Starting phenix.real_space_refine
on Tue Mar  3 15:34:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tat_10427/03_2026/6tat_10427.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tat_10427/03_2026/6tat_10427.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tat_10427/03_2026/6tat_10427.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tat_10427/03_2026/6tat_10427.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6tat_10427/03_2026/6tat_10427.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tat_10427/03_2026/6tat_10427.map"
  }
  resolution = 3.7
  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=   0.002 sd=   0.014
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      20      5.16       5
     C    4310      2.51       5
     N    1190      2.21       5
     O    1270      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 115 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6790
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1358
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 6, 'TRANS': 157}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 0.93, per 1000 atoms: 0.14
  Number of scatterers: 6790
  At special positions: 0
  Unit cell: (116.592, 112.428, 62.46, 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      20     16.00
     O    1270      8.00
     N    1190      7.00
     C    4310      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=10, symmetry=0
  Number of additional bonds: simple=10, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 345.8 milliseconds
  

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1560

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 0 sheets defined
      68.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 63
      removed outlier: 3.642A  pdb=" N   VAL A  48 " --> pdb=" O   ASP A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 70
      removed outlier: 3.877A  pdb=" N   LEU A  70 " --> pdb=" O   ASP A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 76
    Processing helix  chain 'A' and resid 79 through 86
      removed outlier: 4.079A  pdb=" N   VAL A  83 " --> pdb=" O   SER A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 92
      removed outlier: 3.734A  pdb=" N   ASP A  91 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ALA A  92 " --> pdb=" O   ARG A  89 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 88 through 92'
    Processing helix  chain 'A' and resid 94 through 107
      removed outlier: 3.762A  pdb=" N   PHE A 106 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 120
      removed outlier: 3.786A  pdb=" N   ILE A 115 " --> pdb=" O   PRO A 111 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   PHE A 120 " --> pdb=" O   TYR A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 142
      removed outlier: 3.750A  pdb=" N   PHE A 133 " --> pdb=" O   VAL A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 159
      removed outlier: 3.529A  pdb=" N   ILE A 158 " --> pdb=" O   GLU A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 168
      removed outlier: 3.652A  pdb=" N   GLU A 168 " --> pdb=" O   PRO A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 192
      removed outlier: 4.153A  pdb=" N   LEU A 181 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   LEU A 182 " --> pdb=" O   PHE A 178 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   THR A 187 " --> pdb=" O   ASP A 183 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL A 188 " --> pdb=" O   ARG A 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 63
      removed outlier: 3.642A  pdb=" N   VAL B  48 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 70
      removed outlier: 3.877A  pdb=" N   LEU B  70 " --> pdb=" O   ASP B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 76
    Processing helix  chain 'B' and resid 79 through 86
      removed outlier: 4.079A  pdb=" N   VAL B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 92
      removed outlier: 3.733A  pdb=" N   ASP B  91 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA B  92 " --> pdb=" O   ARG B  89 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 88 through 92'
    Processing helix  chain 'B' and resid 94 through 107
      removed outlier: 3.761A  pdb=" N   PHE B 106 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 120
      removed outlier: 3.786A  pdb=" N   ILE B 115 " --> pdb=" O   PRO B 111 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   PHE B 120 " --> pdb=" O   TYR B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 142
      removed outlier: 3.750A  pdb=" N   PHE B 133 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 159
      removed outlier: 3.529A  pdb=" N   ILE B 158 " --> pdb=" O   GLU B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 163 through 168
      removed outlier: 3.652A  pdb=" N   GLU B 168 " --> pdb=" O   PRO B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 192
      removed outlier: 4.154A  pdb=" N   LEU B 181 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   LEU B 182 " --> pdb=" O   PHE B 178 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   THR B 187 " --> pdb=" O   ASP B 183 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL B 188 " --> pdb=" O   ARG B 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 63
      removed outlier: 3.642A  pdb=" N   VAL C  48 " --> pdb=" O   ASP C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 65 through 70
      removed outlier: 3.876A  pdb=" N   LEU C  70 " --> pdb=" O   ASP C  66 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 76
    Processing helix  chain 'C' and resid 79 through 86
      removed outlier: 4.079A  pdb=" N   VAL C  83 " --> pdb=" O   SER C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 88 through 92
      removed outlier: 3.733A  pdb=" N   ASP C  91 " --> pdb=" O   VAL C  88 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA C  92 " --> pdb=" O   ARG C  89 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 88 through 92'
    Processing helix  chain 'C' and resid 94 through 107
      removed outlier: 3.761A  pdb=" N   PHE C 106 " --> pdb=" O   LEU C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 120
      removed outlier: 3.787A  pdb=" N   ILE C 115 " --> pdb=" O   PRO C 111 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   PHE C 120 " --> pdb=" O   TYR C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 142
      removed outlier: 3.750A  pdb=" N   PHE C 133 " --> pdb=" O   VAL C 129 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 151 through 159
      removed outlier: 3.530A  pdb=" N   ILE C 158 " --> pdb=" O   GLU C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 163 through 168
      removed outlier: 3.652A  pdb=" N   GLU C 168 " --> pdb=" O   PRO C 164 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 192
      removed outlier: 4.154A  pdb=" N   LEU C 181 " --> pdb=" O   THR C 177 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   LEU C 182 " --> pdb=" O   PHE C 178 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   THR C 187 " --> pdb=" O   ASP C 183 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL C 188 " --> pdb=" O   ARG C 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 44 through 63
      removed outlier: 3.642A  pdb=" N   VAL D  48 " --> pdb=" O   ASP D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 65 through 70
      removed outlier: 3.877A  pdb=" N   LEU D  70 " --> pdb=" O   ASP D  66 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 72 through 76
    Processing helix  chain 'D' and resid 79 through 86
      removed outlier: 4.079A  pdb=" N   VAL D  83 " --> pdb=" O   SER D  79 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 88 through 92
      removed outlier: 3.733A  pdb=" N   ASP D  91 " --> pdb=" O   VAL D  88 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA D  92 " --> pdb=" O   ARG D  89 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 88 through 92'
    Processing helix  chain 'D' and resid 94 through 107
      removed outlier: 3.761A  pdb=" N   PHE D 106 " --> pdb=" O   LEU D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 120
      removed outlier: 3.787A  pdb=" N   ILE D 115 " --> pdb=" O   PRO D 111 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   PHE D 120 " --> pdb=" O   TYR D 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 142
      removed outlier: 3.749A  pdb=" N   PHE D 133 " --> pdb=" O   VAL D 129 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 151 through 159
      removed outlier: 3.530A  pdb=" N   ILE D 158 " --> pdb=" O   GLU D 154 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 163 through 168
      removed outlier: 3.652A  pdb=" N   GLU D 168 " --> pdb=" O   PRO D 164 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 177 through 192
      removed outlier: 4.153A  pdb=" N   LEU D 181 " --> pdb=" O   THR D 177 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   LEU D 182 " --> pdb=" O   PHE D 178 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   THR D 187 " --> pdb=" O   ASP D 183 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL D 188 " --> pdb=" O   ARG D 184 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 63
      removed outlier: 3.643A  pdb=" N   VAL E  48 " --> pdb=" O   ASP E  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 65 through 70
      removed outlier: 3.876A  pdb=" N   LEU E  70 " --> pdb=" O   ASP E  66 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 72 through 76
    Processing helix  chain 'E' and resid 79 through 86
      removed outlier: 4.079A  pdb=" N   VAL E  83 " --> pdb=" O   SER E  79 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 88 through 92
      removed outlier: 3.733A  pdb=" N   ASP E  91 " --> pdb=" O   VAL E  88 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA E  92 " --> pdb=" O   ARG E  89 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 88 through 92'
    Processing helix  chain 'E' and resid 94 through 107
      removed outlier: 3.761A  pdb=" N   PHE E 106 " --> pdb=" O   LEU E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 111 through 120
      removed outlier: 3.786A  pdb=" N   ILE E 115 " --> pdb=" O   PRO E 111 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   PHE E 120 " --> pdb=" O   TYR E 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 129 through 142
      removed outlier: 3.749A  pdb=" N   PHE E 133 " --> pdb=" O   VAL E 129 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 151 through 159
      removed outlier: 3.530A  pdb=" N   ILE E 158 " --> pdb=" O   GLU E 154 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 163 through 168
      removed outlier: 3.652A  pdb=" N   GLU E 168 " --> pdb=" O   PRO E 164 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 177 through 192
      removed outlier: 4.153A  pdb=" N   LEU E 181 " --> pdb=" O   THR E 177 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   LEU E 182 " --> pdb=" O   PHE E 178 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   THR E 187 " --> pdb=" O   ASP E 183 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL E 188 " --> pdb=" O   ARG E 184 " (cutoff:3.500A)

    280 hydrogen bonds defined for protein.
    810 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: 0.75

  Time building geometry restraints manager: 0.66 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: 2230
        1.34 -     1.46: 987
        1.46 -     1.57: 3693
        1.57 -     1.68: 0
        1.68 -     1.80: 30
  Bond restraints: 6940
  Sorted by residual:
  bond pdb=" N   GLU D  56 "
       pdb=" CA  GLU D  56 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.25e-02 6.40e+03 5.54e+00
  bond pdb=" N   GLU E  56 "
       pdb=" CA  GLU E  56 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.25e-02 6.40e+03 5.49e+00
  bond pdb=" N   THR A  57 "
       pdb=" CA  THR A  57 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.46e+00
  bond pdb=" N   GLU C  56 "
       pdb=" CA  GLU C  56 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.25e-02 6.40e+03 5.40e+00
  bond pdb=" N   THR E  57 "
       pdb=" CA  THR E  57 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.40e+00
  ... (remaining 6935 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 8376
        1.40 -     2.80: 829
        2.80 -     4.20: 100
        4.20 -     5.60: 10
        5.60 -     7.00: 30
  Bond angle restraints: 9345
  Sorted by residual:
  angle pdb=" CA  THR E 109 "
        pdb=" CB  THR E 109 "
        pdb=" CG2 THR E 109 "
      ideal   model   delta    sigma   weight residual
     110.50  117.50   -7.00 1.70e+00 3.46e-01 1.70e+01
  angle pdb=" CA  THR A 109 "
        pdb=" CB  THR A 109 "
        pdb=" CG2 THR A 109 "
      ideal   model   delta    sigma   weight residual
     110.50  117.49   -6.99 1.70e+00 3.46e-01 1.69e+01
  angle pdb=" CA  THR B 109 "
        pdb=" CB  THR B 109 "
        pdb=" CG2 THR B 109 "
      ideal   model   delta    sigma   weight residual
     110.50  117.48   -6.98 1.70e+00 3.46e-01 1.69e+01
  angle pdb=" CA  THR D 109 "
        pdb=" CB  THR D 109 "
        pdb=" CG2 THR D 109 "
      ideal   model   delta    sigma   weight residual
     110.50  117.46   -6.96 1.70e+00 3.46e-01 1.68e+01
  angle pdb=" CA  THR C 109 "
        pdb=" CB  THR C 109 "
        pdb=" CG2 THR C 109 "
      ideal   model   delta    sigma   weight residual
     110.50  117.44   -6.94 1.70e+00 3.46e-01 1.67e+01
  ... (remaining 9340 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 3705
       17.96 -    35.92: 405
       35.92 -    53.88: 80
       53.88 -    71.84: 10
       71.84 -    89.80: 10
  Dihedral angle restraints: 4210
    sinusoidal: 1805
      harmonic: 2405
  Sorted by residual:
  dihedral pdb=" C   THR A 109 "
           pdb=" N   THR A 109 "
           pdb=" CA  THR A 109 "
           pdb=" CB  THR A 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.55    8.55     0      2.50e+00 1.60e-01 1.17e+01
  dihedral pdb=" CA  LYS C  78 "
           pdb=" C   LYS C  78 "
           pdb=" N   SER C  79 "
           pdb=" CA  SER C  79 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.96  -17.04     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  LYS D  78 "
           pdb=" C   LYS D  78 "
           pdb=" N   SER D  79 "
           pdb=" CA  SER D  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.98  -17.02     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 4207 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 740
       0.048 -    0.095: 184
       0.095 -    0.143: 46
       0.143 -    0.190: 10
       0.190 -    0.238: 10
  Chirality restraints: 990
  Sorted by residual:
  chirality pdb=" CA  THR A 109 "
            pdb=" N   THR A 109 "
            pdb=" C   THR A 109 "
            pdb=" CB  THR A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.29    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CB  THR A 109 "
            pdb=" CA  THR A 109 "
            pdb=" OG1 THR A 109 "
            pdb=" CG2 THR A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CA  THR D 109 "
            pdb=" N   THR D 109 "
            pdb=" C   THR D 109 "
            pdb=" CB  THR D 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.29    0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 987 not shown)

  Planarity restraints: 1205
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN E 163 "    0.047 5.00e-02 4.00e+02   7.13e-02 8.13e+00
        pdb=" N   PRO E 164 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO E 164 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO E 164 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 163 "    0.047 5.00e-02 4.00e+02   7.13e-02 8.12e+00
        pdb=" N   PRO A 164 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO A 164 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 164 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C 163 "   -0.047 5.00e-02 4.00e+02   7.12e-02 8.12e+00
        pdb=" N   PRO C 164 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO C 164 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO C 164 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1202 not shown)

  Histogram of nonbonded interaction distances:
        0.72 -     1.56: 20
        1.56 -     2.39: 70
        2.39 -     3.23: 5927
        3.23 -     4.06: 14324
        4.06 -     4.90: 25022
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 45363
  Sorted by model distance:
  nonbonded pdb=" N   PRO A 111 "
            pdb=" CZ  ARG B 190 "
     model   vdw
     0.722 2.680
  nonbonded pdb=" CZ  ARG A 190 "
            pdb=" N   PRO E 111 "
     model   vdw
     0.722 2.680
  nonbonded pdb=" N   PRO B 111 "
            pdb=" CZ  ARG C 190 "
     model   vdw
     0.723 2.680
  nonbonded pdb=" N   PRO C 111 "
            pdb=" CZ  ARG D 190 "
     model   vdw
     0.723 2.680
  nonbonded pdb=" N   PRO D 111 "
            pdb=" CZ  ARG E 190 "
     model   vdw
     0.723 2.680
  ... (remaining 45358 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: 0.02
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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.260
  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:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.280
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
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      :  0.025   0.868   6950  Z= 2.491
  Angle     :  0.913   7.000   9345  Z= 0.557
  Chirality :  0.051   0.238    990
  Planarity :  0.008   0.071   1205
  Dihedral  : 15.557  89.801   2650
  Min Nonbonded Distance : 0.722

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  7.57 %
    Favored  : 91.76 %
  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: -4.23 (0.20), residues: 810
  helix: -2.87 (0.16), residues: 425
  sheet:  None (None), residues: 0
  loop : -2.67 (0.24), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 172 
 TYR   0.029   0.002   TYR A 126 
 PHE   0.009   0.001   PHE B 178 
 TRP   0.008   0.001   TRP A  85 
 HIS   0.002   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 6940)
  covalent geometry    : angle       0.91337 ( 9345)
  hydrogen bonds       : bond        0.18333 (  280)
  hydrogen bonds       : angle       6.46865 (  810)
  Misc. bond           : bond        0.65340 (   10)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 190
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A   88 VAL cc_start: 0.8863 (t) cc_final: 0.8652 (t)
REVERT: B   64 ILE cc_start: 0.8539 (mm) cc_final: 0.8332 (mt)
REVERT: B  148 ARG cc_start: 0.8476 (ttt180) cc_final: 0.8254 (tpp80)
REVERT: B  175 VAL cc_start: 0.8795 (t) cc_final: 0.8549 (p)
REVERT: B  192 ARG cc_start: 0.7155 (ttt180) cc_final: 0.6830 (ttt180)
REVERT: C   64 ILE cc_start: 0.8696 (mm) cc_final: 0.8399 (mt)
REVERT: C   88 VAL cc_start: 0.8715 (t) cc_final: 0.8425 (m)
REVERT: C   93 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8758 (mmmm)
REVERT: D   64 ILE cc_start: 0.8594 (mm) cc_final: 0.8369 (mt)
REVERT: D  148 ARG cc_start: 0.8141 (ttt180) cc_final: 0.7807 (mtp180)
REVERT: D  159 TYR cc_start: 0.8035 (t80) cc_final: 0.7690 (t80)
REVERT: E   64 ILE cc_start: 0.8562 (mm) cc_final: 0.8133 (mt)
  outliers start: 5
  outliers final: 4
  residues processed: 195
  average time/residue: 0.1410
  time to fit residues: 32.3451
Evaluate side-chains
  139 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 135
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain C residue   57 THR
Chi-restraints excluded: chain D residue   57 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 105 HIS
B 105 HIS
C 105 HIS
D 105 HIS
E 105 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.117394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.105284 restraints weight = 10969.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.108170 restraints weight = 6156.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.110194 restraints weight = 3928.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.111601 restraints weight = 2713.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.112680 restraints weight = 1996.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6950  Z= 0.141
  Angle     :  0.545   8.717   9345  Z= 0.287
  Chirality :  0.040   0.143    990
  Planarity :  0.006   0.054   1205
  Dihedral  :  4.283  17.887    919
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 12.43 %
    Favored  : 86.62 %
  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: -2.21 (0.26), residues: 810
  helix: -0.76 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -2.39 (0.27), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.030   0.001   ARG A 190 
 TYR   0.021   0.002   TYR A 166 
 PHE   0.017   0.001   PHE E 120 
 TRP   0.005   0.001   TRP E  95 
 HIS   0.003   0.001   HIS B 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6940)
  covalent geometry    : angle       0.54456 ( 9345)
  hydrogen bonds       : bond        0.03831 (  280)
  hydrogen bonds       : angle       3.75436 (  810)
  Misc. bond           : bond        0.00256 (   10)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 144
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: B   49 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8116 (m-30)
REVERT: B   64 ILE cc_start: 0.8651 (mm) cc_final: 0.8409 (mt)
REVERT: B  175 VAL cc_start: 0.8896 (t) cc_final: 0.8629 (p)
REVERT: B  192 ARG cc_start: 0.6931 (ttt180) cc_final: 0.6686 (ttt180)
REVERT: C   49 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7726 (m-30)
REVERT: C   64 ILE cc_start: 0.8658 (mm) cc_final: 0.8232 (mt)
REVERT: C   88 VAL cc_start: 0.8748 (t) cc_final: 0.8547 (m)
REVERT: C   93 LYS cc_start: 0.9039 (mmmt) cc_final: 0.8820 (mmmm)
REVERT: C  104 ASP cc_start: 0.8359 (t70) cc_final: 0.7926 (t0)
REVERT: C  168 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8329 (mt-10)
REVERT: D   49 ASP cc_start: 0.8039 (t0) cc_final: 0.7664 (m-30)
REVERT: D   64 ILE cc_start: 0.8677 (mm) cc_final: 0.8303 (mt)
REVERT: D  104 ASP cc_start: 0.8428 (t70) cc_final: 0.8095 (t0)
REVERT: D  159 TYR cc_start: 0.8153 (t80) cc_final: 0.7803 (t80)
REVERT: E   64 ILE cc_start: 0.8670 (mm) cc_final: 0.8204 (mt)
REVERT: E   88 VAL cc_start: 0.8706 (t) cc_final: 0.8484 (m)
REVERT: E  127 ASP cc_start: 0.8151 (m-30) cc_final: 0.7932 (m-30)
  outliers start: 7
  outliers final: 2
  residues processed: 146
  average time/residue: 0.1190
  time to fit residues: 21.1549
Evaluate side-chains
  138 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 134
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ASP
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   49 ASP
Chi-restraints excluded: chain E residue  141 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 32 optimal weight:    7.9990
   chunk 37 optimal weight:    0.8980
   chunk 68 optimal weight:    4.9990
   chunk 55 optimal weight:    0.4980
   chunk 75 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 63 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
D  45 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.116512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.104105 restraints weight = 10947.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.106971 restraints weight = 6174.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.109004 restraints weight = 3973.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.110493 restraints weight = 2778.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.111519 restraints weight = 2054.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6950  Z= 0.136
  Angle     :  0.521   8.150   9345  Z= 0.268
  Chirality :  0.039   0.131    990
  Planarity :  0.006   0.054   1205
  Dihedral  :  3.733  13.055    915
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 14.46 %
    Favored  : 83.78 %
  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: -0.97 (0.29), residues: 810
  helix:  0.31 (0.25), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.91 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.031   0.001   ARG A 190 
 TYR   0.015   0.002   TYR B 166 
 PHE   0.013   0.001   PHE E 120 
 TRP   0.003   0.001   TRP E  95 
 HIS   0.005   0.001   HIS D 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6940)
  covalent geometry    : angle       0.52057 ( 9345)
  hydrogen bonds       : bond        0.03557 (  280)
  hydrogen bonds       : angle       3.39570 (  810)
  Misc. bond           : bond        0.00266 (   10)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 135
  time to evaluate  : 0.272 
Fit side-chains
REVERT: B   49 ASP cc_start: 0.8305 (t0) cc_final: 0.8097 (m-30)
REVERT: B   64 ILE cc_start: 0.8700 (mm) cc_final: 0.8472 (mt)
REVERT: B  192 ARG cc_start: 0.6944 (ttt180) cc_final: 0.6721 (ttt180)
REVERT: C   49 ASP cc_start: 0.7946 (t0) cc_final: 0.7714 (m-30)
REVERT: C   64 ILE cc_start: 0.8716 (mm) cc_final: 0.8210 (mt)
REVERT: C   93 LYS cc_start: 0.9075 (mmmt) cc_final: 0.8843 (mmmm)
REVERT: C  104 ASP cc_start: 0.8355 (t70) cc_final: 0.8049 (t0)
REVERT: D   49 ASP cc_start: 0.8026 (t0) cc_final: 0.7655 (m-30)
REVERT: D   64 ILE cc_start: 0.8711 (mm) cc_final: 0.8364 (mt)
REVERT: D  118 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7702 (tm-30)
REVERT: D  159 TYR cc_start: 0.8263 (t80) cc_final: 0.7784 (t80)
REVERT: D  173 HIS cc_start: 0.8182 (OUTLIER) cc_final: 0.7833 (p-80)
REVERT: E   64 ILE cc_start: 0.8717 (mm) cc_final: 0.8233 (mt)
REVERT: E   88 VAL cc_start: 0.8750 (t) cc_final: 0.8525 (m)
REVERT: E  127 ASP cc_start: 0.8247 (m-30) cc_final: 0.8043 (m-30)
REVERT: E  173 HIS cc_start: 0.8271 (OUTLIER) cc_final: 0.7930 (p-80)
  outliers start: 13
  outliers final: 5
  residues processed: 143
  average time/residue: 0.1206
  time to fit residues: 21.1498
Evaluate side-chains
  138 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  109 THR
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  173 HIS
Chi-restraints excluded: chain E residue  179 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 36 optimal weight:    0.2980
   chunk 14 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0000
   chunk 28 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.0588

-------------------------------------------------------------------------------
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 = 0.3397 r_free = 0.3397 target = 0.116503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.103213 restraints weight = 11071.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.106377 restraints weight = 6040.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.108578 restraints weight = 3809.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.110108 restraints weight = 2629.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.111269 restraints weight = 1938.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6950  Z= 0.126
  Angle     :  0.506   8.402   9345  Z= 0.259
  Chirality :  0.039   0.142    990
  Planarity :  0.006   0.052   1205
  Dihedral  :  3.671  16.952    915
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.43 %
    Favored  : 80.41 %
  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: -0.44 (0.30), residues: 810
  helix:  0.75 (0.26), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.68 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.026   0.001   ARG C 190 
 TYR   0.017   0.002   TYR A 166 
 PHE   0.010   0.001   PHE E 120 
 TRP   0.003   0.001   TRP E  84 
 HIS   0.006   0.001   HIS C 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6940)
  covalent geometry    : angle       0.50588 ( 9345)
  hydrogen bonds       : bond        0.03162 (  280)
  hydrogen bonds       : angle       3.29068 (  810)
  Misc. bond           : bond        0.00226 (   10)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 0.314 
Fit side-chains
REVERT: B   49 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.8055 (m-30)
REVERT: B   64 ILE cc_start: 0.8683 (mm) cc_final: 0.8451 (mt)
REVERT: B  192 ARG cc_start: 0.6954 (ttt180) cc_final: 0.6696 (ttt180)
REVERT: C   49 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7626 (m-30)
REVERT: C   64 ILE cc_start: 0.8708 (mm) cc_final: 0.8178 (mt)
REVERT: C   93 LYS cc_start: 0.9117 (mmmt) cc_final: 0.8891 (mmmm)
REVERT: C  104 ASP cc_start: 0.8355 (t70) cc_final: 0.8038 (t0)
REVERT: C  168 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8348 (mt-10)
REVERT: D   64 ILE cc_start: 0.8663 (mm) cc_final: 0.8297 (mt)
REVERT: D  159 TYR cc_start: 0.8284 (t80) cc_final: 0.7848 (t80)
REVERT: D  173 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7832 (p-80)
REVERT: E   64 ILE cc_start: 0.8665 (mm) cc_final: 0.8222 (mt)
REVERT: E   88 VAL cc_start: 0.8840 (t) cc_final: 0.8513 (m)
REVERT: E  173 HIS cc_start: 0.8257 (OUTLIER) cc_final: 0.7902 (p-80)
  outliers start: 16
  outliers final: 7
  residues processed: 143
  average time/residue: 0.1259
  time to fit residues: 22.1263
Evaluate side-chains
  143 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain B residue   49 ASP
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   49 ASP
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  109 THR
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  173 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    0.1980
   chunk 3 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.6388

-------------------------------------------------------------------------------
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 = 0.3358 r_free = 0.3358 target = 0.113990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.100690 restraints weight = 11215.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.103786 restraints weight = 6151.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.105972 restraints weight = 3902.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.107464 restraints weight = 2703.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.108623 restraints weight = 2000.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6950  Z= 0.158
  Angle     :  0.538   7.908   9345  Z= 0.275
  Chirality :  0.040   0.139    990
  Planarity :  0.005   0.051   1205
  Dihedral  :  3.745  16.918    915
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 18.11 %
    Favored  : 79.19 %
  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: -0.14 (0.31), residues: 810
  helix:  0.93 (0.26), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.45 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.025   0.001   ARG A 190 
 TYR   0.016   0.002   TYR B 166 
 PHE   0.013   0.001   PHE E 120 
 TRP   0.004   0.001   TRP E  84 
 HIS   0.008   0.002   HIS B 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 6940)
  covalent geometry    : angle       0.53755 ( 9345)
  hydrogen bonds       : bond        0.03904 (  280)
  hydrogen bonds       : angle       3.31726 (  810)
  Misc. bond           : bond        0.00194 (   10)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.316 
Fit side-chains
REVERT: B   49 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.8065 (m-30)
REVERT: B   64 ILE cc_start: 0.8660 (mm) cc_final: 0.8393 (mt)
REVERT: B  174 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7274 (tm-30)
REVERT: B  192 ARG cc_start: 0.7155 (ttt180) cc_final: 0.6933 (ttt180)
REVERT: C   49 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7649 (m-30)
REVERT: C   64 ILE cc_start: 0.8702 (mm) cc_final: 0.8132 (mt)
REVERT: C   67 LYS cc_start: 0.8796 (tmtt) cc_final: 0.8390 (tttm)
REVERT: C   93 LYS cc_start: 0.9139 (mmmt) cc_final: 0.8892 (mmmm)
REVERT: C  104 ASP cc_start: 0.8361 (t70) cc_final: 0.8086 (t0)
REVERT: D  159 TYR cc_start: 0.8320 (t80) cc_final: 0.7776 (t80)
REVERT: D  173 HIS cc_start: 0.8333 (OUTLIER) cc_final: 0.8022 (p-80)
REVERT: D  174 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7319 (tm-30)
REVERT: E   64 ILE cc_start: 0.8692 (mm) cc_final: 0.8254 (mt)
REVERT: E   88 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8641 (m)
REVERT: E  173 HIS cc_start: 0.8318 (OUTLIER) cc_final: 0.8001 (p-80)
  outliers start: 20
  outliers final: 10
  residues processed: 145
  average time/residue: 0.1240
  time to fit residues: 22.1616
Evaluate side-chains
  143 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain B residue   49 ASP
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   49 ASP
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  109 THR
Chi-restraints excluded: chain D residue   49 ASP
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  173 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0980
   chunk 43 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
E 105 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.117405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.104655 restraints weight = 11138.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.107669 restraints weight = 6192.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.109776 restraints weight = 3943.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.111263 restraints weight = 2729.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.112347 restraints weight = 2005.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6950  Z= 0.117
  Angle     :  0.509   8.303   9345  Z= 0.260
  Chirality :  0.039   0.151    990
  Planarity :  0.005   0.052   1205
  Dihedral  :  3.647  17.791    915
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.73 %
    Favored  : 77.84 %
  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:  0.00 (0.31), residues: 810
  helix:  1.03 (0.26), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.35 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.001   ARG D 190 
 TYR   0.015   0.001   TYR D 166 
 PHE   0.006   0.001   PHE E 120 
 TRP   0.004   0.001   TRP E  84 
 HIS   0.008   0.001   HIS B 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6940)
  covalent geometry    : angle       0.50879 ( 9345)
  hydrogen bonds       : bond        0.02728 (  280)
  hydrogen bonds       : angle       3.21968 (  810)
  Misc. bond           : bond        0.00228 (   10)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: B   49 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.8033 (m-30)
REVERT: B   64 ILE cc_start: 0.8615 (mm) cc_final: 0.8333 (mt)
REVERT: B  124 GLN cc_start: 0.7953 (tt0) cc_final: 0.7549 (pt0)
REVERT: B  192 ARG cc_start: 0.7226 (ttt180) cc_final: 0.6955 (ttt180)
REVERT: C   49 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7398 (m-30)
REVERT: C   52 ILE cc_start: 0.8429 (mm) cc_final: 0.7994 (tp)
REVERT: C   56 GLU cc_start: 0.8281 (tp30) cc_final: 0.8069 (tp30)
REVERT: C   64 ILE cc_start: 0.8656 (mm) cc_final: 0.8086 (mt)
REVERT: C   93 LYS cc_start: 0.9132 (mmmt) cc_final: 0.8891 (mmmm)
REVERT: C  104 ASP cc_start: 0.8372 (t70) cc_final: 0.8108 (t0)
REVERT: D   64 ILE cc_start: 0.8628 (mm) cc_final: 0.8230 (mt)
REVERT: D  159 TYR cc_start: 0.8288 (t80) cc_final: 0.7819 (t80)
REVERT: D  173 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7805 (p-80)
REVERT: E   64 ILE cc_start: 0.8661 (mm) cc_final: 0.8199 (mt)
REVERT: E   88 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8528 (m)
REVERT: E  173 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7871 (p-80)
  outliers start: 18
  outliers final: 8
  residues processed: 144
  average time/residue: 0.1204
  time to fit residues: 21.3230
Evaluate side-chains
  141 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain B residue   49 ASP
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   49 ASP
Chi-restraints excluded: chain C residue  109 THR
Chi-restraints excluded: chain D residue   49 ASP
Chi-restraints excluded: chain D residue  105 HIS
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  109 THR
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  173 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0010
   chunk 8 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 46 optimal weight:   10.0000
   chunk 9 optimal weight:    0.0370
   chunk 64 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   overall best weight:    0.9066

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

Flipped N/Q/H residues before XYZ refinement:
C 105 HIS
E 105 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.117389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.104696 restraints weight = 11016.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.107678 restraints weight = 6162.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.109718 restraints weight = 3943.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.111198 restraints weight = 2737.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.112279 restraints weight = 2020.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6950  Z= 0.119
  Angle     :  0.512   7.816   9345  Z= 0.261
  Chirality :  0.039   0.136    990
  Planarity :  0.006   0.060   1205
  Dihedral  :  3.569  18.198    915
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 20.95 %
    Favored  : 76.62 %
  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:  0.21 (0.31), residues: 810
  helix:  1.17 (0.26), residues: 455
  sheet:  None (None), residues: 0
  loop : -1.25 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG C 190 
 TYR   0.016   0.001   TYR B 166 
 PHE   0.008   0.001   PHE D 120 
 TRP   0.004   0.001   TRP E  84 
 HIS   0.007   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6940)
  covalent geometry    : angle       0.51189 ( 9345)
  hydrogen bonds       : bond        0.02920 (  280)
  hydrogen bonds       : angle       3.18211 (  810)
  Misc. bond           : bond        0.00207 (   10)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.208 
Fit side-chains
REVERT: B   49 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.8043 (m-30)
REVERT: B   64 ILE cc_start: 0.8627 (mm) cc_final: 0.8344 (mt)
REVERT: B  124 GLN cc_start: 0.7939 (tt0) cc_final: 0.7585 (pt0)
REVERT: B  174 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7313 (tm-30)
REVERT: C   49 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7649 (m-30)
REVERT: C   64 ILE cc_start: 0.8664 (mm) cc_final: 0.8090 (mt)
REVERT: C   67 LYS cc_start: 0.8725 (tmtt) cc_final: 0.8299 (tttm)
REVERT: C   93 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8923 (mmmm)
REVERT: C  104 ASP cc_start: 0.8376 (t70) cc_final: 0.8142 (t0)
REVERT: D  173 HIS cc_start: 0.8195 (OUTLIER) cc_final: 0.7872 (p-80)
REVERT: E   64 ILE cc_start: 0.8678 (mm) cc_final: 0.8196 (mt)
REVERT: E   88 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8535 (m)
REVERT: E  173 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.7909 (p-80)
  outliers start: 18
  outliers final: 10
  residues processed: 142
  average time/residue: 0.1077
  time to fit residues: 19.0275
Evaluate side-chains
  140 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain B residue   49 ASP
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   49 ASP
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain D residue   49 ASP
Chi-restraints excluded: chain D residue  105 HIS
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  173 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 38 optimal weight:    7.9990
   chunk 40 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 74 optimal weight:    2.9990
   chunk 78 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
E 105 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.113852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.100607 restraints weight = 11222.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.103660 restraints weight = 6209.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.105765 restraints weight = 3959.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.107334 restraints weight = 2754.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.108434 restraints weight = 2030.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6950  Z= 0.167
  Angle     :  0.560   7.921   9345  Z= 0.285
  Chirality :  0.042   0.211    990
  Planarity :  0.006   0.066   1205
  Dihedral  :  3.796  18.609    915
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.54 %
    Favored  : 76.49 %
  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:  0.26 (0.32), residues: 810
  helix:  1.12 (0.26), residues: 455
  sheet:  None (None), residues: 0
  loop : -1.08 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG D 190 
 TYR   0.019   0.002   TYR C 166 
 PHE   0.012   0.001   PHE E 120 
 TRP   0.004   0.001   TRP E  84 
 HIS   0.008   0.002   HIS C 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 6940)
  covalent geometry    : angle       0.55989 ( 9345)
  hydrogen bonds       : bond        0.04031 (  280)
  hydrogen bonds       : angle       3.27842 (  810)
  Misc. bond           : bond        0.00158 (   10)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.260 
Fit side-chains
REVERT: B   49 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.8027 (m-30)
REVERT: B   64 ILE cc_start: 0.8660 (mm) cc_final: 0.8395 (mt)
REVERT: B  124 GLN cc_start: 0.7991 (tt0) cc_final: 0.7595 (pt0)
REVERT: B  184 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.7845 (ttp-110)
REVERT: B  192 ARG cc_start: 0.7530 (ttt180) cc_final: 0.7226 (ttt180)
REVERT: C   49 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7624 (m-30)
REVERT: C   56 GLU cc_start: 0.8194 (tp30) cc_final: 0.7979 (tp30)
REVERT: C   64 ILE cc_start: 0.8695 (mm) cc_final: 0.8071 (mt)
REVERT: C   67 LYS cc_start: 0.8766 (tmtt) cc_final: 0.8360 (tttm)
REVERT: C   93 LYS cc_start: 0.9146 (mmmt) cc_final: 0.8895 (mmmm)
REVERT: C  104 ASP cc_start: 0.8390 (t70) cc_final: 0.8131 (t0)
REVERT: D  159 TYR cc_start: 0.8370 (t80) cc_final: 0.7949 (t80)
REVERT: D  173 HIS cc_start: 0.8324 (OUTLIER) cc_final: 0.8048 (p-80)
REVERT: E   64 ILE cc_start: 0.8701 (mm) cc_final: 0.8259 (mt)
REVERT: E   88 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8670 (m)
REVERT: E  104 ASP cc_start: 0.8244 (t70) cc_final: 0.7863 (t0)
REVERT: E  173 HIS cc_start: 0.8266 (OUTLIER) cc_final: 0.8019 (p-80)
  outliers start: 22
  outliers final: 11
  residues processed: 144
  average time/residue: 0.1209
  time to fit residues: 21.3388
Evaluate side-chains
  147 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain B residue   49 ASP
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   49 ASP
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   49 ASP
Chi-restraints excluded: chain D residue  105 HIS
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  173 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 22 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
E 105 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.116154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.103732 restraints weight = 11232.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.106608 restraints weight = 6312.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.108656 restraints weight = 4077.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.110067 restraints weight = 2864.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.111145 restraints weight = 2145.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   6950  Z= 0.204
  Angle     :  0.595   7.740   9345  Z= 0.303
  Chirality :  0.043   0.136    990
  Planarity :  0.005   0.049   1205
  Dihedral  :  4.035  19.534    915
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.81 %
    Favored  : 76.22 %
  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:  0.23 (0.32), residues: 810
  helix:  1.02 (0.26), residues: 455
  sheet:  None (None), residues: 0
  loop : -0.97 (0.37), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A 190 
 TYR   0.022   0.002   TYR C 166 
 PHE   0.015   0.001   PHE E 120 
 TRP   0.007   0.001   TRP E  84 
 HIS   0.008   0.002   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 6940)
  covalent geometry    : angle       0.59480 ( 9345)
  hydrogen bonds       : bond        0.04581 (  280)
  hydrogen bonds       : angle       3.40437 (  810)
  Misc. bond           : bond        0.00132 (   10)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  104 ASP cc_start: 0.8339 (t70) cc_final: 0.8100 (t0)
REVERT: B   49 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.8035 (m-30)
REVERT: B   64 ILE cc_start: 0.8714 (mm) cc_final: 0.8436 (mt)
REVERT: B   90 ARG cc_start: 0.7979 (mtm110) cc_final: 0.7652 (mtt90)
REVERT: B  117 MET cc_start: 0.7463 (tpp) cc_final: 0.7005 (tpp)
REVERT: B  124 GLN cc_start: 0.7896 (tt0) cc_final: 0.7509 (pt0)
REVERT: B  174 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7164 (tm-30)
REVERT: C   38 ARG cc_start: 0.6896 (mtt180) cc_final: 0.6607 (mtt180)
REVERT: C   49 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7679 (m-30)
REVERT: C   56 GLU cc_start: 0.8150 (tp30) cc_final: 0.7882 (tp30)
REVERT: C   64 ILE cc_start: 0.8739 (mm) cc_final: 0.8088 (mt)
REVERT: C   67 LYS cc_start: 0.8797 (tmtt) cc_final: 0.8398 (tttm)
REVERT: C   93 LYS cc_start: 0.9123 (mmmt) cc_final: 0.8899 (mmmm)
REVERT: C  104 ASP cc_start: 0.8368 (t70) cc_final: 0.8164 (t0)
REVERT: C  166 TYR cc_start: 0.8004 (m-80) cc_final: 0.7659 (m-10)
REVERT: D  173 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.8127 (p-80)
REVERT: E   64 ILE cc_start: 0.8749 (mm) cc_final: 0.8273 (mt)
REVERT: E   88 VAL cc_start: 0.9013 (OUTLIER) cc_final: 0.8732 (m)
REVERT: E  104 ASP cc_start: 0.8239 (t70) cc_final: 0.7836 (t0)
REVERT: E  173 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.8020 (p-80)
REVERT: E  184 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7335 (mtm110)
  outliers start: 22
  outliers final: 14
  residues processed: 148
  average time/residue: 0.1230
  time to fit residues: 22.1701
Evaluate side-chains
  156 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain B residue   49 ASP
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   49 ASP
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  105 HIS
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   49 ASP
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  105 HIS
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  109 THR
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  173 HIS
Chi-restraints excluded: chain E residue  184 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0030
   chunk 41 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.6390

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

Flipped N/Q/H residues before XYZ refinement:
E 105 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.118020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.105232 restraints weight = 11040.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.108222 restraints weight = 6198.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.110320 restraints weight = 3957.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.111797 restraints weight = 2756.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.112857 restraints weight = 2036.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6950  Z= 0.116
  Angle     :  0.527   8.161   9345  Z= 0.269
  Chirality :  0.039   0.186    990
  Planarity :  0.006   0.079   1205
  Dihedral  :  3.755  17.203    915
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 21.76 %
    Favored  : 76.35 %
  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:  0.40 (0.32), residues: 810
  helix:  1.19 (0.26), residues: 455
  sheet:  None (None), residues: 0
  loop : -0.94 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG B 190 
 TYR   0.017   0.001   TYR D 166 
 PHE   0.006   0.001   PHE D 120 
 TRP   0.006   0.001   TRP E  84 
 HIS   0.008   0.001   HIS C 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6940)
  covalent geometry    : angle       0.52654 ( 9345)
  hydrogen bonds       : bond        0.02488 (  280)
  hydrogen bonds       : angle       3.25943 (  810)
  Misc. bond           : bond        0.00225 (   10)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  104 ASP cc_start: 0.8382 (t70) cc_final: 0.8145 (t0)
REVERT: B   49 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.8019 (m-30)
REVERT: B   64 ILE cc_start: 0.8606 (mm) cc_final: 0.8329 (mt)
REVERT: B   90 ARG cc_start: 0.8014 (mtm110) cc_final: 0.7695 (mtt90)
REVERT: B  124 GLN cc_start: 0.7925 (tt0) cc_final: 0.7553 (pt0)
REVERT: B  184 ARG cc_start: 0.8439 (ttm110) cc_final: 0.8237 (ttp-110)
REVERT: C   49 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7356 (m-30)
REVERT: C   52 ILE cc_start: 0.8344 (mm) cc_final: 0.7996 (tp)
REVERT: C   56 GLU cc_start: 0.8208 (tp30) cc_final: 0.7962 (tp30)
REVERT: C   64 ILE cc_start: 0.8608 (mm) cc_final: 0.7975 (mt)
REVERT: C   67 LYS cc_start: 0.8748 (tmtt) cc_final: 0.8334 (tttm)
REVERT: C   93 LYS cc_start: 0.9129 (mmmt) cc_final: 0.8887 (mmmm)
REVERT: C  104 ASP cc_start: 0.8415 (t70) cc_final: 0.8203 (t0)
REVERT: D  159 TYR cc_start: 0.8351 (t80) cc_final: 0.8025 (t80)
REVERT: D  173 HIS cc_start: 0.8331 (OUTLIER) cc_final: 0.8035 (p-80)
REVERT: E   64 ILE cc_start: 0.8659 (mm) cc_final: 0.8176 (mt)
REVERT: E   88 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8537 (m)
REVERT: E  104 ASP cc_start: 0.8328 (t70) cc_final: 0.8033 (t0)
REVERT: E  173 HIS cc_start: 0.8249 (OUTLIER) cc_final: 0.7951 (p-80)
  outliers start: 14
  outliers final: 7
  residues processed: 140
  average time/residue: 0.1281
  time to fit residues: 21.8319
Evaluate side-chains
  135 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain B residue   49 ASP
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   49 ASP
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   49 ASP
Chi-restraints excluded: chain D residue  105 HIS
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  109 THR
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  173 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0970
   chunk 34 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 75 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 24 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
E 105 HIS
E 124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.118315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.105529 restraints weight = 11114.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.108541 restraints weight = 6241.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.110628 restraints weight = 3998.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.112123 restraints weight = 2775.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.113189 restraints weight = 2041.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
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      :  0.003   0.031   6950  Z= 0.110
  Angle     :  0.519   9.169   9345  Z= 0.261
  Chirality :  0.038   0.133    990
  Planarity :  0.006   0.082   1205
  Dihedral  :  3.521  15.237    915
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 22.30 %
    Favored  : 75.95 %
  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:  0.54 (0.32), residues: 810
  helix:  1.30 (0.26), residues: 455
  sheet:  None (None), residues: 0
  loop : -0.88 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG D 190 
 TYR   0.017   0.001   TYR D 166 
 PHE   0.006   0.001   PHE A 106 
 TRP   0.005   0.001   TRP D  84 
 HIS   0.009   0.001   HIS B 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6940)
  covalent geometry    : angle       0.51885 ( 9345)
  hydrogen bonds       : bond        0.02649 (  280)
  hydrogen bonds       : angle       3.18072 (  810)
  Misc. bond           : bond        0.00210 (   10)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1081.93 seconds
wall clock time: 19 minutes 22.53 seconds (1162.53 seconds total)