Starting phenix.real_space_refine
on Tue Mar 11 20:47:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tat_10427/03_2025/6tat_10427.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tat_10427/03_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_10427/03_2025/6tat_10427.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tat_10427/03_2025/6tat_10427.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tat_10427/03_2025/6tat_10427.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tat_10427/03_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 2.88, 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: 1.73
  Conformation dependent library (CDL) restraints added in 954.2 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: 0.78
  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: 1.44

  Time building geometry restraints manager: 2.04 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: 0.06
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:             0.230
  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:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     17.570
  Find NCS groups from input model:        0.140
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.310
-------------------------------------------------------------------------------
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  : 0.834 
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: 0.3330
  time to fit residues: 76.5225
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  : 0.831 
-------------------------------------------------------------------------------
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 = 0.3424 r_free = 0.3424 target = 0.118501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.106354 restraints weight = 10871.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.109292 restraints weight = 6105.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.111320 restraints weight = 3876.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
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   8.644   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  : 0.749 
Fit side-chains
   revert: symmetry clash
REVERT: B   49 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8111 (m-30)
REVERT: B   64 ILE cc_start: 0.8633 (mm) cc_final: 0.8401 (mt)
REVERT: B  175 VAL cc_start: 0.8882 (t) cc_final: 0.8603 (p)
REVERT: B  192 ARG cc_start: 0.6933 (ttt180) cc_final: 0.6691 (ttt180)
REVERT: C   49 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7748 (m-30)
REVERT: C   64 ILE cc_start: 0.8655 (mm) cc_final: 0.8247 (mt)
REVERT: C   88 VAL cc_start: 0.8751 (t) cc_final: 0.8535 (m)
REVERT: C   93 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8774 (mmmm)
REVERT: C  104 ASP cc_start: 0.8324 (t70) cc_final: 0.7907 (t0)
REVERT: C  168 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8317 (mt-10)
REVERT: D   49 ASP cc_start: 0.8054 (t0) cc_final: 0.7677 (m-30)
REVERT: D   64 ILE cc_start: 0.8667 (mm) cc_final: 0.8297 (mt)
REVERT: D  104 ASP cc_start: 0.8391 (t70) cc_final: 0.8063 (t0)
REVERT: D  159 TYR cc_start: 0.8112 (t80) cc_final: 0.7806 (t80)
REVERT: E   64 ILE cc_start: 0.8665 (mm) cc_final: 0.8194 (mt)
REVERT: E   88 VAL cc_start: 0.8694 (t) cc_final: 0.8461 (m)
REVERT: E  117 MET cc_start: 0.8011 (tpp) cc_final: 0.7735 (mmm)
REVERT: E  127 ASP cc_start: 0.8219 (m-30) cc_final: 0.7970 (m-30)
  outliers start: 7
  outliers final: 2
  residues processed: 142
  average time/residue: 0.2760
  time to fit residues: 47.8195
Evaluate side-chains
  136 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 132
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ASP
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   49 ASP
Chi-restraints excluded: chain E residue  141 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 62 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 64 optimal weight:    8.9990
   chunk 30 optimal weight:    0.4980
   chunk 16 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   overall best weight:    1.4584

-------------------------------------------------------------------------------
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 = 0.3380 r_free = 0.3380 target = 0.115452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.102903 restraints weight = 10963.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.105780 restraints weight = 6212.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.107821 restraints weight = 4013.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6940  Z= 0.232
  Angle     :  0.534   8.174   9345  Z= 0.276
  Chirality :  0.040   0.133    990
  Planarity :  0.006   0.052   1205
  Dihedral  :  3.793  13.571    915
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.65 %
    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: -0.99 (0.29), residues: 810
  helix:  0.28 (0.25), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.90 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  84 
 HIS   0.005   0.001   HIS D 173 
 PHE   0.016   0.001   PHE E 120 
 TYR   0.016   0.002   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
  150 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.829 
Fit side-chains
REVERT: B   49 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8096 (m-30)
REVERT: B   64 ILE cc_start: 0.8735 (mm) cc_final: 0.8463 (mt)
REVERT: B  192 ARG cc_start: 0.6987 (ttt180) cc_final: 0.6765 (ttt180)
REVERT: C   49 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7738 (m-30)
REVERT: C   64 ILE cc_start: 0.8759 (mm) cc_final: 0.8278 (mt)
REVERT: C   93 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8856 (mmmm)
REVERT: C  104 ASP cc_start: 0.8361 (t70) cc_final: 0.8035 (t0)
REVERT: D   49 ASP cc_start: 0.8049 (t0) cc_final: 0.7689 (m-30)
REVERT: D   64 ILE cc_start: 0.8751 (mm) cc_final: 0.8388 (mt)
REVERT: D  104 ASP cc_start: 0.8501 (t70) cc_final: 0.8297 (t0)
REVERT: D  159 TYR cc_start: 0.8286 (t80) cc_final: 0.7764 (t80)
REVERT: D  173 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.7878 (p-80)
REVERT: E   64 ILE cc_start: 0.8740 (mm) cc_final: 0.8262 (mt)
REVERT: E   88 VAL cc_start: 0.8774 (t) cc_final: 0.8552 (m)
REVERT: E  117 MET cc_start: 0.8003 (tpp) cc_final: 0.7770 (tpp)
REVERT: E  127 ASP cc_start: 0.8263 (m-30) cc_final: 0.8046 (m-30)
REVERT: E  173 HIS cc_start: 0.8339 (OUTLIER) cc_final: 0.7970 (p-80)
  outliers start: 15
  outliers final: 5
  residues processed: 144
  average time/residue: 0.2628
  time to fit residues: 46.4677
Evaluate side-chains
  137 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
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 C residue   97 ASP
Chi-restraints excluded: chain C residue  109 THR
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain E residue  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:    0.0970
   chunk 63 optimal weight:    5.9990
   chunk 33 optimal weight:    8.9990
   chunk 34 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 23 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 49 optimal weight:    8.9990
   overall best weight:    2.1784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.114992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.102095 restraints weight = 11198.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.105077 restraints weight = 6210.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.107178 restraints weight = 3992.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   6940  Z= 0.305
  Angle     :  0.577   8.069   9345  Z= 0.295
  Chirality :  0.042   0.147    990
  Planarity :  0.006   0.053   1205
  Dihedral  :  3.975  17.664    915
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.43 %
    Favored  : 79.73 %
  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: -0.48 (0.30), residues: 810
  helix:  0.67 (0.26), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.63 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  84 
 HIS   0.006   0.002   HIS C 173 
 PHE   0.018   0.001   PHE E 120 
 TYR   0.018   0.002   TYR B 166 
 ARG   0.026   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
  164 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.736 
Fit side-chains
REVERT: B   49 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.8084 (m-30)
REVERT: B   64 ILE cc_start: 0.8764 (mm) cc_final: 0.8533 (mt)
REVERT: B  168 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8504 (mt-10)
REVERT: B  192 ARG cc_start: 0.7086 (ttt180) cc_final: 0.6817 (ttt180)
REVERT: C   49 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7725 (m-30)
REVERT: C   64 ILE cc_start: 0.8774 (mm) cc_final: 0.8187 (mt)
REVERT: C   93 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8883 (mmmm)
REVERT: C  104 ASP cc_start: 0.8368 (t70) cc_final: 0.8086 (t0)
REVERT: D  104 ASP cc_start: 0.8518 (t70) cc_final: 0.8294 (t0)
REVERT: D  118 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8022 (tm-30)
REVERT: D  159 TYR cc_start: 0.8338 (t80) cc_final: 0.7773 (t80)
REVERT: D  161 LEU cc_start: 0.8008 (mp) cc_final: 0.7777 (mt)
REVERT: D  173 HIS cc_start: 0.8413 (OUTLIER) cc_final: 0.8062 (p-80)
REVERT: D  174 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7630 (tm-30)
REVERT: E   64 ILE cc_start: 0.8774 (mm) cc_final: 0.8297 (mt)
REVERT: E   88 VAL cc_start: 0.8980 (t) cc_final: 0.8697 (m)
REVERT: E  117 MET cc_start: 0.8088 (tpp) cc_final: 0.7833 (tpp)
REVERT: E  173 HIS cc_start: 0.8337 (OUTLIER) cc_final: 0.8030 (p-80)
  outliers start: 21
  outliers final: 12
  residues processed: 153
  average time/residue: 0.2632
  time to fit residues: 49.5728
Evaluate side-chains
  150 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
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   94 THR
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  162 MET
Chi-restraints excluded: chain E residue  173 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 54 optimal weight:    0.3980
   chunk 50 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0570
   chunk 31 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.6098

-------------------------------------------------------------------------------
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 = 0.3396 r_free = 0.3396 target = 0.116602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.103609 restraints weight = 10848.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.106626 restraints weight = 6064.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.108712 restraints weight = 3878.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.2852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6940  Z= 0.163
  Angle     :  0.492   8.337   9345  Z= 0.251
  Chirality :  0.038   0.137    990
  Planarity :  0.006   0.054   1205
  Dihedral  :  3.667  16.116    915
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 19.59 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.90 (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 B 173 
 PHE   0.006   0.001   PHE A 106 
 TYR   0.018   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
  149 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 0.807 
Fit side-chains
REVERT: B   49 ASP cc_start: 0.8245 (t0) cc_final: 0.8033 (m-30)
REVERT: B   64 ILE cc_start: 0.8676 (mm) cc_final: 0.8447 (mt)
REVERT: B  124 GLN cc_start: 0.7877 (tt0) cc_final: 0.7594 (pt0)
REVERT: B  192 ARG cc_start: 0.7387 (ttt180) cc_final: 0.7096 (ttt180)
REVERT: C   49 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7680 (m-30)
REVERT: C   64 ILE cc_start: 0.8676 (mm) cc_final: 0.8095 (mt)
REVERT: C   93 LYS cc_start: 0.9137 (mmmt) cc_final: 0.8892 (mmmm)
REVERT: C  104 ASP cc_start: 0.8361 (t70) cc_final: 0.8076 (t0)
REVERT: D   64 ILE cc_start: 0.8638 (mm) cc_final: 0.8254 (mt)
REVERT: D  159 TYR cc_start: 0.8283 (t80) cc_final: 0.7838 (t80)
REVERT: D  173 HIS cc_start: 0.8346 (OUTLIER) cc_final: 0.8010 (p-80)
REVERT: E   64 ILE cc_start: 0.8681 (mm) cc_final: 0.8220 (mt)
REVERT: E   88 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8506 (m)
REVERT: E  117 MET cc_start: 0.7986 (tpp) cc_final: 0.7718 (tpp)
REVERT: E  173 HIS cc_start: 0.8307 (OUTLIER) cc_final: 0.7959 (p-80)
  outliers start: 14
  outliers final: 5
  residues processed: 145
  average time/residue: 0.2792
  time to fit residues: 49.8479
Evaluate side-chains
  136 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 127
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  105 HIS
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  173 HIS
Chi-restraints excluded: chain E residue   88 VAL
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:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 57 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    2.3386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.115790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.103292 restraints weight = 11126.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.106262 restraints weight = 6221.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.108283 restraints weight = 4000.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.3002

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= 0.324
  Angle     :  0.596   7.838   9345  Z= 0.302
  Chirality :  0.042   0.141    990
  Planarity :  0.006   0.055   1205
  Dihedral  :  3.941  16.944    915
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.00 %
    Favored  : 77.03 %
  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: -0.02 (0.31), residues: 810
  helix:  0.94 (0.26), residues: 455
  sheet:  None (None), residues: 0
  loop : -1.28 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  84 
 HIS   0.008   0.002   HIS C 173 
 PHE   0.017   0.001   PHE E 120 
 TYR   0.020   0.002   TYR B 166 
 ARG   0.023   0.001   ARG A 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
  158 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 0.757 
Fit side-chains
REVERT: B   49 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.8044 (m-30)
REVERT: B   64 ILE cc_start: 0.8752 (mm) cc_final: 0.8467 (mt)
REVERT: B  124 GLN cc_start: 0.7834 (tt0) cc_final: 0.7610 (pt0)
REVERT: B  192 ARG cc_start: 0.7301 (ttt180) cc_final: 0.7059 (ttt180)
REVERT: C   38 ARG cc_start: 0.6862 (mtt180) cc_final: 0.6560 (mtt180)
REVERT: C   49 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7776 (m-30)
REVERT: C   64 ILE cc_start: 0.8771 (mm) cc_final: 0.8128 (mt)
REVERT: C   67 LYS cc_start: 0.8783 (tmtt) cc_final: 0.8378 (tttm)
REVERT: C   93 LYS cc_start: 0.9116 (mmmt) cc_final: 0.8876 (mmmm)
REVERT: C  104 ASP cc_start: 0.8370 (t70) cc_final: 0.8152 (t0)
REVERT: D  159 TYR cc_start: 0.8377 (t80) cc_final: 0.7912 (t80)
REVERT: D  161 LEU cc_start: 0.8138 (mp) cc_final: 0.7909 (mt)
REVERT: D  173 HIS cc_start: 0.8464 (OUTLIER) cc_final: 0.8081 (p-80)
REVERT: E   64 ILE cc_start: 0.8786 (mm) cc_final: 0.8301 (mt)
REVERT: E   88 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8699 (m)
REVERT: E  117 MET cc_start: 0.8015 (tpp) cc_final: 0.7742 (tpp)
REVERT: E  173 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.8018 (p-80)
  outliers start: 22
  outliers final: 12
  residues processed: 147
  average time/residue: 0.2556
  time to fit residues: 46.1657
Evaluate side-chains
  148 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain B residue   49 ASP
Chi-restraints excluded: chain B residue   94 THR
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain 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  109 THR
Chi-restraints excluded: chain D residue   49 ASP
Chi-restraints excluded: chain D residue  105 HIS
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  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:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 45 optimal weight:    0.1980
   chunk 71 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0060
   chunk 73 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 48 optimal weight:    7.9990
   overall best weight:    0.5196

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.118512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.106084 restraints weight = 10889.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.108966 restraints weight = 6195.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.110953 restraints weight = 3992.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6940  Z= 0.165
  Angle     :  0.510   8.272   9345  Z= 0.260
  Chirality :  0.038   0.136    990
  Planarity :  0.006   0.055   1205
  Dihedral  :  3.646  14.667    915
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 21.62 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.07 (0.26), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.23 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  84 
 HIS   0.008   0.001   HIS C 173 
 PHE   0.006   0.001   PHE E 106 
 TYR   0.015   0.001   TYR B 166 
 ARG   0.024   0.001   ARG D 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
  147 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 134
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A  104 ASP cc_start: 0.8160 (t70) cc_final: 0.7838 (t0)
REVERT: B   49 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.8015 (m-30)
REVERT: B   64 ILE cc_start: 0.8697 (mm) cc_final: 0.8442 (mt)
REVERT: C   49 ASP cc_start: 0.7904 (t0) cc_final: 0.7422 (m-30)
REVERT: C   52 ILE cc_start: 0.8412 (mm) cc_final: 0.8008 (tp)
REVERT: C   56 GLU cc_start: 0.8310 (tp30) cc_final: 0.8078 (mm-30)
REVERT: C   64 ILE cc_start: 0.8643 (mm) cc_final: 0.8026 (mt)
REVERT: C   67 LYS cc_start: 0.8728 (tmtt) cc_final: 0.8304 (tttm)
REVERT: C   93 LYS cc_start: 0.9119 (mmmt) cc_final: 0.8874 (mmmm)
REVERT: C  104 ASP cc_start: 0.8382 (t70) cc_final: 0.8132 (t0)
REVERT: D   64 ILE cc_start: 0.8531 (mm) cc_final: 0.8127 (mt)
REVERT: D  159 TYR cc_start: 0.8308 (t80) cc_final: 0.7987 (t80)
REVERT: D  173 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.7981 (p-80)
REVERT: E   64 ILE cc_start: 0.8743 (mm) cc_final: 0.8262 (mt)
REVERT: E   88 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8522 (m)
REVERT: E  117 MET cc_start: 0.7955 (tpp) cc_final: 0.7694 (tpp)
REVERT: E  173 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7931 (p-80)
  outliers start: 13
  outliers final: 6
  residues processed: 143
  average time/residue: 0.2485
  time to fit residues: 44.2751
Evaluate side-chains
  141 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain B residue   49 ASP
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain D residue  105 HIS
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  109 THR
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  173 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 33 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.117321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.104450 restraints weight = 10995.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.107448 restraints weight = 6158.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.109532 restraints weight = 3939.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6940  Z= 0.172
  Angle     :  0.503   7.939   9345  Z= 0.256
  Chirality :  0.038   0.135    990
  Planarity :  0.005   0.053   1205
  Dihedral  :  3.500  13.672    915
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 21.62 %
    Favored  : 76.08 %
  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:  0.34 (0.32), residues: 810
  helix:  1.22 (0.26), residues: 455
  sheet:  None (None), residues: 0
  loop : -1.10 (0.35), residues: 355

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 E 120 
 TYR   0.016   0.001   TYR D 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
  143 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.739 
Fit side-chains
REVERT: A  104 ASP cc_start: 0.8185 (t70) cc_final: 0.7739 (t0)
REVERT: B   49 ASP cc_start: 0.8231 (t0) cc_final: 0.8016 (m-30)
REVERT: B   64 ILE cc_start: 0.8634 (mm) cc_final: 0.8355 (mt)
REVERT: B  124 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7444 (pt0)
REVERT: C   49 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7667 (m-30)
REVERT: C   56 GLU cc_start: 0.8344 (tp30) cc_final: 0.8127 (mm-30)
REVERT: C   64 ILE cc_start: 0.8667 (mm) cc_final: 0.8055 (mt)
REVERT: C   93 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8884 (mmmm)
REVERT: C  104 ASP cc_start: 0.8395 (t70) cc_final: 0.8132 (t0)
REVERT: D  159 TYR cc_start: 0.8352 (t80) cc_final: 0.8060 (t80)
REVERT: D  173 HIS cc_start: 0.8274 (OUTLIER) cc_final: 0.7969 (p-80)
REVERT: E   64 ILE cc_start: 0.8736 (mm) cc_final: 0.8257 (mt)
REVERT: E   88 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8525 (m)
REVERT: E  104 ASP cc_start: 0.8239 (t70) cc_final: 0.7912 (t0)
REVERT: E  117 MET cc_start: 0.7903 (tpp) cc_final: 0.7552 (mmm)
REVERT: E  173 HIS cc_start: 0.8240 (OUTLIER) cc_final: 0.7951 (p-80)
  outliers start: 17
  outliers final: 9
  residues processed: 137
  average time/residue: 0.2471
  time to fit residues: 42.0288
Evaluate side-chains
  137 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
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  124 GLN
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   49 ASP
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  109 THR
Chi-restraints excluded: chain D residue   49 ASP
Chi-restraints excluded: chain D residue  105 HIS
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  109 THR
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  173 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0980
   chunk 56 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0060
   chunk 1 optimal weight:    6.9990
   chunk 33 optimal weight:    8.9990
   chunk 63 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.4996

-------------------------------------------------------------------------------
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 = 0.3440 r_free = 0.3440 target = 0.120050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.107298 restraints weight = 11007.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.110319 restraints weight = 6136.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.112384 restraints weight = 3906.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6940  Z= 0.159
  Angle     :  0.506   8.226   9345  Z= 0.255
  Chirality :  0.038   0.134    990
  Planarity :  0.006   0.055   1205
  Dihedral  :  3.385  12.166    915
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 22.16 %
    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:  0.48 (0.32), residues: 810
  helix:  1.23 (0.26), residues: 460
  sheet:  None (None), residues: 0
  loop : -0.89 (0.36), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  84 
 HIS   0.008   0.001   HIS C 173 
 PHE   0.006   0.001   PHE A 106 
 TYR   0.017   0.001   TYR D 166 
 ARG   0.022   0.001   ARG C 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
  142 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A  104 ASP cc_start: 0.8184 (t70) cc_final: 0.7748 (t0)
REVERT: B   49 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7864 (m-30)
REVERT: B   52 ILE cc_start: 0.8292 (mm) cc_final: 0.7851 (tt)
REVERT: B   64 ILE cc_start: 0.8599 (mm) cc_final: 0.8300 (mt)
REVERT: B  124 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7567 (pt0)
REVERT: B  161 LEU cc_start: 0.8342 (mp) cc_final: 0.8107 (mp)
REVERT: B  192 ARG cc_start: 0.7366 (ttt180) cc_final: 0.7047 (ttt180)
REVERT: C   49 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7677 (m-30)
REVERT: C   56 GLU cc_start: 0.8373 (tp30) cc_final: 0.8151 (mm-30)
REVERT: C   64 ILE cc_start: 0.8629 (mm) cc_final: 0.8020 (mt)
REVERT: C   93 LYS cc_start: 0.9132 (mmmt) cc_final: 0.8881 (mmmm)
REVERT: C  104 ASP cc_start: 0.8391 (t70) cc_final: 0.8121 (t0)
REVERT: D  159 TYR cc_start: 0.8335 (t80) cc_final: 0.8090 (t80)
REVERT: D  173 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.7884 (p-80)
REVERT: E   64 ILE cc_start: 0.8706 (mm) cc_final: 0.8191 (mt)
REVERT: E   88 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8513 (m)
REVERT: E  104 ASP cc_start: 0.8235 (t70) cc_final: 0.7928 (t0)
REVERT: E  117 MET cc_start: 0.7734 (tpp) cc_final: 0.7378 (mmm)
REVERT: E  173 HIS cc_start: 0.8181 (OUTLIER) cc_final: 0.7935 (p-80)
  outliers start: 15
  outliers final: 8
  residues processed: 136
  average time/residue: 0.2830
  time to fit residues: 47.5059
Evaluate side-chains
  135 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain B residue   49 ASP
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  124 GLN
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   49 ASP
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  109 THR
Chi-restraints excluded: chain D residue  105 HIS
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  109 THR
Chi-restraints excluded: chain E residue  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:    7.9990
   chunk 39 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 11 optimal weight:    0.4980
   chunk 60 optimal weight:    5.9990
   chunk 17 optimal weight:    9.9990
   chunk 40 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.7782

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.119075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.106494 restraints weight = 11264.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.109425 restraints weight = 6385.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.111468 restraints weight = 4110.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.3304

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= 0.172
  Angle     :  0.513   8.247   9345  Z= 0.259
  Chirality :  0.038   0.134    990
  Planarity :  0.006   0.061   1205
  Dihedral  :  3.370  11.714    915
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 22.30 %
    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:  0.60 (0.32), residues: 810
  helix:  1.28 (0.26), residues: 460
  sheet:  None (None), residues: 0
  loop : -0.77 (0.36), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  84 
 HIS   0.008   0.001   HIS C 173 
 PHE   0.006   0.001   PHE E 120 
 TYR   0.016   0.001   TYR B 166 
 ARG   0.020   0.001   ARG C 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
  141 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.719 
Fit side-chains
REVERT: A  104 ASP cc_start: 0.8190 (t70) cc_final: 0.7754 (t0)
REVERT: B   49 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.8029 (m-30)
REVERT: B   64 ILE cc_start: 0.8626 (mm) cc_final: 0.8322 (mt)
REVERT: B  117 MET cc_start: 0.7549 (tpp) cc_final: 0.7120 (tpp)
REVERT: B  124 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7543 (pt0)
REVERT: B  161 LEU cc_start: 0.8332 (mp) cc_final: 0.8079 (mp)
REVERT: B  192 ARG cc_start: 0.7376 (ttt180) cc_final: 0.7174 (ttt180)
REVERT: C   49 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7439 (m-30)
REVERT: C   52 ILE cc_start: 0.8384 (mm) cc_final: 0.7964 (tp)
REVERT: C   56 GLU cc_start: 0.8442 (tp30) cc_final: 0.8170 (mm-30)
REVERT: C   64 ILE cc_start: 0.8660 (mm) cc_final: 0.8022 (mt)
REVERT: C   93 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8879 (mmmm)
REVERT: C  104 ASP cc_start: 0.8400 (t70) cc_final: 0.8148 (t0)
REVERT: D  159 TYR cc_start: 0.8336 (t80) cc_final: 0.8075 (t80)
REVERT: D  173 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7895 (p-80)
REVERT: D  174 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7378 (tm-30)
REVERT: E   64 ILE cc_start: 0.8735 (mm) cc_final: 0.8199 (mt)
REVERT: E   88 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8533 (m)
REVERT: E  104 ASP cc_start: 0.8243 (t70) cc_final: 0.7956 (t0)
REVERT: E  117 MET cc_start: 0.7768 (tpp) cc_final: 0.7400 (mmm)
REVERT: E  173 HIS cc_start: 0.8168 (OUTLIER) cc_final: 0.7917 (p-80)
  outliers start: 16
  outliers final: 9
  residues processed: 137
  average time/residue: 0.2636
  time to fit residues: 44.3058
Evaluate side-chains
  141 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
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 B residue  124 GLN
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  105 HIS
Chi-restraints excluded: chain D residue  173 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  109 THR
Chi-restraints excluded: chain E residue  124 GLN
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:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 49 optimal weight:    8.9990
   chunk 33 optimal weight:    8.9990
   chunk 26 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 20 optimal weight:    0.0000
   chunk 37 optimal weight:    0.6980
   overall best weight:    1.4988

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.116442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.103319 restraints weight = 11246.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.106375 restraints weight = 6195.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.108475 restraints weight = 3927.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.3298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6940  Z= 0.231
  Angle     :  0.547   7.890   9345  Z= 0.275
  Chirality :  0.040   0.135    990
  Planarity :  0.006   0.053   1205
  Dihedral  :  3.539  12.524    915
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 21.89 %
    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:  0.61 (0.32), residues: 810
  helix:  1.25 (0.26), residues: 460
  sheet:  None (None), residues: 0
  loop : -0.71 (0.37), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D  84 
 HIS   0.008   0.002   HIS C 173 
 PHE   0.010   0.001   PHE E 120 
 TYR   0.018   0.002   TYR B 166 
 ARG   0.019   0.001   ARG C 190 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2077.75 seconds
wall clock time: 36 minutes 59.28 seconds (2219.28 seconds total)