Starting phenix.real_space_refine
on Tue Mar  3 16:46:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7t4f_25675/03_2026/7t4f_25675.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t4f_25675/03_2026/7t4f_25675.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t4f_25675/03_2026/7t4f_25675.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t4f_25675/03_2026/7t4f_25675.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7t4f_25675/03_2026/7t4f_25675.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t4f_25675/03_2026/7t4f_25675.map"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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    4516      2.51       5
     N    1216      2.21       5
     O    1472      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7224
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1806
          Classifications: {'peptide': 245}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 232}
    Chain: "B"
      Number of atoms: 1806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1806
          Classifications: {'peptide': 245}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 232}
    Chain: "C"
      Number of atoms: 1806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1806
          Classifications: {'peptide': 245}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 232}
    Chain: "D"
      Number of atoms: 1806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1806
          Classifications: {'peptide': 245}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 232}
  Time building chain proxies: 1.62, per 1000 atoms: 0.22
  Number of scatterers: 7224
  At special positions: 0
  Unit cell: (108.9, 108.9, 127.6, 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    1472      8.00
     N    1216      7.00
     C    4516      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 209.9 milliseconds
  

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1776

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 16 sheets defined
      8.2% alpha, 44.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 103
    Processing helix  chain 'A' and resid 151 through 156
    Processing helix  chain 'B' and resid 90 through 103
    Processing helix  chain 'B' and resid 151 through 156
      removed outlier: 3.556A  pdb=" N   SER B 156 " --> pdb=" O   GLU B 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 103
    Processing helix  chain 'C' and resid 151 through 156
      removed outlier: 3.504A  pdb=" N   SER C 156 " --> pdb=" O   GLU C 153 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 103
    Processing helix  chain 'D' and resid 151 through 156
    Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39
      removed outlier: 4.601A  pdb=" N   LEU A  17 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   ALA A 107 " --> pdb=" O   TYR A  20 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   LYS A 142 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ILE A 127 " --> pdb=" O   THR A 140 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   THR A 140 " --> pdb=" O   ILE A 127 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   LYS A 129 " --> pdb=" O   THR A 138 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   THR A 138 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   VAL A 131 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 8.402A  pdb=" N   VAL A 136 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   SER A  81 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   LEU A  45 " --> pdb=" O   SER A  81 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   THR A  83 " --> pdb=" O   LYS A  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 39
      removed outlier: 4.601A  pdb=" N   LEU A  17 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   ALA A 107 " --> pdb=" O   TYR A  20 " (cutoff:3.500A)
      removed outlier: 17.808A  pdb=" N   ARG A 121 " --> pdb=" O   ASP C  56 " (cutoff:3.500A)
      removed outlier: 14.231A  pdb=" N   ASP C  56 " --> pdb=" O   ARG A 121 " (cutoff:3.500A)
      removed outlier: 12.286A  pdb=" N   TRP A 123 " --> pdb=" O   SER C  54 " (cutoff:3.500A)
      removed outlier: 9.384A  pdb=" N   SER C  54 " --> pdb=" O   TRP A 123 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   SER A 125 " --> pdb=" O   ALA C  52 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   THR C  51 " --> pdb=" O   LYS C  75 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   LYS C  75 " --> pdb=" O   THR C  51 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   GLU C  53 " --> pdb=" O   GLY C  73 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 56
      removed outlier: 6.744A  pdb=" N   THR A  51 " --> pdb=" O   LYS A  75 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   LYS A  75 " --> pdb=" O   THR A  51 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   GLU A  53 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 167
    Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 174
      removed outlier: 6.687A  pdb=" N   THR A 171 " --> pdb=" O   THR A 242 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   THR A 244 " --> pdb=" O   THR A 171 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   VAL A 173 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 38
      removed outlier: 5.449A  pdb=" N   ALA B 107 " --> pdb=" O   TYR B  20 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   LYS B 142 " --> pdb=" O   SER B 125 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   ILE B 127 " --> pdb=" O   THR B 140 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   THR B 140 " --> pdb=" O   ILE B 127 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   LYS B 129 " --> pdb=" O   THR B 138 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   THR B 138 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ASP B  44 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   ALA B  85 " --> pdb=" O   VAL B  42 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   VAL B  42 " --> pdb=" O   ALA B  85 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 38
      removed outlier: 5.449A  pdb=" N   ALA B 107 " --> pdb=" O   TYR B  20 " (cutoff:3.500A)
      removed outlier: 17.775A  pdb=" N   ARG B 121 " --> pdb=" O   ASP D  56 " (cutoff:3.500A)
      removed outlier: 14.331A  pdb=" N   ASP D  56 " --> pdb=" O   ARG B 121 " (cutoff:3.500A)
      removed outlier: 12.231A  pdb=" N   TRP B 123 " --> pdb=" O   SER D  54 " (cutoff:3.500A)
      removed outlier: 9.286A  pdb=" N   SER D  54 " --> pdb=" O   TRP B 123 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   SER B 125 " --> pdb=" O   ALA D  52 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   THR D  51 " --> pdb=" O   LYS D  75 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   LYS D  75 " --> pdb=" O   THR D  51 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   GLU D  53 " --> pdb=" O   GLY D  73 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 51 through 56
      removed outlier: 6.715A  pdb=" N   THR B  51 " --> pdb=" O   LYS B  75 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   LYS B  75 " --> pdb=" O   THR B  51 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   GLU B  53 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 167
    Processing sheet with id=AB1, first strand: chain 'B' and resid 170 through 174
      removed outlier: 6.688A  pdb=" N   THR B 171 " --> pdb=" O   THR B 242 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   THR B 244 " --> pdb=" O   THR B 171 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   VAL B 173 " --> pdb=" O   THR B 244 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 36 through 38
      removed outlier: 5.478A  pdb=" N   ALA C 107 " --> pdb=" O   TYR C  20 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   LYS C 142 " --> pdb=" O   SER C 125 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   ILE C 127 " --> pdb=" O   THR C 140 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   THR C 140 " --> pdb=" O   ILE C 127 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   LYS C 129 " --> pdb=" O   THR C 138 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   THR C 138 " --> pdb=" O   LYS C 129 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   VAL C 131 " --> pdb=" O   VAL C 136 " (cutoff:3.500A)
      removed outlier: 8.448A  pdb=" N   VAL C 136 " --> pdb=" O   VAL C 131 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   SER C  81 " --> pdb=" O   LEU C  45 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   LEU C  45 " --> pdb=" O   SER C  81 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   THR C  83 " --> pdb=" O   LYS C  43 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 163 through 167
    Processing sheet with id=AB4, first strand: chain 'C' and resid 170 through 174
      removed outlier: 6.688A  pdb=" N   THR C 171 " --> pdb=" O   THR C 242 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   THR C 244 " --> pdb=" O   THR C 171 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   VAL C 173 " --> pdb=" O   THR C 244 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 36 through 38
      removed outlier: 5.322A  pdb=" N   ALA D 107 " --> pdb=" O   TYR D  20 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   LYS D 142 " --> pdb=" O   SER D 125 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   ILE D 127 " --> pdb=" O   THR D 140 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   THR D 140 " --> pdb=" O   ILE D 127 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   LYS D 129 " --> pdb=" O   THR D 138 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   THR D 138 " --> pdb=" O   LYS D 129 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ASP D  44 " --> pdb=" O   THR D  83 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   ALA D  85 " --> pdb=" O   VAL D  42 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   VAL D  42 " --> pdb=" O   ALA D  85 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 163 through 167
    Processing sheet with id=AB7, first strand: chain 'D' and resid 170 through 174
      removed outlier: 6.688A  pdb=" N   THR D 171 " --> pdb=" O   THR D 242 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   THR D 244 " --> pdb=" O   THR D 171 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   VAL D 173 " --> pdb=" O   THR D 244 " (cutoff:3.500A)

    296 hydrogen bonds defined for protein.
    768 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: 1.08

  Time building geometry restraints manager: 0.80 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.19 -     1.31: 1249
        1.31 -     1.44: 1883
        1.44 -     1.56: 4196
        1.56 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 7368
  Sorted by residual:
  bond pdb=" C   PRO B   9 "
       pdb=" O   PRO B   9 "
    ideal  model  delta    sigma   weight residual
    1.233  1.187  0.046 1.16e-02 7.43e+03 1.55e+01
  bond pdb=" C   PRO D   9 "
       pdb=" O   PRO D   9 "
    ideal  model  delta    sigma   weight residual
    1.233  1.189  0.044 1.19e-02 7.06e+03 1.37e+01
  bond pdb=" N   VAL D  10 "
       pdb=" CA  VAL D  10 "
    ideal  model  delta    sigma   weight residual
    1.456  1.498 -0.042 1.14e-02 7.69e+03 1.35e+01
  bond pdb=" N   VAL C  10 "
       pdb=" CA  VAL C  10 "
    ideal  model  delta    sigma   weight residual
    1.459  1.502 -0.043 1.19e-02 7.06e+03 1.31e+01
  bond pdb=" CA  ALA A  13 "
       pdb=" CB  ALA A  13 "
    ideal  model  delta    sigma   weight residual
    1.527  1.477  0.050 1.44e-02 4.82e+03 1.20e+01
  ... (remaining 7363 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 9700
        1.78 -     3.55: 305
        3.55 -     5.33: 49
        5.33 -     7.11: 8
        7.11 -     8.88: 2
  Bond angle restraints: 10064
  Sorted by residual:
  angle pdb=" N   GLY B  12 "
        pdb=" CA  GLY B  12 "
        pdb=" C   GLY B  12 "
      ideal   model   delta    sigma   weight residual
     114.67  121.24   -6.57 1.10e+00 8.26e-01 3.57e+01
  angle pdb=" N   PRO D   9 "
        pdb=" CA  PRO D   9 "
        pdb=" CB  PRO D   9 "
      ideal   model   delta    sigma   weight residual
     103.35   98.89    4.46 8.70e-01 1.32e+00 2.62e+01
  angle pdb=" C   THR C  15 "
        pdb=" CA  THR C  15 "
        pdb=" CB  THR C  15 "
      ideal   model   delta    sigma   weight residual
     109.53  117.59   -8.06 1.69e+00 3.50e-01 2.27e+01
  angle pdb=" C   LYS C  11 "
        pdb=" CA  LYS C  11 "
        pdb=" CB  LYS C  11 "
      ideal   model   delta    sigma   weight residual
     109.68  118.56   -8.88 2.05e+00 2.38e-01 1.88e+01
  angle pdb=" C   GLY B 147 "
        pdb=" N   ARG B 148 "
        pdb=" CA  ARG B 148 "
      ideal   model   delta    sigma   weight residual
     121.83  128.46   -6.63 1.56e+00 4.11e-01 1.81e+01
  ... (remaining 10059 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 3958
       17.68 -    35.35: 298
       35.35 -    53.02: 71
       53.02 -    70.70: 24
       70.70 -    88.37: 9
  Dihedral angle restraints: 4360
    sinusoidal: 1588
      harmonic: 2772
  Sorted by residual:
  dihedral pdb=" CA  ASP C  64 "
           pdb=" CB  ASP C  64 "
           pdb=" CG  ASP C  64 "
           pdb=" OD1 ASP C  64 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.53   57.53     1      2.00e+01 2.50e-03 1.11e+01
  dihedral pdb=" CB  GLU C 135 "
           pdb=" CG  GLU C 135 "
           pdb=" CD  GLU C 135 "
           pdb=" OE1 GLU C 135 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.37   88.37     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CG  ARG B 139 "
           pdb=" CD  ARG B 139 "
           pdb=" NE  ARG B 139 "
           pdb=" CZ  ARG B 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -133.84   43.84     2      1.50e+01 4.44e-03 1.02e+01
  ... (remaining 4357 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 883
       0.046 -    0.092: 177
       0.092 -    0.138: 110
       0.138 -    0.184: 14
       0.184 -    0.230: 8
  Chirality restraints: 1192
  Sorted by residual:
  chirality pdb=" CA  VAL C 228 "
            pdb=" N   VAL C 228 "
            pdb=" C   VAL C 228 "
            pdb=" CB  VAL C 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CA  VAL A  10 "
            pdb=" N   VAL A  10 "
            pdb=" C   VAL A  10 "
            pdb=" CB  VAL A  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CA  VAL B  10 "
            pdb=" N   VAL B  10 "
            pdb=" C   VAL B  10 "
            pdb=" CB  VAL B  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 1189 not shown)

  Planarity restraints: 1292
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B  13 "   -0.013 2.00e-02 2.50e+03   2.74e-02 7.50e+00
        pdb=" C   ALA B  13 "    0.047 2.00e-02 2.50e+03
        pdb=" O   ALA B  13 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLY B  14 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B  14 "    0.011 2.00e-02 2.50e+03   2.34e-02 5.45e+00
        pdb=" C   GLY B  14 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   GLY B  14 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR B  15 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D  13 "   -0.010 2.00e-02 2.50e+03   2.00e-02 3.99e+00
        pdb=" C   ALA D  13 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ALA D  13 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLY D  14 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1289 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 901
        2.76 -     3.30: 6247
        3.30 -     3.83: 11438
        3.83 -     4.37: 12925
        4.37 -     4.90: 23496
  Nonbonded interactions: 55007
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 108 "
            pdb=" OD1 ASN B 145 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" ND2 ASN A  29 "
            pdb=" OD1 ASP A 192 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" OG  SER A 126 "
            pdb=" OE2 GLU C  49 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OH  TYR A 108 "
            pdb=" OD1 ASN A 145 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OG  SER B  32 "
            pdb=" OG  SER B 194 "
     model   vdw
     2.337 3.040
  ... (remaining 55002 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.020
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.940
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6873
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      :  0.004   0.050   7368  Z= 0.320
  Angle     :  0.701   8.884  10064  Z= 0.474
  Chirality :  0.052   0.230   1192
  Planarity :  0.004   0.043   1292
  Dihedral  : 14.605  88.374   2584
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 12.18 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.25), residues: 972
  helix:  2.35 (0.64), residues: 54
  sheet:  1.09 (0.23), residues: 494
  loop : -0.82 (0.25), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 148 
 TYR   0.007   0.001   TYR A 108 
 PHE   0.010   0.001   PHE B  82 
 TRP   0.009   0.001   TRP A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 7368)
  covalent geometry    : angle       0.70126 (10064)
  hydrogen bonds       : bond        0.16742 (  269)
  hydrogen bonds       : angle       6.85127 (  768)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A    8 MET cc_start: 0.8168 (mtm) cc_final: 0.7897 (mtm)
REVERT: A   11 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.7037 (mmmt)
REVERT: B   11 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.6947 (mmpt)
REVERT: C   31 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8864 (mm)
REVERT: C  148 ARG cc_start: 0.8413 (ttt180) cc_final: 0.6756 (mmp80)
REVERT: D   43 LYS cc_start: 0.8722 (mtpp) cc_final: 0.7805 (mmtm)
REVERT: D  151 MET cc_start: 0.9054 (mmm) cc_final: 0.8804 (mmm)
  outliers start: 19
  outliers final: 7
  residues processed: 108
  average time/residue: 0.5694
  time to fit residues: 64.6428
Evaluate side-chains
  98 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 LYS
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   11 LYS
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain D residue   46 THR
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:   30.0000
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.0010
   chunk 45 optimal weight:   40.0000
   chunk 74 optimal weight:    7.9990
   overall best weight:    2.9994

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

Flipped N/Q/H residues before XYZ refinement:
D 177 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.193938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.107104 restraints weight = 7846.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 2.38
r_work: 0.3107 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.1377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   7368  Z= 0.206
  Angle     :  0.570   6.352  10064  Z= 0.305
  Chirality :  0.049   0.157   1192
  Planarity :  0.005   0.033   1292
  Dihedral  :  5.692  56.686   1048
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 12.31 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.25), residues: 972
  helix:  1.71 (0.70), residues: 56
  sheet:  0.97 (0.23), residues: 496
  loop : -0.92 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 106 
 TYR   0.010   0.001   TYR B 108 
 PHE   0.021   0.002   PHE A 120 
 TRP   0.013   0.002   TRP D  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 ( 7368)
  covalent geometry    : angle       0.57047 (10064)
  hydrogen bonds       : bond        0.04387 (  269)
  hydrogen bonds       : angle       5.53144 (  768)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A    8 MET cc_start: 0.8313 (mtm) cc_final: 0.8109 (mtm)
REVERT: A   31 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7990 (mm)
REVERT: A   38 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8028 (ttt90)
REVERT: A  135 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8382 (mt-10)
REVERT: B   11 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.7304 (mmpt)
REVERT: B   91 GLN cc_start: 0.8750 (mm110) cc_final: 0.8441 (mm110)
REVERT: C   11 LYS cc_start: 0.8650 (mtmt) cc_final: 0.8386 (mttt)
REVERT: C   31 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8684 (mm)
REVERT: C   43 LYS cc_start: 0.8862 (mtpp) cc_final: 0.7504 (mmtt)
REVERT: C  134 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8335 (mtpm)
REVERT: C  148 ARG cc_start: 0.8592 (ttt180) cc_final: 0.6317 (tpp-160)
REVERT: D   43 LYS cc_start: 0.8795 (mtpp) cc_final: 0.7675 (mmtm)
  outliers start: 21
  outliers final: 10
  residues processed: 89
  average time/residue: 0.7207
  time to fit residues: 66.7673
Evaluate side-chains
  91 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   11 LYS
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   44 ASP
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   46 THR
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 5 optimal weight:    0.4980
   chunk 57 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 54 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 93 optimal weight:   30.0000
   chunk 94 optimal weight:    4.9990
   chunk 41 optimal weight:   30.0000
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A   5 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.194589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.108374 restraints weight = 7826.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.37
r_work: 0.3141 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7368  Z= 0.115
  Angle     :  0.467   4.551  10064  Z= 0.250
  Chirality :  0.046   0.153   1192
  Planarity :  0.004   0.037   1292
  Dihedral  :  4.776  54.651   1040
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 12.44 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.25), residues: 972
  helix:  1.90 (0.69), residues: 56
  sheet:  0.88 (0.23), residues: 494
  loop : -0.86 (0.25), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 139 
 TYR   0.008   0.001   TYR B 108 
 PHE   0.013   0.002   PHE B  82 
 TRP   0.009   0.001   TRP C  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7368)
  covalent geometry    : angle       0.46722 (10064)
  hydrogen bonds       : bond        0.03225 (  269)
  hydrogen bonds       : angle       4.87537 (  768)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8133 (ttt90)
REVERT: B   11 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.7353 (mmpt)
REVERT: B   41 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8632 (mttp)
REVERT: B   91 GLN cc_start: 0.8674 (mm110) cc_final: 0.8350 (mm110)
REVERT: C   43 LYS cc_start: 0.8796 (mtpp) cc_final: 0.7348 (mmtt)
REVERT: C  134 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8302 (mtpm)
REVERT: C  148 ARG cc_start: 0.8612 (ttt180) cc_final: 0.6357 (tpp-160)
REVERT: D   43 LYS cc_start: 0.8690 (mtpp) cc_final: 0.7537 (mmtm)
  outliers start: 20
  outliers final: 7
  residues processed: 94
  average time/residue: 0.6694
  time to fit residues: 65.8153
Evaluate side-chains
  85 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain B residue   11 LYS
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain C residue   44 ASP
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 68 optimal weight:   50.0000
   chunk 46 optimal weight:   20.0000
   chunk 64 optimal weight:    7.9990
   chunk 45 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 54 optimal weight:    0.5980
   chunk 34 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    2.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.193666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.107084 restraints weight = 7871.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.39
r_work: 0.3111 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   7368  Z= 0.196
  Angle     :  0.549   6.736  10064  Z= 0.291
  Chirality :  0.048   0.162   1192
  Planarity :  0.005   0.040   1292
  Dihedral  :  4.825  56.376   1034
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 13.21 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.26), residues: 972
  helix:  1.64 (0.70), residues: 56
  sheet:  0.68 (0.22), residues: 514
  loop : -0.80 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 139 
 TYR   0.010   0.001   TYR B 108 
 PHE   0.020   0.002   PHE A 120 
 TRP   0.012   0.002   TRP D  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 7368)
  covalent geometry    : angle       0.54865 (10064)
  hydrogen bonds       : bond        0.03907 (  269)
  hydrogen bonds       : angle       5.03948 (  768)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8013 (ttt90)
REVERT: A  212 MET cc_start: 0.4935 (OUTLIER) cc_final: 0.4371 (tpt)
REVERT: B   11 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.7443 (mmpt)
REVERT: B   41 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8679 (mttp)
REVERT: B   91 GLN cc_start: 0.8717 (mm110) cc_final: 0.8362 (mm110)
REVERT: C   31 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8671 (mm)
REVERT: C   43 LYS cc_start: 0.8812 (mtpp) cc_final: 0.7559 (mmtt)
REVERT: C  134 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8296 (mtpm)
REVERT: C  148 ARG cc_start: 0.8554 (ttt180) cc_final: 0.6377 (tpp-160)
REVERT: D   43 LYS cc_start: 0.8729 (mtpp) cc_final: 0.7615 (mmtm)
  outliers start: 20
  outliers final: 11
  residues processed: 89
  average time/residue: 0.7388
  time to fit residues: 68.5545
Evaluate side-chains
  91 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  212 MET
Chi-restraints excluded: chain B residue   11 LYS
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   44 ASP
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   46 THR
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 70 optimal weight:   20.0000
   chunk 49 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 44 optimal weight:   50.0000
   chunk 92 optimal weight:   40.0000
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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 = 0.4186 r_free = 0.4186 target = 0.194047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.107896 restraints weight = 7855.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.34
r_work: 0.3123 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7368  Z= 0.152
  Angle     :  0.495   5.072  10064  Z= 0.264
  Chirality :  0.047   0.154   1192
  Planarity :  0.005   0.041   1292
  Dihedral  :  4.605  58.308   1034
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 14.74 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.26), residues: 972
  helix:  1.77 (0.70), residues: 56
  sheet:  0.73 (0.23), residues: 512
  loop : -0.84 (0.27), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 121 
 TYR   0.009   0.001   TYR B 108 
 PHE   0.017   0.002   PHE A 120 
 TRP   0.010   0.002   TRP D  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 7368)
  covalent geometry    : angle       0.49452 (10064)
  hydrogen bonds       : bond        0.03412 (  269)
  hydrogen bonds       : angle       4.81686 (  768)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8151 (ttt90)
REVERT: A  140 THR cc_start: 0.8937 (m) cc_final: 0.8719 (m)
REVERT: B   11 LYS cc_start: 0.8837 (mmmm) cc_final: 0.7402 (mmpt)
REVERT: B   41 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8671 (mttp)
REVERT: B   91 GLN cc_start: 0.8697 (mm110) cc_final: 0.8337 (mm110)
REVERT: C   31 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8682 (mm)
REVERT: C   43 LYS cc_start: 0.8848 (mtpp) cc_final: 0.7566 (mmtt)
REVERT: C  134 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8317 (mtpm)
REVERT: C  148 ARG cc_start: 0.8580 (ttt180) cc_final: 0.6356 (tpp-160)
REVERT: D   29 ASN cc_start: 0.8761 (t0) cc_final: 0.8513 (t0)
REVERT: D   43 LYS cc_start: 0.8714 (mtpp) cc_final: 0.7641 (mmtm)
  outliers start: 21
  outliers final: 13
  residues processed: 91
  average time/residue: 0.7057
  time to fit residues: 67.1007
Evaluate side-chains
  93 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   44 ASP
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   46 THR
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 51 optimal weight:    7.9990
   chunk 41 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 44 optimal weight:    8.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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 = 0.4167 r_free = 0.4167 target = 0.192729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.106528 restraints weight = 7898.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.40
r_work: 0.3114 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7368  Z= 0.163
  Angle     :  0.514   5.660  10064  Z= 0.273
  Chirality :  0.047   0.157   1192
  Planarity :  0.005   0.043   1292
  Dihedral  :  4.459  59.407   1030
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 15.13 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.26), residues: 972
  helix:  1.69 (0.69), residues: 56
  sheet:  0.76 (0.23), residues: 508
  loop : -0.82 (0.27), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 121 
 TYR   0.009   0.001   TYR B 108 
 PHE   0.018   0.002   PHE A 120 
 TRP   0.010   0.002   TRP D  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 7368)
  covalent geometry    : angle       0.51447 (10064)
  hydrogen bonds       : bond        0.03550 (  269)
  hydrogen bonds       : angle       4.85690 (  768)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8016 (ttt90)
REVERT: A  140 THR cc_start: 0.8908 (m) cc_final: 0.8701 (m)
REVERT: B   11 LYS cc_start: 0.8840 (mmmm) cc_final: 0.7343 (mmpt)
REVERT: B   41 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8650 (mttp)
REVERT: B   91 GLN cc_start: 0.8670 (mm110) cc_final: 0.8278 (mm110)
REVERT: C   31 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8678 (mm)
REVERT: C   43 LYS cc_start: 0.8803 (mtpp) cc_final: 0.7533 (mmtt)
REVERT: C  134 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8300 (mtpm)
REVERT: C  148 ARG cc_start: 0.8534 (ttt180) cc_final: 0.6320 (tpp-160)
REVERT: D   29 ASN cc_start: 0.8766 (t0) cc_final: 0.8494 (t0)
REVERT: D   43 LYS cc_start: 0.8707 (mtpp) cc_final: 0.7615 (mmtm)
  outliers start: 21
  outliers final: 14
  residues processed: 92
  average time/residue: 0.7156
  time to fit residues: 68.6063
Evaluate side-chains
  94 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   44 ASP
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   46 THR
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 40 optimal weight:   30.0000
   chunk 59 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 6 optimal weight:    0.2980
   chunk 66 optimal weight:    8.9990
   chunk 67 optimal weight:   10.0000
   chunk 94 optimal weight:   50.0000
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   overall best weight:    2.6386

-------------------------------------------------------------------------------
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 = 0.4179 r_free = 0.4179 target = 0.193399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.107234 restraints weight = 7873.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.39
r_work: 0.3113 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7368  Z= 0.179
  Angle     :  0.525   5.664  10064  Z= 0.279
  Chirality :  0.047   0.157   1192
  Planarity :  0.005   0.043   1292
  Dihedral  :  4.515  59.827   1030
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.38 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.26), residues: 972
  helix:  1.64 (0.69), residues: 56
  sheet:  0.75 (0.23), residues: 496
  loop : -0.80 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 139 
 TYR   0.010   0.001   TYR B 108 
 PHE   0.019   0.002   PHE A 120 
 TRP   0.011   0.002   TRP D  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 7368)
  covalent geometry    : angle       0.52494 (10064)
  hydrogen bonds       : bond        0.03651 (  269)
  hydrogen bonds       : angle       4.87758 (  768)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8040 (ttt90)
REVERT: B   11 LYS cc_start: 0.8881 (mmmm) cc_final: 0.7428 (mmpt)
REVERT: B   41 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8683 (mttp)
REVERT: B   91 GLN cc_start: 0.8701 (mm110) cc_final: 0.8315 (mm110)
REVERT: C   31 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8690 (mm)
REVERT: C   43 LYS cc_start: 0.8821 (mtpp) cc_final: 0.7565 (mmtt)
REVERT: C  134 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8318 (mtpm)
REVERT: C  148 ARG cc_start: 0.8567 (ttt180) cc_final: 0.6386 (tpp-160)
REVERT: D   29 ASN cc_start: 0.8777 (t0) cc_final: 0.8563 (t0)
REVERT: D   43 LYS cc_start: 0.8717 (mtpp) cc_final: 0.7638 (mmtm)
  outliers start: 20
  outliers final: 15
  residues processed: 90
  average time/residue: 0.7065
  time to fit residues: 66.3539
Evaluate side-chains
  93 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   44 ASP
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   46 THR
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 74 optimal weight:    0.5980
   chunk 41 optimal weight:   50.0000
   chunk 27 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 55 optimal weight:   10.0000
   chunk 87 optimal weight:    3.9990
   chunk 80 optimal weight:    0.7980
   chunk 40 optimal weight:   30.0000
   chunk 7 optimal weight:    7.9990
   chunk 42 optimal weight:    8.9990
   overall best weight:    1.8384

-------------------------------------------------------------------------------
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 = 0.4171 r_free = 0.4171 target = 0.193050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.107221 restraints weight = 7864.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.38
r_work: 0.3114 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7368  Z= 0.133
  Angle     :  0.478   5.028  10064  Z= 0.255
  Chirality :  0.046   0.152   1192
  Planarity :  0.004   0.045   1292
  Dihedral  :  4.303  58.758   1030
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.28 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.26), residues: 972
  helix:  1.79 (0.69), residues: 56
  sheet:  0.81 (0.24), residues: 494
  loop : -0.76 (0.26), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 121 
 TYR   0.008   0.001   TYR B 108 
 PHE   0.015   0.002   PHE A 120 
 TRP   0.008   0.001   TRP D  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7368)
  covalent geometry    : angle       0.47826 (10064)
  hydrogen bonds       : bond        0.03192 (  269)
  hydrogen bonds       : angle       4.71256 (  768)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8136 (ttt90)
REVERT: B   11 LYS cc_start: 0.8857 (mmmm) cc_final: 0.7384 (mmpt)
REVERT: B   41 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8671 (mttp)
REVERT: B   91 GLN cc_start: 0.8656 (mm110) cc_final: 0.8268 (mm110)
REVERT: C   31 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8669 (mm)
REVERT: C   43 LYS cc_start: 0.8821 (mtpp) cc_final: 0.7533 (mmtt)
REVERT: C  134 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8310 (mtpm)
REVERT: C  148 ARG cc_start: 0.8533 (ttt180) cc_final: 0.6355 (tpp-160)
REVERT: D   29 ASN cc_start: 0.8746 (t0) cc_final: 0.8465 (t0)
REVERT: D   43 LYS cc_start: 0.8709 (mtpp) cc_final: 0.7618 (mmtm)
  outliers start: 20
  outliers final: 13
  residues processed: 92
  average time/residue: 0.6770
  time to fit residues: 65.1385
Evaluate side-chains
  92 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   41 LYS
Chi-restraints excluded: chain C residue   44 ASP
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 59 optimal weight:   10.0000
   chunk 54 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 64 optimal weight:    8.9990
   chunk 27 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 89 optimal weight:    9.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 = 0.4164 r_free = 0.4164 target = 0.192323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.106475 restraints weight = 7806.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.34
r_work: 0.3112 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7368  Z= 0.176
  Angle     :  0.522   5.825  10064  Z= 0.278
  Chirality :  0.047   0.159   1192
  Planarity :  0.005   0.062   1292
  Dihedral  :  4.500  59.325   1030
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 16.15 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.26), residues: 972
  helix:  1.63 (0.69), residues: 56
  sheet:  0.76 (0.24), residues: 496
  loop : -0.83 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 139 
 TYR   0.010   0.001   TYR B 108 
 PHE   0.019   0.002   PHE A 120 
 TRP   0.011   0.002   TRP D  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 7368)
  covalent geometry    : angle       0.52230 (10064)
  hydrogen bonds       : bond        0.03621 (  269)
  hydrogen bonds       : angle       4.85257 (  768)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A   31 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.8026 (mm)
REVERT: A   38 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8035 (ttt90)
REVERT: B   11 LYS cc_start: 0.8870 (mmmm) cc_final: 0.7407 (mmpt)
REVERT: B   41 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8688 (mttp)
REVERT: B   91 GLN cc_start: 0.8763 (mm110) cc_final: 0.8370 (mm110)
REVERT: C   31 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8701 (mm)
REVERT: C   43 LYS cc_start: 0.8801 (mtpp) cc_final: 0.7524 (mmtt)
REVERT: C  134 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8318 (mtpm)
REVERT: C  148 ARG cc_start: 0.8545 (ttt180) cc_final: 0.6360 (tpp-160)
REVERT: D   29 ASN cc_start: 0.8781 (t0) cc_final: 0.8486 (t0)
REVERT: D   43 LYS cc_start: 0.8724 (mtpp) cc_final: 0.7638 (mmtm)
  outliers start: 21
  outliers final: 15
  residues processed: 88
  average time/residue: 0.7120
  time to fit residues: 65.3608
Evaluate side-chains
  94 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   44 ASP
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   46 THR
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 19 optimal weight:   20.0000
   chunk 24 optimal weight:    7.9990
   chunk 45 optimal weight:    6.9990
   chunk 20 optimal weight:   30.0000
   chunk 90 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0770
   overall best weight:    1.3742

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.193630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.107919 restraints weight = 7877.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 2.37
r_work: 0.3132 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7368  Z= 0.108
  Angle     :  0.456   4.789  10064  Z= 0.244
  Chirality :  0.045   0.150   1192
  Planarity :  0.005   0.058   1292
  Dihedral  :  4.195  58.232   1030
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.54 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.26), residues: 972
  helix:  1.81 (0.68), residues: 56
  sheet:  0.82 (0.24), residues: 494
  loop : -0.73 (0.26), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 121 
 TYR   0.007   0.001   TYR B 108 
 PHE   0.013   0.001   PHE B  82 
 TRP   0.008   0.001   TRP D  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7368)
  covalent geometry    : angle       0.45595 (10064)
  hydrogen bonds       : bond        0.02927 (  269)
  hydrogen bonds       : angle       4.60864 (  768)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8128 (ttt90)
REVERT: A  140 THR cc_start: 0.8886 (m) cc_final: 0.8583 (m)
REVERT: B   11 LYS cc_start: 0.8851 (mmmm) cc_final: 0.7400 (mmpt)
REVERT: B   41 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8665 (mttp)
REVERT: B   91 GLN cc_start: 0.8644 (mm110) cc_final: 0.8262 (mm110)
REVERT: C   31 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8687 (mm)
REVERT: C   41 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8144 (mttt)
REVERT: C   43 LYS cc_start: 0.8756 (mtpp) cc_final: 0.7443 (mmtt)
REVERT: C  134 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8303 (mtpm)
REVERT: C  148 ARG cc_start: 0.8559 (ttt180) cc_final: 0.6413 (tpp-160)
REVERT: D   29 ASN cc_start: 0.8746 (t0) cc_final: 0.8459 (t0)
REVERT: D   43 LYS cc_start: 0.8694 (mtpp) cc_final: 0.7597 (mmtm)
  outliers start: 17
  outliers final: 11
  residues processed: 88
  average time/residue: 0.7294
  time to fit residues: 66.8834
Evaluate side-chains
  92 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   41 LYS
Chi-restraints excluded: chain C residue   44 ASP
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   46 THR
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 42 optimal weight:   20.0000
   chunk 83 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 41 optimal weight:   50.0000
   chunk 56 optimal weight:    0.0980
   chunk 47 optimal weight:   40.0000
   chunk 68 optimal weight:   30.0000
   chunk 35 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   overall best weight:    1.4188

-------------------------------------------------------------------------------
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 = 0.4176 r_free = 0.4176 target = 0.193632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.107886 restraints weight = 7864.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 2.39
r_work: 0.3136 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7368  Z= 0.110
  Angle     :  0.459   4.825  10064  Z= 0.244
  Chirality :  0.045   0.150   1192
  Planarity :  0.005   0.057   1292
  Dihedral  :  4.168  57.799   1030
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.79 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.26), residues: 972
  helix:  1.83 (0.68), residues: 56
  sheet:  0.83 (0.24), residues: 494
  loop : -0.73 (0.26), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 121 
 TYR   0.008   0.001   TYR B 108 
 PHE   0.013   0.001   PHE A 120 
 TRP   0.008   0.001   TRP D  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7368)
  covalent geometry    : angle       0.45910 (10064)
  hydrogen bonds       : bond        0.02945 (  269)
  hydrogen bonds       : angle       4.58160 (  768)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3660.42 seconds
wall clock time: 62 minutes 42.10 seconds (3762.10 seconds total)