Starting phenix.real_space_refine
on Tue Feb 11 21:17:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tat_10427/02_2025/6tat_10427.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tat_10427/02_2025/6tat_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6tat_10427/02_2025/6tat_10427.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tat_10427/02_2025/6tat_10427.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tat_10427/02_2025/6tat_10427.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tat_10427/02_2025/6tat_10427.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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:
    C, B, E, D
  Time building chain proxies: 2.84, per 1000 atoms: 0.42
  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: 1.81
  Conformation dependent library (CDL) restraints added in 996.8 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: 0.58
  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: 1.46

  Time building geometry restraints manager: 1.95 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     16.260
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.720
-------------------------------------------------------------------------------
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      :  0.005   0.039   6940  Z= 0.301
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.008   0.001   TRP A  85 
 HIS   0.002   0.001   HIS A 173 
 PHE   0.009   0.001   PHE B 178 
 TYR   0.029   0.002   TYR A 126 
 ARG   0.003   0.000   ARG D 172 

*********************** 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  : 0.812 
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: 0.7156 (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: 0.7689 (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: 0.3366
  time to fit residues: 77.4976
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  : 0.792 
-------------------------------------------------------------------------------
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 67 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0060
   chunk 62 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0970
   chunk 72 optimal weight:    0.0010
   overall best weight:    0.7802

-------------------------------------------------------------------------------
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 = 0.3425 r_free = 0.3425 target = 0.118601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.105708 restraints weight = 10845.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.108721 restraints weight = 5892.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.110964 restraints weight = 3749.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6940  Z= 0.186
  Angle     :  0.535   8.643   9345  Z= 0.281
  Chirality :  0.039   0.146    990
  Planarity :  0.006   0.054   1205
  Dihedral  :  4.281  18.324    919
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 12.16 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.26), residues: 810
  helix: -0.79 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -2.41 (0.27), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  85 
 HIS   0.003   0.001   HIS B 173 
 PHE   0.015   0.001   PHE E 120 
 TYR   0.020   0.002   TYR B 166 
 ARG   0.035   0.002   ARG A 190 

*********************** 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
  147 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 140
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
REVERT: B   49 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8094 (m-30)
REVERT: B   64 ILE cc_start: 0.8606 (mm) cc_final: 0.8398 (mt)
REVERT: B  175 VAL cc_start: 0.8847 (t) cc_final: 0.8581 (p)
REVERT: B  192 ARG cc_start: 0.6970 (ttt180) cc_final: 0.6720 (ttt180)
REVERT: C   49 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7705 (m-30)
REVERT: C   64 ILE cc_start: 0.8634 (mm) cc_final: 0.8246 (mt)
REVERT: C   88 VAL cc_start: 0.8761 (t) cc_final: 0.8544 (m)
REVERT: C   93 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8786 (mmmm)
REVERT: C  104 ASP cc_start: 0.8340 (t70) cc_final: 0.7914 (t0)
REVERT: C  126 TYR cc_start: 0.5896 (p90) cc_final: 0.5685 (p90)
REVERT: C  168 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8305 (mt-10)
REVERT: D   49 ASP cc_start: 0.8031 (t0) cc_final: 0.7643 (m-30)
REVERT: D   64 ILE cc_start: 0.8629 (mm) cc_final: 0.8286 (mt)
REVERT: D  104 ASP cc_start: 0.8422 (t70) cc_final: 0.8088 (t0)
REVERT: D  118 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.8001 (tm-30)
REVERT: D  159 TYR cc_start: 0.8126 (t80) cc_final: 0.7815 (t80)
REVERT: E   64 ILE cc_start: 0.8640 (mm) cc_final: 0.8194 (mt)
REVERT: E   88 VAL cc_start: 0.8691 (t) cc_final: 0.8447 (m)
REVERT: E  117 MET cc_start: 0.7994 (tpp) cc_final: 0.7702 (mmm)
REVERT: E  127 ASP cc_start: 0.8252 (m-30) cc_final: 0.7987 (m-30)
  outliers start: 7
  outliers final: 2
  residues processed: 142
  average time/residue: 0.2816
  time to fit residues: 49.0818
Evaluate side-chains
  136 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 131
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
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 D residue  118 GLU
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 48 optimal weight:    8.9990
   chunk 62 optimal weight:    7.9990
   chunk 57 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 64 optimal weight:   10.0000
   chunk 30 optimal weight:    0.4980
   chunk 16 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0670
   chunk 26 optimal weight:    0.9990
   overall best weight:    1.1124

-------------------------------------------------------------------------------
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 = 0.3401 r_free = 0.3401 target = 0.116918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.104475 restraints weight = 10922.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.107387 restraints weight = 6164.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.109413 restraints weight = 3960.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6940  Z= 0.202
  Angle     :  0.516   8.197   9345  Z= 0.266
  Chirality :  0.039   0.131    990
  Planarity :  0.006   0.054   1205
  Dihedral  :  3.674  12.690    915
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.92 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.29), residues: 810
  helix:  0.33 (0.25), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.89 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E  95 
 HIS   0.005   0.001   HIS E 173 
 PHE   0.013   0.001   PHE E 120 
 TYR   0.016   0.001   TYR B 166 
 ARG   0.031   0.001   ARG A 190 

*********************** 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
  146 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 ILE cc_start: 0.8060 (mt) cc_final: 0.7856 (mm)
REVERT: B   49 ASP cc_start: 0.8310 (t0) cc_final: 0.8104 (m-30)
REVERT: B   64 ILE cc_start: 0.8705 (mm) cc_final: 0.8467 (mt)
REVERT: B  192 ARG cc_start: 0.6936 (ttt180) cc_final: 0.6717 (ttt180)
REVERT: C   49 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7734 (m-30)
REVERT: C   64 ILE cc_start: 0.8710 (mm) cc_final: 0.8245 (mt)
REVERT: C   93 LYS cc_start: 0.9083 (mmmt) cc_final: 0.8843 (mmmm)
REVERT: C  104 ASP cc_start: 0.8360 (t70) cc_final: 0.8026 (t0)
REVERT: D   49 ASP cc_start: 0.8047 (t0) cc_final: 0.7676 (m-30)
REVERT: D   64 ILE cc_start: 0.8729 (mm) cc_final: 0.8367 (mt)
REVERT: D  159 TYR cc_start: 0.8274 (t80) cc_final: 0.7817 (t80)
REVERT: D  173 HIS cc_start: 0.8159 (OUTLIER) cc_final: 0.7825 (p-80)
REVERT: E   64 ILE cc_start: 0.8721 (mm) cc_final: 0.8238 (mt)
REVERT: E   88 VAL cc_start: 0.8757 (t) cc_final: 0.8526 (m)
REVERT: E  117 MET cc_start: 0.7967 (tpp) cc_final: 0.7732 (tpp)
REVERT: E  127 ASP cc_start: 0.8240 (m-30) cc_final: 0.8029 (m-30)
REVERT: E  173 HIS cc_start: 0.8316 (OUTLIER) cc_final: 0.7968 (p-80)
  outliers start: 13
  outliers final: 5
  residues processed: 142
  average time/residue: 0.2803
  time to fit residues: 48.4950
Evaluate side-chains
  135 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 127
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  141 LEU
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain E residue  109 THR
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  173 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 63 optimal weight:    6.9990
   chunk 33 optimal weight:    8.9990
   chunk 34 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 49 optimal weight:    8.9990
   overall best weight:    2.5186

-------------------------------------------------------------------------------
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 = 0.3325 r_free = 0.3325 target = 0.111843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.099196 restraints weight = 11256.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.102007 restraints weight = 6466.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.103976 restraints weight = 4238.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   6940  Z= 0.340
  Angle     :  0.605   8.052   9345  Z= 0.309
  Chirality :  0.043   0.147    990
  Planarity :  0.006   0.051   1205
  Dihedral  :  4.002  16.089    915
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 18.38 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.30), residues: 810
  helix:  0.68 (0.26), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.59 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  95 
 HIS   0.006   0.002   HIS C 173 
 PHE   0.021   0.002   PHE E 120 
 TYR   0.017   0.002   TYR B 166 
 ARG   0.025   0.001   ARG A 190 

*********************** 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
  160 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 0.848 
Fit side-chains
REVERT: A  115 ILE cc_start: 0.8227 (mt) cc_final: 0.8024 (mm)
REVERT: B   49 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.8073 (m-30)
REVERT: B   64 ILE cc_start: 0.8805 (mm) cc_final: 0.8551 (mt)
REVERT: B  168 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8461 (mt-10)
REVERT: B  192 ARG cc_start: 0.7100 (ttt180) cc_final: 0.6814 (ttt180)
REVERT: C   49 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7714 (m-30)
REVERT: C   64 ILE cc_start: 0.8790 (mm) cc_final: 0.8185 (mt)
REVERT: C   93 LYS cc_start: 0.9133 (mmmt) cc_final: 0.8904 (mmmm)
REVERT: C  104 ASP cc_start: 0.8376 (t70) cc_final: 0.8088 (t0)
REVERT: D  159 TYR cc_start: 0.8328 (t80) cc_final: 0.7703 (t80)
REVERT: D  173 HIS cc_start: 0.8434 (OUTLIER) cc_final: 0.8108 (p-80)
REVERT: D  174 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7716 (tm-30)
REVERT: E   64 ILE cc_start: 0.8781 (mm) cc_final: 0.8319 (mt)
REVERT: E   88 VAL cc_start: 0.8994 (t) cc_final: 0.8718 (m)
REVERT: E  117 MET cc_start: 0.8067 (tpp) cc_final: 0.7820 (tpp)
REVERT: E  173 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.8061 (p-80)
  outliers start: 21
  outliers final: 11
  residues processed: 152
  average time/residue: 0.2712
  time to fit residues: 50.6482
Evaluate side-chains
  148 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
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  141 LEU
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain E residue  109 THR
Chi-restraints excluded: chain E residue  141 LEU
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 7 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0670
   chunk 17 optimal weight:    8.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.7922

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.119863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.107179 restraints weight = 10831.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.110226 restraints weight = 6006.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.112345 restraints weight = 3844.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6940  Z= 0.176
  Angle     :  0.508   8.344   9345  Z= 0.260
  Chirality :  0.039   0.137    990
  Planarity :  0.006   0.054   1205
  Dihedral  :  3.750  15.716    915
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.46 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.31), residues: 810
  helix:  0.89 (0.26), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.49 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E  84 
 HIS   0.008   0.001   HIS C 173 
 PHE   0.006   0.001   PHE D 120 
 TYR   0.013   0.001   TYR B 166 
 ARG   0.026   0.001   ARG C 190 

*********************** 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
  150 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.750 
Fit side-chains
REVERT: B   49 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.8050 (m-30)
REVERT: B   64 ILE cc_start: 0.8739 (mm) cc_final: 0.8478 (mt)
REVERT: B  192 ARG cc_start: 0.7379 (ttt180) cc_final: 0.7094 (ttt180)
REVERT: C   49 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7724 (m-30)
REVERT: C   64 ILE cc_start: 0.8701 (mm) cc_final: 0.8109 (mt)
REVERT: C   93 LYS cc_start: 0.9114 (mmmt) cc_final: 0.8888 (mmmm)
REVERT: C  104 ASP cc_start: 0.8358 (t70) cc_final: 0.8076 (t0)
REVERT: C  189 GLU cc_start: 0.7572 (tp30) cc_final: 0.7345 (tp30)
REVERT: D   64 ILE cc_start: 0.8686 (mm) cc_final: 0.8281 (mt)
REVERT: D  104 ASP cc_start: 0.8476 (t70) cc_final: 0.8259 (t0)
REVERT: D  159 TYR cc_start: 0.8280 (t80) cc_final: 0.7808 (t80)
REVERT: D  173 HIS cc_start: 0.8332 (OUTLIER) cc_final: 0.7963 (p-80)
REVERT: E   64 ILE cc_start: 0.8723 (mm) cc_final: 0.8241 (mt)
REVERT: E   88 VAL cc_start: 0.8892 (t) cc_final: 0.8570 (m)
REVERT: E  117 MET cc_start: 0.8025 (tpp) cc_final: 0.7776 (tpp)
REVERT: E  173 HIS cc_start: 0.8262 (OUTLIER) cc_final: 0.7958 (p-80)
  outliers start: 17
  outliers final: 8
  residues processed: 145
  average time/residue: 0.2672
  time to fit residues: 47.8307
Evaluate side-chains
  140 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
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 C residue   37 VAL
Chi-restraints excluded: chain C residue   49 ASP
Chi-restraints excluded: chain D residue  105 HIS
Chi-restraints excluded: chain D residue  141 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0000
   chunk 5 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0020
   chunk 42 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    1.1998

-------------------------------------------------------------------------------
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 = 0.3382 r_free = 0.3382 target = 0.115523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.102487 restraints weight = 11030.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.105564 restraints weight = 6085.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.107694 restraints weight = 3851.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.2948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6940  Z= 0.207
  Angle     :  0.521   8.148   9345  Z= 0.266
  Chirality :  0.039   0.138    990
  Planarity :  0.006   0.055   1205
  Dihedral  :  3.693  16.578    915
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.00 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.31), residues: 810
  helix:  0.99 (0.26), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.28 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E  84 
 HIS   0.008   0.001   HIS B 173 
 PHE   0.009   0.001   PHE E 120 
 TYR   0.018   0.002   TYR B 166 
 ARG   0.024   0.001   ARG D 190 

*********************** 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: 23
    poor density    : 129
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
REVERT: B   49 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.8031 (m-30)
REVERT: B   64 ILE cc_start: 0.8679 (mm) cc_final: 0.8402 (mt)
REVERT: B  124 GLN cc_start: 0.7935 (tt0) cc_final: 0.7494 (pt0)
REVERT: B  192 ARG cc_start: 0.7406 (ttt180) cc_final: 0.7093 (ttt180)
REVERT: C   49 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7693 (m-30)
REVERT: C   64 ILE cc_start: 0.8696 (mm) cc_final: 0.8094 (mt)
REVERT: C   93 LYS cc_start: 0.9149 (mmmt) cc_final: 0.8928 (mmmm)
REVERT: C  104 ASP cc_start: 0.8368 (t70) cc_final: 0.8154 (t0)
REVERT: D  104 ASP cc_start: 0.8540 (t70) cc_final: 0.8317 (t0)
REVERT: D  159 TYR cc_start: 0.8323 (t80) cc_final: 0.7842 (t80)
REVERT: D  173 HIS cc_start: 0.8343 (OUTLIER) cc_final: 0.7936 (p-80)
REVERT: E   64 ILE cc_start: 0.8705 (mm) cc_final: 0.8246 (mt)
REVERT: E   88 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8555 (m)
REVERT: E  117 MET cc_start: 0.7986 (tpp) cc_final: 0.7704 (tpp)
REVERT: E  173 HIS cc_start: 0.8345 (OUTLIER) cc_final: 0.8027 (p-80)
  outliers start: 23
  outliers final: 12
  residues processed: 144
  average time/residue: 0.2737
  time to fit residues: 48.2660
Evaluate side-chains
  143 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
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  141 LEU
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  105 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0570
   chunk 71 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   overall best weight:    1.2900

-------------------------------------------------------------------------------
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 = 0.3436 r_free = 0.3436 target = 0.118437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.105715 restraints weight = 10864.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.108733 restraints weight = 6008.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.110835 restraints weight = 3833.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.3013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6940  Z= 0.211
  Angle     :  0.522   7.937   9345  Z= 0.267
  Chirality :  0.040   0.164    990
  Planarity :  0.005   0.051   1205
  Dihedral  :  3.719  19.096    915
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 21.35 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.31), residues: 810
  helix:  1.03 (0.26), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.17 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E  84 
 HIS   0.008   0.001   HIS B 173 
 PHE   0.009   0.001   PHE E 120 
 TYR   0.021   0.002   TYR B 166 
 ARG   0.023   0.001   ARG A 190 

*********************** 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
  151 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 0.812 
Fit side-chains
REVERT: B   49 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.8037 (m-30)
REVERT: B   64 ILE cc_start: 0.8693 (mm) cc_final: 0.8405 (mt)
REVERT: B  124 GLN cc_start: 0.7879 (tt0) cc_final: 0.7499 (pt0)
REVERT: B  192 ARG cc_start: 0.7569 (ttt180) cc_final: 0.7249 (ttt180)
REVERT: C   49 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7724 (m-30)
REVERT: C   64 ILE cc_start: 0.8697 (mm) cc_final: 0.8085 (mt)
REVERT: C   67 LYS cc_start: 0.8747 (tmtt) cc_final: 0.8318 (tttm)
REVERT: C   93 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8891 (mmmm)
REVERT: C  104 ASP cc_start: 0.8362 (t70) cc_final: 0.8153 (t0)
REVERT: C  189 GLU cc_start: 0.7562 (tp30) cc_final: 0.7346 (tp30)
REVERT: D  104 ASP cc_start: 0.8539 (t70) cc_final: 0.8335 (t0)
REVERT: D  159 TYR cc_start: 0.8330 (t80) cc_final: 0.7889 (t80)
REVERT: D  173 HIS cc_start: 0.8331 (OUTLIER) cc_final: 0.7962 (p-80)
REVERT: E   64 ILE cc_start: 0.8730 (mm) cc_final: 0.8245 (mt)
REVERT: E   88 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8588 (m)
REVERT: E  117 MET cc_start: 0.7988 (tpp) cc_final: 0.7702 (tpp)
REVERT: E  173 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.7992 (p-80)
  outliers start: 21
  outliers final: 14
  residues processed: 144
  average time/residue: 0.2657
  time to fit residues: 47.2339
Evaluate side-chains
  147 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
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 C residue  105 HIS
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  141 LEU
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 33 optimal weight:    8.9990
   chunk 42 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 = 0.3404 r_free = 0.3404 target = 0.115884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.103435 restraints weight = 11076.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.106365 restraints weight = 6204.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.108366 restraints weight = 3991.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.3106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6940  Z= 0.302
  Angle     :  0.584   7.931   9345  Z= 0.297
  Chirality :  0.042   0.149    990
  Planarity :  0.005   0.049   1205
  Dihedral  :  3.966  20.525    915
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 20.95 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.32), residues: 810
  helix:  1.02 (0.26), residues: 455
  sheet:  None (None), residues: 0
  loop : -1.05 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  84 
 HIS   0.008   0.002   HIS A 173 
 PHE   0.015   0.001   PHE E 120 
 TYR   0.020   0.002   TYR B 166 
 ARG   0.022   0.001   ARG A 190 

*********************** 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
  159 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.835 
Fit side-chains
REVERT: A  115 ILE cc_start: 0.8172 (mt) cc_final: 0.7966 (mm)
REVERT: B   49 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.8034 (m-30)
REVERT: B   64 ILE cc_start: 0.8733 (mm) cc_final: 0.8455 (mt)
REVERT: B  124 GLN cc_start: 0.7894 (tt0) cc_final: 0.7425 (pt0)
REVERT: B  184 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.7260 (mtm-85)
REVERT: C   38 ARG cc_start: 0.6869 (mtt180) cc_final: 0.6550 (mtt180)
REVERT: C   49 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7677 (m-30)
REVERT: C   64 ILE cc_start: 0.8755 (mm) cc_final: 0.8114 (mt)
REVERT: C   67 LYS cc_start: 0.8794 (tmtt) cc_final: 0.8392 (tttm)
REVERT: C   93 LYS cc_start: 0.9134 (mmmt) cc_final: 0.8898 (mmmm)
REVERT: C  104 ASP cc_start: 0.8362 (t70) cc_final: 0.8139 (t0)
REVERT: D   64 ILE cc_start: 0.8633 (mm) cc_final: 0.8350 (mm)
REVERT: D  104 ASP cc_start: 0.8577 (t70) cc_final: 0.8365 (t0)
REVERT: D  155 LEU cc_start: 0.8005 (tt) cc_final: 0.7757 (tp)
REVERT: D  159 TYR cc_start: 0.8364 (t80) cc_final: 0.7910 (t80)
REVERT: D  173 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.8073 (p-80)
REVERT: E   64 ILE cc_start: 0.8769 (mm) cc_final: 0.8289 (mt)
REVERT: E   88 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8721 (m)
REVERT: E  173 HIS cc_start: 0.8396 (OUTLIER) cc_final: 0.8117 (p-80)
  outliers start: 25
  outliers final: 17
  residues processed: 150
  average time/residue: 0.2694
  time to fit residues: 49.7682
Evaluate side-chains
  154 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
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   94 THR
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  107 SER
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 C residue  109 THR
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  141 LEU
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 56 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 33 optimal weight:    8.9990
   chunk 63 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3390 r_free = 0.3390 target = 0.116297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.103227 restraints weight = 11062.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.106236 restraints weight = 6109.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.108362 restraints weight = 3879.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6940  Z= 0.190
  Angle     :  0.531   8.155   9345  Z= 0.270
  Chirality :  0.039   0.135    990
  Planarity :  0.005   0.053   1205
  Dihedral  :  3.794  19.638    915
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 22.03 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.32), residues: 810
  helix:  1.13 (0.26), residues: 455
  sheet:  None (None), residues: 0
  loop : -1.05 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  84 
 HIS   0.008   0.001   HIS A 173 
 PHE   0.008   0.001   PHE E 120 
 TYR   0.017   0.002   TYR B 166 
 ARG   0.023   0.001   ARG A 190 

*********************** 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
  144 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.886 
Fit side-chains
REVERT: B   49 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7994 (m-30)
REVERT: B   64 ILE cc_start: 0.8709 (mm) cc_final: 0.8461 (mt)
REVERT: B  124 GLN cc_start: 0.7880 (tt0) cc_final: 0.7480 (pt0)
REVERT: C   49 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7384 (m-30)
REVERT: C   52 ILE cc_start: 0.8373 (mm) cc_final: 0.7957 (tp)
REVERT: C   56 GLU cc_start: 0.8355 (tp30) cc_final: 0.8152 (mm-30)
REVERT: C   64 ILE cc_start: 0.8665 (mm) cc_final: 0.8031 (mt)
REVERT: C   67 LYS cc_start: 0.8758 (tmtt) cc_final: 0.8339 (tttm)
REVERT: C   93 LYS cc_start: 0.9154 (mmmt) cc_final: 0.8909 (mmmm)
REVERT: C  104 ASP cc_start: 0.8385 (t70) cc_final: 0.8138 (t0)
REVERT: D  104 ASP cc_start: 0.8582 (t70) cc_final: 0.8377 (t0)
REVERT: D  159 TYR cc_start: 0.8338 (t80) cc_final: 0.7908 (t80)
REVERT: D  173 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.7991 (p-80)
REVERT: E   64 ILE cc_start: 0.8702 (mm) cc_final: 0.8223 (mt)
REVERT: E   88 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8568 (m)
REVERT: E  117 MET cc_start: 0.8035 (tpp) cc_final: 0.7604 (mmm)
REVERT: E  173 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7973 (p-80)
REVERT: E  184 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7925 (ttm170)
  outliers start: 18
  outliers final: 12
  residues processed: 138
  average time/residue: 0.2652
  time to fit residues: 45.3397
Evaluate side-chains
  143 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
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  105 HIS
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   49 ASP
Chi-restraints excluded: chain C residue  105 HIS
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  141 LEU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 39 optimal weight:    0.2980
   chunk 71 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0000
   chunk 17 optimal weight:    9.9990
   chunk 40 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   overall best weight:    0.7386

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

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

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 = 0.117496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.104301 restraints weight = 11283.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.107401 restraints weight = 6198.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.109547 restraints weight = 3931.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.3245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6940  Z= 0.173
  Angle     :  0.527   8.612   9345  Z= 0.264
  Chirality :  0.039   0.134    990
  Planarity :  0.005   0.056   1205
  Dihedral  :  3.581  17.770    915
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 22.16 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.32), residues: 810
  helix:  1.23 (0.26), residues: 455
  sheet:  None (None), residues: 0
  loop : -0.99 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  84 
 HIS   0.008   0.001   HIS A 173 
 PHE   0.006   0.001   PHE A 106 
 TYR   0.017   0.001   TYR D 166 
 ARG   0.022   0.001   ARG D 190 

********************** 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
  143 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A  130 ILE cc_start: 0.6118 (OUTLIER) cc_final: 0.5861 (tt)
REVERT: B   49 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7992 (m-30)
REVERT: B   64 ILE cc_start: 0.8632 (mm) cc_final: 0.8348 (mt)
REVERT: B  124 GLN cc_start: 0.7922 (tt0) cc_final: 0.7558 (pt0)
REVERT: B  161 LEU cc_start: 0.8349 (mp) cc_final: 0.8095 (mp)
REVERT: C   49 ASP cc_start: 0.7860 (t0) cc_final: 0.7358 (m-30)
REVERT: C   52 ILE cc_start: 0.8323 (mm) cc_final: 0.7892 (tp)
REVERT: C   56 GLU cc_start: 0.8354 (tp30) cc_final: 0.8127 (mm-30)
REVERT: C   64 ILE cc_start: 0.8626 (mm) cc_final: 0.7978 (mt)
REVERT: C   93 LYS cc_start: 0.9160 (mmmt) cc_final: 0.8906 (mmmm)
REVERT: C  104 ASP cc_start: 0.8385 (t70) cc_final: 0.8135 (t0)
REVERT: D  104 ASP cc_start: 0.8583 (t70) cc_final: 0.8380 (t0)
REVERT: D  159 TYR cc_start: 0.8322 (t80) cc_final: 0.7918 (t80)
REVERT: D  173 HIS cc_start: 0.8223 (OUTLIER) cc_final: 0.7907 (p-80)
REVERT: E   64 ILE cc_start: 0.8725 (mm) cc_final: 0.8232 (mt)
REVERT: E   88 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8538 (m)
REVERT: E  104 ASP cc_start: 0.8270 (t70) cc_final: 0.8006 (t0)
REVERT: E  117 MET cc_start: 0.7985 (tpp) cc_final: 0.7697 (tpp)
REVERT: E  173 HIS cc_start: 0.8252 (OUTLIER) cc_final: 0.7994 (p-80)
REVERT: E  184 ARG cc_start: 0.8102 (ttm110) cc_final: 0.7880 (ttm170)
  outliers start: 17
  outliers final: 11
  residues processed: 138
  average time/residue: 0.2659
  time to fit residues: 45.1886
Evaluate side-chains
  142 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain B residue   49 ASP
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue  105 HIS
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  141 LEU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 49 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 71 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0470
   chunk 20 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.8682

-------------------------------------------------------------------------------
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 = 0.3408 r_free = 0.3408 target = 0.117493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.104331 restraints weight = 11148.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.107421 restraints weight = 6121.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.109569 restraints weight = 3879.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6940  Z= 0.179
  Angle     :  0.524   7.845   9345  Z= 0.262
  Chirality :  0.039   0.135    990
  Planarity :  0.006   0.057   1205
  Dihedral  :  3.524  16.823    915
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 22.70 %
    Favored  : 75.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.32), residues: 810
  helix:  1.21 (0.26), residues: 460
  sheet:  None (None), residues: 0
  loop : -0.84 (0.37), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  84 
 HIS   0.008   0.001   HIS A 173 
 PHE   0.006   0.001   PHE E 120 
 TYR   0.017   0.001   TYR D 166 
 ARG   0.021   0.001   ARG D 190 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2007.00 seconds
wall clock time: 36 minutes 57.77 seconds (2217.77 seconds total)