24_46482.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d24_46482/02_2026/9d24_46482.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d24_46482/02_2026/9d24_46482.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d24_46482/02_2026/9d24_46482.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d24_46482/02_2026/9d24_46482.map"
  }
  resolution = 2.98
  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    2355      2.51       5
     N     605      2.21       5
     O     680      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3645
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 729
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 4, 'TRANS': 89}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 0.36, per 1000 atoms: 0.10
  Number of scatterers: 3645
  At special positions: 0
  Unit cell: (90.072, 73.392, 40.866, 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     680      8.00
     N     605      7.00
     C    2355      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: 0.15
  Conformation dependent library (CDL) restraints added in 79.8 milliseconds
  

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  890

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 48.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 16
      removed outlier: 6.596A  pdb=" N   MET B  13 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 8.126A  pdb=" N   VAL D  16 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   LYS B  15 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   MET A  13 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 8.128A  pdb=" N   VAL B  16 " --> pdb=" O   MET A  13 " (cutoff:3.500A)
      removed outlier: 6.251A  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 21
      removed outlier: 6.128A  pdb=" N   ALA B  19 " --> pdb=" O   VAL D  20 " (cutoff:3.500A)
      removed outlier: 6.132A  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 35
      removed outlier: 6.465A  pdb=" N   ALA B  25 " --> pdb=" O   ILE D  26 " (cutoff:3.500A)
      removed outlier: 7.814A  pdb=" N   VAL D  28 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ASN B  27 " --> pdb=" O   VAL D  28 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   VAL D  30 " --> pdb=" O   ASN B  27 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   ALA B  29 " --> pdb=" O   VAL D  30 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   VAL D  32 " --> pdb=" O   ALA B  29 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   HIS B  31 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   ARG D  34 " --> pdb=" O   HIS B  31 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   PHE B  33 " --> pdb=" O   ARG D  34 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ALA A  25 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
      removed outlier: 7.816A  pdb=" N   VAL B  28 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   ASN A  27 " --> pdb=" O   VAL B  28 " (cutoff:3.500A)
      removed outlier: 7.634A  pdb=" N   VAL B  30 " --> pdb=" O   ASN A  27 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   ALA A  29 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   VAL B  32 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   HIS A  31 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   ARG B  34 " --> pdb=" O   HIS A  31 " (cutoff:3.500A)
      removed outlier: 6.604A  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: 6.323A  pdb=" N   THR A  59 " --> pdb=" O   ALA C  60 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   GLU C  62 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   GLU A  61 " --> pdb=" O   GLU C  62 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   THR C  59 " --> pdb=" O   ALA E  60 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   GLU E  62 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   GLU C  61 " --> pdb=" O   GLU E  62 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 65 through 66
      removed outlier: 6.289A  pdb=" N   VAL B  65 " --> pdb=" O   GLU D  66 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   VAL A  65 " --> pdb=" O   GLU B  66 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 70 through 73
      removed outlier: 6.565A  pdb=" N   LYS A  70 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 7.812A  pdb=" N   ILE C  73 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLU A  72 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   LYS C  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   ILE E  73 " --> pdb=" O   LYS C  70 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   GLU C  72 " --> pdb=" O   ILE E  73 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 76 through 80
      removed outlier: 6.911A  pdb=" N   SER B  77 " --> pdb=" O   LYS D  76 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   TYR D  78 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   SER A  77 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   TYR B  78 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
      removed outlier: 9.244A  pdb=" N   LYS A  76 " --> pdb=" O   SER C  77 " (cutoff:3.500A)
      removed outlier: 9.676A  pdb=" N   TRP C  79 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   TYR A  78 " --> pdb=" O   TRP C  79 " (cutoff:3.500A)
      removed outlier: 9.254A  pdb=" N   LYS C  76 " --> pdb=" O   SER E  77 " (cutoff:3.500A)
      removed outlier: 9.684A  pdb=" N   TRP E  79 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
      removed outlier: 5.617A  pdb=" N   TYR C  78 " --> pdb=" O   TRP E  79 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 83 through 84
      removed outlier: 6.900A  pdb=" N   GLY B  83 " --> pdb=" O   ILE D  84 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   GLY A  83 " --> pdb=" O   ILE B  84 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 92 through 99
      removed outlier: 6.848A  pdb=" N   VAL B  93 " --> pdb=" O   VAL D  94 " (cutoff:3.500A)
      removed outlier: 7.944A  pdb=" N   THR D  96 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   PHE B  95 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   ASN D  98 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   ALA B  97 " --> pdb=" O   ASN D  98 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   VAL A  93 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 7.948A  pdb=" N   THR B  96 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   PHE A  95 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   ASN B  98 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   ALA A  97 " --> pdb=" O   ASN B  98 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 103 through 110
      removed outlier: 6.771A  pdb=" N   LEU D 110 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   LEU B 110 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ARG A 104 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 7.645A  pdb=" N   ILE C 107 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   THR A 106 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   ALA C 109 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   ALA A 108 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ARG C 104 " --> pdb=" O   TYR E 105 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   ILE E 107 " --> pdb=" O   ARG C 104 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   THR C 106 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   ALA E 109 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   ALA C 108 " --> pdb=" O   ALA E 109 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 118 through 123
      removed outlier: 5.829A  pdb=" N   THR B 118 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   VAL D 121 " --> pdb=" O   THR B 118 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ALA B 120 " --> pdb=" O   VAL D 121 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   THR D 123 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   VAL B 122 " --> pdb=" O   THR D 123 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   THR A 118 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
      removed outlier: 7.538A  pdb=" N   VAL B 121 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ALA A 120 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   THR B 123 " --> pdb=" O   ALA A 120 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   VAL A 122 " --> pdb=" O   THR B 123 " (cutoff:3.500A)

    86 hydrogen bonds defined for protein.
    258 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: 0.31

  Time building geometry restraints manager: 0.21 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: 1150
        1.34 -     1.46: 637
        1.46 -     1.57: 1933
        1.57 -     1.69: 0
        1.69 -     1.80: 10
  Bond restraints: 3730
  Sorted by residual:
  bond pdb=" CA  SER C  23 "
       pdb=" C   SER C  23 "
    ideal  model  delta    sigma   weight residual
    1.524  1.534 -0.010 1.26e-02 6.30e+03 6.24e-01
  bond pdb=" CA  SER E  23 "
       pdb=" C   SER E  23 "
    ideal  model  delta    sigma   weight residual
    1.524  1.534 -0.010 1.26e-02 6.30e+03 6.03e-01
  bond pdb=" N   GLU E  63 "
       pdb=" CA  GLU E  63 "
    ideal  model  delta    sigma   weight residual
    1.460  1.470 -0.010 1.42e-02 4.96e+03 5.13e-01
  bond pdb=" CA  SER A  23 "
       pdb=" C   SER A  23 "
    ideal  model  delta    sigma   weight residual
    1.524  1.533 -0.009 1.26e-02 6.30e+03 5.13e-01
  bond pdb=" N   GLU C  63 "
       pdb=" CA  GLU C  63 "
    ideal  model  delta    sigma   weight residual
    1.460  1.470 -0.010 1.42e-02 4.96e+03 5.05e-01
  ... (remaining 3725 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.10: 4794
        1.10 -     2.21: 212
        2.21 -     3.31: 49
        3.31 -     4.41: 15
        4.41 -     5.51: 5
  Bond angle restraints: 5075
  Sorted by residual:
  angle pdb=" C   GLU B  62 "
        pdb=" N   GLU B  63 "
        pdb=" CA  GLU B  63 "
      ideal   model   delta    sigma   weight residual
     122.82  125.86   -3.04 1.42e+00 4.96e-01 4.57e+00
  angle pdb=" C   GLU E  62 "
        pdb=" N   GLU E  63 "
        pdb=" CA  GLU E  63 "
      ideal   model   delta    sigma   weight residual
     122.82  125.86   -3.04 1.42e+00 4.96e-01 4.57e+00
  angle pdb=" C   GLU D  62 "
        pdb=" N   GLU D  63 "
        pdb=" CA  GLU D  63 "
      ideal   model   delta    sigma   weight residual
     122.82  125.84   -3.02 1.42e+00 4.96e-01 4.52e+00
  angle pdb=" C   GLU C  62 "
        pdb=" N   GLU C  63 "
        pdb=" CA  GLU C  63 "
      ideal   model   delta    sigma   weight residual
     122.82  125.82   -3.00 1.42e+00 4.96e-01 4.48e+00
  angle pdb=" C   GLU A  62 "
        pdb=" N   GLU A  63 "
        pdb=" CA  GLU A  63 "
      ideal   model   delta    sigma   weight residual
     122.82  125.81   -2.99 1.42e+00 4.96e-01 4.42e+00
  ... (remaining 5070 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.17: 1925
       10.17 -    20.34: 165
       20.34 -    30.51: 50
       30.51 -    40.67: 40
       40.67 -    50.84: 20
  Dihedral angle restraints: 2200
    sinusoidal: 825
      harmonic: 1375
  Sorted by residual:
  dihedral pdb=" CG  ARG A 104 "
           pdb=" CD  ARG A 104 "
           pdb=" NE  ARG A 104 "
           pdb=" CZ  ARG A 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   42.06   47.94     2      1.50e+01 4.44e-03 1.18e+01
  dihedral pdb=" CG  ARG B 104 "
           pdb=" CD  ARG B 104 "
           pdb=" NE  ARG B 104 "
           pdb=" CZ  ARG B 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   42.06   47.94     2      1.50e+01 4.44e-03 1.18e+01
  dihedral pdb=" CG  ARG C 104 "
           pdb=" CD  ARG C 104 "
           pdb=" NE  ARG C 104 "
           pdb=" CZ  ARG C 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   42.07   47.93     2      1.50e+01 4.44e-03 1.18e+01
  ... (remaining 2197 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 266
       0.025 -    0.051: 180
       0.051 -    0.076: 54
       0.076 -    0.101: 43
       0.101 -    0.127: 52
  Chirality restraints: 595
  Sorted by residual:
  chirality pdb=" CA  SER B  85 "
            pdb=" N   SER B  85 "
            pdb=" C   SER B  85 "
            pdb=" CB  SER B  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.01e-01
  chirality pdb=" CA  SER D  85 "
            pdb=" N   SER D  85 "
            pdb=" C   SER D  85 "
            pdb=" CB  SER D  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 3.98e-01
  chirality pdb=" CA  SER A  85 "
            pdb=" N   SER A  85 "
            pdb=" C   SER A  85 "
            pdb=" CB  SER A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 3.97e-01
  ... (remaining 592 not shown)

  Planarity restraints: 630
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C 101 "    0.034 5.00e-02 4.00e+02   5.20e-02 4.32e+00
        pdb=" N   PRO C 102 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO C 102 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C 102 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY E 101 "    0.034 5.00e-02 4.00e+02   5.20e-02 4.32e+00
        pdb=" N   PRO E 102 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO E 102 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO E 102 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 101 "    0.034 5.00e-02 4.00e+02   5.19e-02 4.31e+00
        pdb=" N   PRO A 102 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 102 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 102 "    0.029 5.00e-02 4.00e+02
  ... (remaining 627 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 341
        2.76 -     3.29: 3337
        3.29 -     3.83: 6397
        3.83 -     4.36: 7475
        4.36 -     4.90: 14159
  Nonbonded interactions: 31709
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  23 "
            pdb=" O   GLY C  22 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OG  SER C  23 "
            pdb=" O   GLY E  22 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   GLY B  22 "
            pdb=" OG  SER D  23 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   GLY A  22 "
            pdb=" OG  SER B  23 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OH  TYR A 114 "
            pdb=" OG1 THR C 119 "
     model   vdw
     2.252 3.040
  ... (remaining 31704 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:             2.170
  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:          0.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.260
  Find NCS groups from input model:        0.020
  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:7.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
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      :  0.002   0.022   3730  Z= 0.105
  Angle     :  0.584   5.515   5075  Z= 0.301
  Chirality :  0.050   0.127    595
  Planarity :  0.008   0.052    630
  Dihedral  : 11.317  50.843   1310
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.82 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.32 (0.36), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 104 
 TYR   0.015   0.001   TYR A 114 
 PHE   0.008   0.001   PHE A  33 
 TRP   0.002   0.001   TRP B  79 
 HIS   0.001   0.001   HIS C  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 3730)
  covalent geometry    : angle       0.58405 ( 5075)
  hydrogen bonds       : bond        0.16181 (   86)
  hydrogen bonds       : angle       9.51798 (  258)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.098 
Fit side-chains
REVERT: D   70 LYS cc_start: 0.8424 (ttpt) cc_final: 0.8099 (tttt)
  outliers start: 0
  outliers final: 1
  residues processed: 55
  average time/residue: 0.4060
  time to fit residues: 22.9817
Evaluate side-chains
  51 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   63 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.1980
   overall best weight:    2.4388

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

Flipped N/Q/H residues before XYZ refinement:
A 124 ASN
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 124 ASN
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 124 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.120190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.098379 restraints weight = 4247.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.39
r_work: 0.3386 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.063   3730  Z= 0.354
  Angle     :  0.794   6.542   5075  Z= 0.427
  Chirality :  0.058   0.179    595
  Planarity :  0.007   0.043    630
  Dihedral  :  9.947 171.554    508
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  :  9.23 %
    Favored  : 85.64 %
  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: -2.42 (0.36), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.84 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG B 104 
 TYR   0.023   0.003   TYR A 114 
 PHE   0.021   0.004   PHE C  33 
 TRP   0.013   0.002   TRP A  79 
 HIS   0.003   0.001   HIS E  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00897 ( 3730)
  covalent geometry    : angle       0.79445 ( 5075)
  hydrogen bonds       : bond        0.03905 (   86)
  hydrogen bonds       : angle       5.56683 (  258)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 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: 20
    poor density    : 38
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A   63 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7723 (pt0)
REVERT: C   63 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7738 (pt0)
REVERT: C   89 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8163 (mt-10)
REVERT: E   63 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8008 (pt0)
  outliers start: 20
  outliers final: 6
  residues processed: 48
  average time/residue: 0.3973
  time to fit residues: 19.8321
Evaluate side-chains
  45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 GLU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   63 GLU
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain E residue   63 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0980
   chunk 4 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0770
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
C 124 ASN
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.128571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.108882 restraints weight = 4016.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 2.08
r_work: 0.3578 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3460 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3730  Z= 0.127
  Angle     :  0.607   5.672   5075  Z= 0.323
  Chirality :  0.052   0.151    595
  Planarity :  0.005   0.036    630
  Dihedral  :  5.665  19.770    505
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 11.54 %
    Favored  : 85.38 %
  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: -2.47 (0.36), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 104 
 TYR   0.017   0.002   TYR A 114 
 PHE   0.010   0.002   PHE E  87 
 TRP   0.003   0.001   TRP B  79 
 HIS   0.002   0.000   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3730)
  covalent geometry    : angle       0.60681 ( 5075)
  hydrogen bonds       : bond        0.02508 (   86)
  hydrogen bonds       : angle       5.12928 (  258)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 33
  time to evaluate  : 0.125 
Fit side-chains
REVERT: C   89 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8141 (mt-10)
REVERT: D   70 LYS cc_start: 0.8417 (ttpt) cc_final: 0.7861 (tttt)
REVERT: E   13 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.5987 (tmt)
  outliers start: 12
  outliers final: 4
  residues processed: 37
  average time/residue: 0.3047
  time to fit residues: 11.8657
Evaluate side-chains
  37 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain E residue   13 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.125486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.104647 restraints weight = 4090.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 2.13
r_work: 0.3505 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3384 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3730  Z= 0.213
  Angle     :  0.658   6.096   5075  Z= 0.352
  Chirality :  0.054   0.149    595
  Planarity :  0.005   0.040    630
  Dihedral  :  5.861  20.197    505
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 11.54 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.36 (0.36), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 104 
 TYR   0.018   0.002   TYR C 114 
 PHE   0.016   0.003   PHE E  87 
 TRP   0.004   0.001   TRP D  79 
 HIS   0.002   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 3730)
  covalent geometry    : angle       0.65760 ( 5075)
  hydrogen bonds       : bond        0.02616 (   86)
  hydrogen bonds       : angle       4.99052 (  258)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 32
  time to evaluate  : 0.196 
Fit side-chains
REVERT: D   70 LYS cc_start: 0.8412 (ttpt) cc_final: 0.7893 (tttt)
  outliers start: 13
  outliers final: 6
  residues processed: 37
  average time/residue: 0.2845
  time to fit residues: 11.1753
Evaluate side-chains
  38 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D 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:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0570
   chunk 37 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 2 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.8900

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

Flipped N/Q/H residues before XYZ refinement:
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.126765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.106156 restraints weight = 3968.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 2.18
r_work: 0.3545 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.3061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3730  Z= 0.153
  Angle     :  0.608   5.994   5075  Z= 0.325
  Chirality :  0.052   0.144    595
  Planarity :  0.005   0.041    630
  Dihedral  :  5.699  18.998    505
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 11.79 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.41 (0.36), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 104 
 TYR   0.016   0.002   TYR C 114 
 PHE   0.010   0.002   PHE E  87 
 TRP   0.003   0.001   TRP D  79 
 HIS   0.002   0.000   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 3730)
  covalent geometry    : angle       0.60829 ( 5075)
  hydrogen bonds       : bond        0.02174 (   86)
  hydrogen bonds       : angle       4.83656 (  258)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 33
  time to evaluate  : 0.080 
Fit side-chains
REVERT: D   70 LYS cc_start: 0.8349 (ttpt) cc_final: 0.7822 (tttt)
REVERT: D   93 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8867 (t)
REVERT: E   13 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.5791 (tmt)
  outliers start: 12
  outliers final: 4
  residues processed: 39
  average time/residue: 0.2258
  time to fit residues: 9.2926
Evaluate side-chains
  38 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.124138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.103471 restraints weight = 4076.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 2.12
r_work: 0.3507 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3730  Z= 0.213
  Angle     :  0.647   6.397   5075  Z= 0.347
  Chirality :  0.054   0.146    595
  Planarity :  0.005   0.042    630
  Dihedral  :  5.830  19.251    505
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 11.28 %
    Favored  : 85.64 %
  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: -2.40 (0.36), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 104 
 TYR   0.017   0.002   TYR C 114 
 PHE   0.015   0.003   PHE E  87 
 TRP   0.004   0.001   TRP C  79 
 HIS   0.003   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 3730)
  covalent geometry    : angle       0.64688 ( 5075)
  hydrogen bonds       : bond        0.02403 (   86)
  hydrogen bonds       : angle       4.87396 (  258)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 32
  time to evaluate  : 0.134 
Fit side-chains
  outliers start: 12
  outliers final: 6
  residues processed: 37
  average time/residue: 0.3454
  time to fit residues: 13.4305
Evaluate side-chains
  35 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 29
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.127596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.107367 restraints weight = 4043.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.06
r_work: 0.3555 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3438 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.3279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3730  Z= 0.149
  Angle     :  0.605   6.204   5075  Z= 0.324
  Chirality :  0.052   0.142    595
  Planarity :  0.005   0.042    630
  Dihedral  :  5.680  18.405    505
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 11.79 %
    Favored  : 85.38 %
  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: -2.43 (0.36), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.84 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 104 
 TYR   0.015   0.002   TYR C 114 
 PHE   0.010   0.002   PHE E  87 
 TRP   0.002   0.000   TRP A  79 
 HIS   0.002   0.000   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 3730)
  covalent geometry    : angle       0.60453 ( 5075)
  hydrogen bonds       : bond        0.02081 (   86)
  hydrogen bonds       : angle       4.77540 (  258)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 31
  time to evaluate  : 0.120 
Fit side-chains
REVERT: D   63 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7488 (tt0)
REVERT: D   70 LYS cc_start: 0.8363 (ttpt) cc_final: 0.7878 (tttt)
REVERT: D   93 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8887 (t)
  outliers start: 11
  outliers final: 4
  residues processed: 36
  average time/residue: 0.3668
  time to fit residues: 13.8093
Evaluate side-chains
  37 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.125237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.104646 restraints weight = 4040.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 2.12
r_work: 0.3517 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3398 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3730  Z= 0.181
  Angle     :  0.622   6.337   5075  Z= 0.334
  Chirality :  0.053   0.144    595
  Planarity :  0.005   0.041    630
  Dihedral  :  5.711  18.682    505
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 12.05 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.39 (0.36), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 104 
 TYR   0.016   0.002   TYR C 114 
 PHE   0.013   0.002   PHE E  87 
 TRP   0.002   0.001   TRP A  79 
 HIS   0.003   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 3730)
  covalent geometry    : angle       0.62179 ( 5075)
  hydrogen bonds       : bond        0.02199 (   86)
  hydrogen bonds       : angle       4.77043 (  258)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 29
  time to evaluate  : 0.078 
Fit side-chains
REVERT: D   63 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7459 (tt0)
  outliers start: 11
  outliers final: 6
  residues processed: 35
  average time/residue: 0.2817
  time to fit residues: 10.3862
Evaluate side-chains
  36 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 15 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.127220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.106917 restraints weight = 4010.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 2.10
r_work: 0.3557 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3439 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3730  Z= 0.145
  Angle     :  0.597   6.148   5075  Z= 0.320
  Chirality :  0.052   0.141    595
  Planarity :  0.005   0.042    630
  Dihedral  :  5.623  18.409    505
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 12.56 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.41 (0.36), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 104 
 TYR   0.015   0.002   TYR A 114 
 PHE   0.010   0.002   PHE E  87 
 TRP   0.002   0.000   TRP A  79 
 HIS   0.002   0.000   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 3730)
  covalent geometry    : angle       0.59729 ( 5075)
  hydrogen bonds       : bond        0.02007 (   86)
  hydrogen bonds       : angle       4.70368 (  258)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.099 
Fit side-chains
REVERT: D   63 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7871 (pt0)
REVERT: D   70 LYS cc_start: 0.8316 (ttpt) cc_final: 0.7797 (tttt)
REVERT: D   93 VAL cc_start: 0.9117 (OUTLIER) cc_final: 0.8878 (t)
  outliers start: 9
  outliers final: 4
  residues processed: 37
  average time/residue: 0.3829
  time to fit residues: 14.8439
Evaluate side-chains
  38 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 41 optimal weight:    0.0970
   chunk 37 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0970
   chunk 21 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 23 optimal weight:    0.1980
   overall best weight:    0.3776

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

Flipped N/Q/H residues before XYZ refinement:
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.132401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.112400 restraints weight = 4106.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 2.24
r_work: 0.3626 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3502 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3730  Z= 0.104
  Angle     :  0.560   5.723   5075  Z= 0.300
  Chirality :  0.051   0.135    595
  Planarity :  0.005   0.044    630
  Dihedral  :  5.286  17.014    505
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 13.85 %
    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: -2.46 (0.36), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 104 
 TYR   0.014   0.001   TYR A 114 
 PHE   0.008   0.001   PHE A  95 
 TRP   0.002   0.000   TRP A  79 
 HIS   0.002   0.000   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 3730)
  covalent geometry    : angle       0.56002 ( 5075)
  hydrogen bonds       : bond        0.01687 (   86)
  hydrogen bonds       : angle       4.59519 (  258)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.091 
Fit side-chains
REVERT: D   63 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7773 (pt0)
REVERT: D   70 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7650 (tttt)
  outliers start: 6
  outliers final: 3
  residues processed: 36
  average time/residue: 0.4782
  time to fit residues: 17.7903
Evaluate side-chains
  36 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue  117 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 20 optimal weight:    6.9990
   chunk 2 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.128038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.107209 restraints weight = 4128.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 2.20
r_work: 0.3531 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.3421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3730  Z= 0.173
  Angle     :  0.609   6.214   5075  Z= 0.327
  Chirality :  0.053   0.141    595
  Planarity :  0.005   0.042    630
  Dihedral  :  5.547  18.503    505
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.33 %
    Favored  : 84.87 %
  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: -2.40 (0.36), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 104 
 TYR   0.016   0.002   TYR C 114 
 PHE   0.013   0.002   PHE E  87 
 TRP   0.002   0.000   TRP A  79 
 HIS   0.002   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 3730)
  covalent geometry    : angle       0.60902 ( 5075)
  hydrogen bonds       : bond        0.02062 (   86)
  hydrogen bonds       : angle       4.62668 (  258)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1008.76 seconds
wall clock time: 17 minutes 56.72 seconds (1076.72 seconds total)