Starting phenix.real_space_refine
on Thu Mar 13 09:58:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vvz_43573/03_2025/8vvz_43573.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vvz_43573/03_2025/8vvz_43573.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vvz_43573/03_2025/8vvz_43573.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vvz_43573/03_2025/8vvz_43573.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vvz_43573/03_2025/8vvz_43573.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vvz_43573/03_2025/8vvz_43573.cif"
  }
  resolution = 3.41
  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=   0.044
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      30      5.16       5
     C    5658      2.51       5
     N    1488      2.21       5
     O    1680      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8856
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1476
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1476
          Classifications: {'peptide': 184}
          Link IDs: {'PTRANS': 3, 'TRANS': 180}
    Chain: "B"
      Number of atoms: 1476
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1476
          Classifications: {'peptide': 184}
          Link IDs: {'PTRANS': 3, 'TRANS': 180}
  Restraints were copied for chains:
    C, E, D, F
  Time building chain proxies: 7.83, per 1000 atoms: 0.88
  Number of scatterers: 8856
  At special positions: 0
  Unit cell: (119.463, 116.779, 92.6177, 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      30     16.00
     O    1680      8.00
     N    1488      7.00
     C    5658      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: 2.45
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 0 sheets defined
      74.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 29
    Processing helix  chain 'A' and resid 31 through 35
    Processing helix  chain 'A' and resid 45 through 61
      removed outlier: 3.731A  pdb=" N   LYS A  49 " --> pdb=" O   ASP A  45 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   ALA A  50 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
      removed outlier: 5.490A  pdb=" N   GLU A  51 " --> pdb=" O   TRP A  47 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   ARG A  52 " --> pdb=" O   LYS A  48 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LYS A  55 " --> pdb=" O   GLU A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 70
      removed outlier: 4.056A  pdb=" N   ASN A  68 " --> pdb=" O   SER A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 87
      removed outlier: 3.532A  pdb=" N   LEU A  80 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 104
    Processing helix  chain 'A' and resid 112 through 130
    Processing helix  chain 'A' and resid 135 through 146
      removed outlier: 3.840A  pdb=" N   THR A 146 " --> pdb=" O   HIS A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 151
      removed outlier: 6.305A  pdb=" N   CYS A 150 " --> pdb=" O   LEU A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 162
    Processing helix  chain 'A' and resid 167 through 184
      removed outlier: 4.141A  pdb=" N   ILE A 180 " --> pdb=" O   LEU A 176 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   LYS A 181 " --> pdb=" O   ASP A 177 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ILE A 182 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 29
    Processing helix  chain 'B' and resid 31 through 35
    Processing helix  chain 'B' and resid 44 through 61
      removed outlier: 3.886A  pdb=" N   ALA B  50 " --> pdb=" O   SER B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 71
      removed outlier: 3.626A  pdb=" N   PHE B  69 " --> pdb=" O   PHE B  66 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   THR B  71 " --> pdb=" O   ASN B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 88
    Processing helix  chain 'B' and resid 91 through 104
    Processing helix  chain 'B' and resid 112 through 130
    Processing helix  chain 'B' and resid 135 through 146
    Processing helix  chain 'B' and resid 148 through 150
      No H-bonds generated for 'chain 'B' and resid 148 through 150'
    Processing helix  chain 'B' and resid 151 through 160
    Processing helix  chain 'B' and resid 167 through 186
    Processing helix  chain 'C' and resid 14 through 29
    Processing helix  chain 'C' and resid 31 through 35
    Processing helix  chain 'C' and resid 45 through 61
      removed outlier: 3.730A  pdb=" N   LYS C  49 " --> pdb=" O   ASP C  45 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   ALA C  50 " --> pdb=" O   SER C  46 " (cutoff:3.500A)
      removed outlier: 5.490A  pdb=" N   GLU C  51 " --> pdb=" O   TRP C  47 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   ARG C  52 " --> pdb=" O   LYS C  48 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LYS C  55 " --> pdb=" O   GLU C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 70
      removed outlier: 4.056A  pdb=" N   ASN C  68 " --> pdb=" O   SER C  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 75 through 87
      removed outlier: 3.533A  pdb=" N   LEU C  80 " --> pdb=" O   ALA C  76 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 104
    Processing helix  chain 'C' and resid 112 through 130
    Processing helix  chain 'C' and resid 135 through 146
      removed outlier: 3.840A  pdb=" N   THR C 146 " --> pdb=" O   HIS C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 151
      removed outlier: 6.305A  pdb=" N   CYS C 150 " --> pdb=" O   LEU C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 152 through 162
    Processing helix  chain 'C' and resid 167 through 184
      removed outlier: 4.142A  pdb=" N   ILE C 180 " --> pdb=" O   LEU C 176 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   LYS C 181 " --> pdb=" O   ASP C 177 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ILE C 182 " --> pdb=" O   GLN C 178 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 14 through 29
    Processing helix  chain 'D' and resid 31 through 35
    Processing helix  chain 'D' and resid 44 through 61
      removed outlier: 3.886A  pdb=" N   ALA D  50 " --> pdb=" O   SER D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 71
      removed outlier: 3.627A  pdb=" N   PHE D  69 " --> pdb=" O   PHE D  66 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   THR D  71 " --> pdb=" O   ASN D  68 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 75 through 88
    Processing helix  chain 'D' and resid 91 through 104
    Processing helix  chain 'D' and resid 112 through 130
    Processing helix  chain 'D' and resid 135 through 146
    Processing helix  chain 'D' and resid 148 through 150
      No H-bonds generated for 'chain 'D' and resid 148 through 150'
    Processing helix  chain 'D' and resid 151 through 160
    Processing helix  chain 'D' and resid 167 through 186
    Processing helix  chain 'E' and resid 14 through 29
    Processing helix  chain 'E' and resid 31 through 35
    Processing helix  chain 'E' and resid 45 through 61
      removed outlier: 3.730A  pdb=" N   LYS E  49 " --> pdb=" O   ASP E  45 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   ALA E  50 " --> pdb=" O   SER E  46 " (cutoff:3.500A)
      removed outlier: 5.490A  pdb=" N   GLU E  51 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   ARG E  52 " --> pdb=" O   LYS E  48 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LYS E  55 " --> pdb=" O   GLU E  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 70
      removed outlier: 4.056A  pdb=" N   ASN E  68 " --> pdb=" O   SER E  65 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 75 through 87
      removed outlier: 3.533A  pdb=" N   LEU E  80 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 91 through 104
    Processing helix  chain 'E' and resid 112 through 130
    Processing helix  chain 'E' and resid 135 through 146
      removed outlier: 3.840A  pdb=" N   THR E 146 " --> pdb=" O   HIS E 142 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 147 through 151
      removed outlier: 6.304A  pdb=" N   CYS E 150 " --> pdb=" O   LEU E 147 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 152 through 162
    Processing helix  chain 'E' and resid 167 through 184
      removed outlier: 4.141A  pdb=" N   ILE E 180 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   LYS E 181 " --> pdb=" O   ASP E 177 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ILE E 182 " --> pdb=" O   GLN E 178 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 14 through 29
    Processing helix  chain 'F' and resid 31 through 35
    Processing helix  chain 'F' and resid 44 through 61
      removed outlier: 3.886A  pdb=" N   ALA F  50 " --> pdb=" O   SER F  46 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 66 through 71
      removed outlier: 3.626A  pdb=" N   PHE F  69 " --> pdb=" O   PHE F  66 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   THR F  71 " --> pdb=" O   ASN F  68 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 75 through 88
    Processing helix  chain 'F' and resid 91 through 104
    Processing helix  chain 'F' and resid 112 through 130
    Processing helix  chain 'F' and resid 135 through 146
    Processing helix  chain 'F' and resid 148 through 150
      No H-bonds generated for 'chain 'F' and resid 148 through 150'
    Processing helix  chain 'F' and resid 151 through 160
    Processing helix  chain 'F' and resid 167 through 186

    531 hydrogen bonds defined for protein.
    1512 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: 2.14

  Time building geometry restraints manager: 2.87 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: 2892
        1.34 -     1.46: 1784
        1.46 -     1.58: 4258
        1.58 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 8982
  Sorted by residual:
  bond pdb=" N   GLY E  37 "
       pdb=" CA  GLY E  37 "
    ideal  model  delta    sigma   weight residual
    1.443  1.450 -0.007 1.17e-02 7.31e+03 3.61e-01
  bond pdb=" N   SER C  72 "
       pdb=" CA  SER C  72 "
    ideal  model  delta    sigma   weight residual
    1.457  1.464 -0.007 1.29e-02 6.01e+03 2.85e-01
  bond pdb=" N   GLY A  37 "
       pdb=" CA  GLY A  37 "
    ideal  model  delta    sigma   weight residual
    1.443  1.449 -0.006 1.17e-02 7.31e+03 2.85e-01
  bond pdb=" N   SER A  72 "
       pdb=" CA  SER A  72 "
    ideal  model  delta    sigma   weight residual
    1.457  1.464 -0.007 1.29e-02 6.01e+03 2.80e-01
  bond pdb=" N   GLY C  37 "
       pdb=" CA  GLY C  37 "
    ideal  model  delta    sigma   weight residual
    1.443  1.449 -0.006 1.17e-02 7.31e+03 2.69e-01
  ... (remaining 8977 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 11818
        0.98 -     1.95: 218
        1.95 -     2.93: 45
        2.93 -     3.91: 12
        3.91 -     4.88: 3
  Bond angle restraints: 12096
  Sorted by residual:
  angle pdb=" C   THR E  71 "
        pdb=" N   SER E  72 "
        pdb=" CA  SER E  72 "
      ideal   model   delta    sigma   weight residual
     121.54  126.42   -4.88 1.91e+00 2.74e-01 6.54e+00
  angle pdb=" C   THR A  71 "
        pdb=" N   SER A  72 "
        pdb=" CA  SER A  72 "
      ideal   model   delta    sigma   weight residual
     121.54  126.42   -4.88 1.91e+00 2.74e-01 6.53e+00
  angle pdb=" C   THR C  71 "
        pdb=" N   SER C  72 "
        pdb=" CA  SER C  72 "
      ideal   model   delta    sigma   weight residual
     121.54  126.35   -4.81 1.91e+00 2.74e-01 6.34e+00
  angle pdb=" CA  SER A  72 "
        pdb=" C   SER A  72 "
        pdb=" N   ASP A  73 "
      ideal   model   delta    sigma   weight residual
     116.84  119.45   -2.61 1.71e+00 3.42e-01 2.32e+00
  angle pdb=" CA  SER E  72 "
        pdb=" C   SER E  72 "
        pdb=" N   ASP E  73 "
      ideal   model   delta    sigma   weight residual
     116.84  119.43   -2.59 1.71e+00 3.42e-01 2.30e+00
  ... (remaining 12091 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 5002
       17.57 -    35.14: 470
       35.14 -    52.72: 78
       52.72 -    70.29: 12
       70.29 -    87.86: 12
  Dihedral angle restraints: 5574
    sinusoidal: 2292
      harmonic: 3282
  Sorted by residual:
  dihedral pdb=" CG  ARG D 101 "
           pdb=" CD  ARG D 101 "
           pdb=" NE  ARG D 101 "
           pdb=" CZ  ARG D 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -135.55  -44.45     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" CG  ARG B 101 "
           pdb=" CD  ARG B 101 "
           pdb=" NE  ARG B 101 "
           pdb=" CZ  ARG B 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.57  -44.43     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" CG  ARG F 101 "
           pdb=" CD  ARG F 101 "
           pdb=" NE  ARG F 101 "
           pdb=" CZ  ARG F 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.64  -44.36     2      1.50e+01 4.44e-03 1.04e+01
  ... (remaining 5571 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 918
       0.024 -    0.048: 315
       0.048 -    0.071: 138
       0.071 -    0.095: 34
       0.095 -    0.119: 23
  Chirality restraints: 1428
  Sorted by residual:
  chirality pdb=" CA  ILE D  74 "
            pdb=" N   ILE D  74 "
            pdb=" C   ILE D  74 "
            pdb=" CB  ILE D  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.54e-01
  chirality pdb=" CA  ILE F  74 "
            pdb=" N   ILE F  74 "
            pdb=" C   ILE F  74 "
            pdb=" CB  ILE F  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.48e-01
  chirality pdb=" CA  ILE C  74 "
            pdb=" N   ILE C  74 "
            pdb=" C   ILE C  74 "
            pdb=" CB  ILE C  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.37e-01
  ... (remaining 1425 not shown)

  Planarity restraints: 1512
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C  31 "    0.006 2.00e-02 2.50e+03   1.26e-02 1.59e+00
        pdb=" C   VAL C  31 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   VAL C  31 "    0.008 2.00e-02 2.50e+03
        pdb=" N   LEU C  32 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E  31 "    0.006 2.00e-02 2.50e+03   1.25e-02 1.55e+00
        pdb=" C   VAL E  31 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   VAL E  31 "    0.008 2.00e-02 2.50e+03
        pdb=" N   LEU E  32 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  31 "    0.006 2.00e-02 2.50e+03   1.23e-02 1.51e+00
        pdb=" C   VAL A  31 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   VAL A  31 "    0.008 2.00e-02 2.50e+03
        pdb=" N   LEU A  32 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1509 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1884
        2.79 -     3.31: 8791
        3.31 -     3.84: 13923
        3.84 -     4.37: 15987
        4.37 -     4.90: 27618
  Nonbonded interactions: 68203
  Sorted by model distance:
  nonbonded pdb=" O   GLY F 153 "
            pdb=" OG1 THR F 156 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   GLY D 153 "
            pdb=" OG1 THR D 156 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   GLY B 153 "
            pdb=" OG1 THR B 156 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   LYS E   4 "
            pdb=" OH  TYR E  61 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   LYS A   4 "
            pdb=" OH  TYR A  61 "
     model   vdw
     2.259 3.040
  ... (remaining 68198 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             11.650
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.110
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.020
  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:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
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      :  0.001   0.012   8982  Z= 0.079
  Angle     :  0.369   4.883  12096  Z= 0.214
  Chirality :  0.032   0.119   1428
  Planarity :  0.002   0.017   1512
  Dihedral  : 14.143  87.859   3414
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  2.19 (0.27), residues: 1092
  helix:  1.93 (0.20), residues: 759
  sheet:  None (None), residues: 0
  loop :  0.46 (0.38), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  47 
 HIS   0.001   0.000   HIS F 116 
 PHE   0.005   0.001   PHE C 120 
 TYR   0.005   0.001   TYR D  87 
 ARG   0.002   0.000   ARG E  89 

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 308
  time to evaluate  : 1.142 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 ASP cc_start: 0.8495 (t0) cc_final: 0.8237 (t0)
REVERT: A   36 ASP cc_start: 0.8175 (p0) cc_final: 0.7838 (p0)
REVERT: A  100 LYS cc_start: 0.8432 (mttt) cc_final: 0.8093 (mttp)
REVERT: A  138 ASP cc_start: 0.8532 (t0) cc_final: 0.7505 (m-30)
REVERT: B   51 GLU cc_start: 0.7827 (tp30) cc_final: 0.7549 (tp30)
REVERT: B   60 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8251 (tm-30)
REVERT: B   61 TYR cc_start: 0.7580 (m-80) cc_final: 0.7120 (m-80)
REVERT: B   78 GLN cc_start: 0.8534 (mt0) cc_final: 0.7987 (mp10)
REVERT: B  100 LYS cc_start: 0.7056 (mptt) cc_final: 0.6121 (mmtm)
REVERT: C   11 ASP cc_start: 0.8830 (t0) cc_final: 0.8241 (t0)
REVERT: C   51 GLU cc_start: 0.8631 (tp30) cc_final: 0.8343 (tp30)
REVERT: C   78 GLN cc_start: 0.8740 (mt0) cc_final: 0.8035 (mm-40)
REVERT: C   89 ARG cc_start: 0.8002 (ttp-110) cc_final: 0.7471 (ptt-90)
REVERT: C  102 LEU cc_start: 0.7908 (tp) cc_final: 0.7620 (tp)
REVERT: C  103 LEU cc_start: 0.8695 (mp) cc_final: 0.8326 (mt)
REVERT: C  138 ASP cc_start: 0.8578 (t0) cc_final: 0.7980 (t0)
REVERT: C  159 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7883 (mt-10)
REVERT: D    6 ASN cc_start: 0.8302 (m-40) cc_final: 0.7901 (t0)
REVERT: D   48 LYS cc_start: 0.8270 (mmtp) cc_final: 0.7802 (mmtm)
REVERT: D   49 LYS cc_start: 0.8161 (mtpp) cc_final: 0.7917 (tptp)
REVERT: D   61 TYR cc_start: 0.7696 (m-80) cc_final: 0.7145 (m-80)
REVERT: D  133 LYS cc_start: 0.8591 (mttm) cc_final: 0.8296 (mtmm)
REVERT: D  151 TYR cc_start: 0.8631 (m-80) cc_final: 0.8358 (m-80)
REVERT: D  183 LYS cc_start: 0.7721 (mmtm) cc_final: 0.7405 (mtpt)
REVERT: E   11 ASP cc_start: 0.8648 (t0) cc_final: 0.8446 (t0)
REVERT: E   34 VAL cc_start: 0.8372 (t) cc_final: 0.8108 (t)
REVERT: E   51 GLU cc_start: 0.8620 (tp30) cc_final: 0.8418 (tp30)
REVERT: E   77 ARG cc_start: 0.8066 (ttm170) cc_final: 0.7805 (ttm170)
REVERT: E   78 GLN cc_start: 0.8744 (mt0) cc_final: 0.8483 (mt0)
REVERT: E  135 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7656 (pm20)
REVERT: E  173 ASN cc_start: 0.8467 (t0) cc_final: 0.7231 (m-40)
REVERT: E  185 ASP cc_start: 0.8487 (t70) cc_final: 0.8270 (m-30)
REVERT: F   11 ASP cc_start: 0.8406 (t0) cc_final: 0.8097 (p0)
REVERT: F   32 LEU cc_start: 0.8027 (tt) cc_final: 0.7734 (tt)
REVERT: F   48 LYS cc_start: 0.8390 (mmtp) cc_final: 0.8089 (tptp)
REVERT: F   59 ILE cc_start: 0.8142 (mt) cc_final: 0.7695 (mm)
REVERT: F  111 MET cc_start: 0.8768 (ttp) cc_final: 0.8412 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 308
  average time/residue: 0.2371
  time to fit residues: 95.8876
Evaluate side-chains
  210 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 81 optimal weight:    0.0980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0060
   chunk 84 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 98 optimal weight:    4.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
B   6 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.144016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.117113 restraints weight = 12265.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 2.48
r_work: 0.3191 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8982  Z= 0.181
  Angle     :  0.467   4.443  12096  Z= 0.250
  Chirality :  0.037   0.176   1428
  Planarity :  0.003   0.038   1512
  Dihedral  :  3.165  15.211   1176
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  7.42 %
    Favored  : 91.46 %
  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:  2.26 (0.26), residues: 1092
  helix:  1.97 (0.19), residues: 768
  sheet:  None (None), residues: 0
  loop :  0.49 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  47 
 HIS   0.002   0.000   HIS E 116 
 PHE   0.011   0.001   PHE E  66 
 TYR   0.012   0.002   TYR E  87 
 ARG   0.007   0.001   ARG B  52 

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 215
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   60 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8107 (tm-30)
REVERT: B   61 TYR cc_start: 0.7963 (m-80) cc_final: 0.7336 (m-80)
REVERT: B  100 LYS cc_start: 0.7474 (mptt) cc_final: 0.6378 (mmtp)
REVERT: C   11 ASP cc_start: 0.8675 (t0) cc_final: 0.8107 (t0)
REVERT: C   74 ILE cc_start: 0.8352 (mt) cc_final: 0.8083 (tp)
REVERT: C   78 GLN cc_start: 0.8916 (mt0) cc_final: 0.8575 (mm-40)
REVERT: C   89 ARG cc_start: 0.7960 (ttp-110) cc_final: 0.7674 (ptt-90)
REVERT: C  103 LEU cc_start: 0.8848 (mp) cc_final: 0.8425 (mt)
REVERT: C  159 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8010 (mt-10)
REVERT: C  173 ASN cc_start: 0.8502 (t0) cc_final: 0.8245 (t0)
REVERT: C  183 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8557 (tttt)
REVERT: D   49 LYS cc_start: 0.7917 (mtpp) cc_final: 0.7709 (tptp)
REVERT: D  111 MET cc_start: 0.8742 (ttp) cc_final: 0.8463 (ttm)
REVERT: E    6 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7647 (m-40)
REVERT: E   11 ASP cc_start: 0.8556 (t0) cc_final: 0.8301 (t0)
REVERT: E   77 ARG cc_start: 0.8594 (ttm170) cc_final: 0.8283 (ttm170)
REVERT: E   78 GLN cc_start: 0.8959 (mt0) cc_final: 0.8726 (mt0)
REVERT: E  138 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7580 (m-30)
REVERT: E  173 ASN cc_start: 0.8637 (t0) cc_final: 0.7752 (m110)
REVERT: F   30 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7251 (m-30)
REVERT: F   59 ILE cc_start: 0.8760 (mt) cc_final: 0.8296 (mm)
REVERT: F   64 ASP cc_start: 0.7836 (m-30) cc_final: 0.7570 (m-30)
REVERT: F  152 ASP cc_start: 0.7479 (t0) cc_final: 0.7060 (t0)
  outliers start: 11
  outliers final: 4
  residues processed: 219
  average time/residue: 0.2492
  time to fit residues: 71.5057
Evaluate side-chains
  195 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 188
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain E residue    6 ASN
Chi-restraints excluded: chain E residue   73 ASP
Chi-restraints excluded: chain E residue  138 ASP
Chi-restraints excluded: chain F residue   30 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 20 optimal weight:    0.1980
   chunk 24 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0970
   chunk 91 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
B   6 ASN
C  29 GLN
F  78 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.134294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.109040 restraints weight = 12100.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 2.03
r_work: 0.3055 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8982  Z= 0.242
  Angle     :  0.486   6.505  12096  Z= 0.255
  Chirality :  0.038   0.179   1428
  Planarity :  0.003   0.034   1512
  Dihedral  :  3.287  15.207   1176
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  9.55 %
    Favored  : 89.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.27 (0.26), residues: 1092
  helix:  2.07 (0.19), residues: 750
  sheet:  None (None), residues: 0
  loop :  0.32 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  47 
 HIS   0.002   0.001   HIS D 116 
 PHE   0.013   0.001   PHE B  20 
 TYR   0.013   0.002   TYR C  87 
 ARG   0.008   0.001   ARG B  52 

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 187
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 ASP cc_start: 0.8675 (t0) cc_final: 0.8435 (t0)
REVERT: A   60 GLU cc_start: 0.8904 (tp30) cc_final: 0.8622 (tp30)
REVERT: A  134 ILE cc_start: 0.8697 (mt) cc_final: 0.8455 (mt)
REVERT: B  100 LYS cc_start: 0.7730 (mptt) cc_final: 0.6560 (mmtt)
REVERT: C   11 ASP cc_start: 0.8887 (t0) cc_final: 0.8343 (t0)
REVERT: C   74 ILE cc_start: 0.8467 (mt) cc_final: 0.8247 (tp)
REVERT: C   78 GLN cc_start: 0.9142 (mt0) cc_final: 0.8779 (mm-40)
REVERT: C   89 ARG cc_start: 0.8111 (ttp-110) cc_final: 0.7494 (ptt-90)
REVERT: C  102 LEU cc_start: 0.8937 (tp) cc_final: 0.8612 (tp)
REVERT: C  103 LEU cc_start: 0.8876 (mp) cc_final: 0.8413 (mt)
REVERT: C  159 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8206 (mt-10)
REVERT: C  183 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8674 (tttt)
REVERT: D    6 ASN cc_start: 0.8162 (t0) cc_final: 0.7914 (t0)
REVERT: D   49 LYS cc_start: 0.7913 (mtpp) cc_final: 0.7709 (tptp)
REVERT: D   51 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7814 (mm-30)
REVERT: E   11 ASP cc_start: 0.8515 (t0) cc_final: 0.8294 (t0)
REVERT: E   39 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6938 (tpp)
REVERT: E   59 ILE cc_start: 0.9303 (mt) cc_final: 0.9059 (mp)
REVERT: E   77 ARG cc_start: 0.8656 (ttm170) cc_final: 0.8280 (ttm170)
REVERT: E   78 GLN cc_start: 0.9042 (mt0) cc_final: 0.8806 (mt0)
REVERT: E  138 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7788 (m-30)
REVERT: E  173 ASN cc_start: 0.8639 (t0) cc_final: 0.7813 (m110)
REVERT: F   30 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7595 (m-30)
REVERT: F   59 ILE cc_start: 0.8881 (mt) cc_final: 0.8599 (mm)
REVERT: F   60 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8137 (tp30)
  outliers start: 13
  outliers final: 7
  residues processed: 192
  average time/residue: 0.2649
  time to fit residues: 66.3953
Evaluate side-chains
  195 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 184
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 ASN
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain D residue  183 LYS
Chi-restraints excluded: chain E residue   39 MET
Chi-restraints excluded: chain E residue   73 ASP
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  138 ASP
Chi-restraints excluded: chain F residue   30 ASP
Chi-restraints excluded: chain F residue   60 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0980
   chunk 13 optimal weight:    0.7980
   chunk 63 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   chunk 103 optimal weight:    0.0770
   chunk 95 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
B   6 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.136978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.111986 restraints weight = 11964.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 2.01
r_work: 0.3052 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8982  Z= 0.149
  Angle     :  0.433   6.730  12096  Z= 0.230
  Chirality :  0.036   0.179   1428
  Planarity :  0.003   0.040   1512
  Dihedral  :  3.199  14.472   1176
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 11.38 %
    Favored  : 87.09 %
  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:  2.50 (0.26), residues: 1092
  helix:  2.25 (0.19), residues: 750
  sheet:  None (None), residues: 0
  loop :  0.40 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  47 
 HIS   0.002   0.000   HIS B 142 
 PHE   0.008   0.001   PHE B  20 
 TYR   0.013   0.002   TYR B  61 
 ARG   0.009   0.001   ARG B  52 

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 214
  time to evaluate  : 1.119 
Fit side-chains
REVERT: A   11 ASP cc_start: 0.8722 (t0) cc_final: 0.8426 (t0)
REVERT: A   60 GLU cc_start: 0.8904 (tp30) cc_final: 0.8620 (tp30)
REVERT: A  127 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8385 (tt)
REVERT: B   61 TYR cc_start: 0.8019 (m-80) cc_final: 0.7159 (m-80)
REVERT: B   78 GLN cc_start: 0.8601 (mt0) cc_final: 0.7781 (mp10)
REVERT: B  100 LYS cc_start: 0.7611 (mptt) cc_final: 0.6381 (mmtt)
REVERT: C   11 ASP cc_start: 0.8859 (t0) cc_final: 0.8317 (t0)
REVERT: C   74 ILE cc_start: 0.8420 (mt) cc_final: 0.8192 (tp)
REVERT: C   78 GLN cc_start: 0.9124 (mt0) cc_final: 0.8759 (mm-40)
REVERT: C   89 ARG cc_start: 0.8078 (ttp-110) cc_final: 0.7496 (ptt-90)
REVERT: C  102 LEU cc_start: 0.8826 (tp) cc_final: 0.8568 (tp)
REVERT: C  103 LEU cc_start: 0.8910 (mp) cc_final: 0.8513 (mt)
REVERT: C  159 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8421 (mt-10)
REVERT: C  173 ASN cc_start: 0.8593 (t0) cc_final: 0.8320 (t0)
REVERT: C  178 GLN cc_start: 0.9153 (tm-30) cc_final: 0.8297 (tm-30)
REVERT: C  183 LYS cc_start: 0.8960 (mmmt) cc_final: 0.8488 (mmmm)
REVERT: D   49 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7724 (tptp)
REVERT: D   51 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7745 (mm-30)
REVERT: E   11 ASP cc_start: 0.8506 (t0) cc_final: 0.8283 (t0)
REVERT: E   59 ILE cc_start: 0.9210 (mt) cc_final: 0.8960 (mp)
REVERT: E   77 ARG cc_start: 0.8612 (ttm170) cc_final: 0.8206 (ttm170)
REVERT: E   78 GLN cc_start: 0.9073 (mt0) cc_final: 0.8817 (mt0)
REVERT: E  138 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7852 (m-30)
REVERT: E  173 ASN cc_start: 0.8634 (t0) cc_final: 0.7821 (m110)
REVERT: F   59 ILE cc_start: 0.8783 (mt) cc_final: 0.8413 (mm)
REVERT: F   60 GLU cc_start: 0.8263 (tp30) cc_final: 0.7897 (tp30)
  outliers start: 15
  outliers final: 5
  residues processed: 223
  average time/residue: 0.2488
  time to fit residues: 74.0534
Evaluate side-chains
  194 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 187
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain D residue  183 LYS
Chi-restraints excluded: chain E residue   73 ASP
Chi-restraints excluded: chain E residue  138 ASP
Chi-restraints excluded: chain F residue   31 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 84 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 105 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 91 optimal weight:    0.6980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B   6 ASN
C  29 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.134959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.109931 restraints weight = 11832.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 2.00
r_work: 0.3016 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
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      :  0.003   0.036   8982  Z= 0.200
  Angle     :  0.465   7.107  12096  Z= 0.245
  Chirality :  0.037   0.179   1428
  Planarity :  0.003   0.044   1512
  Dihedral  :  3.266  14.307   1176
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.53 %
    Favored  : 83.94 %
  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:  2.50 (0.26), residues: 1092
  helix:  2.26 (0.19), residues: 750
  sheet:  None (None), residues: 0
  loop :  0.39 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  47 
 HIS   0.002   0.001   HIS C 142 
 PHE   0.010   0.001   PHE B  20 
 TYR   0.012   0.002   TYR B  61 
 ARG   0.010   0.001   ARG B  52 

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 194
  time to evaluate  : 1.286 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.8895 (tp30) cc_final: 0.8570 (tp30)
REVERT: A  127 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8436 (tt)
REVERT: A  134 ILE cc_start: 0.8805 (mt) cc_final: 0.8506 (mt)
REVERT: B   60 GLU cc_start: 0.8631 (tp30) cc_final: 0.8154 (tp30)
REVERT: B   61 TYR cc_start: 0.8099 (m-80) cc_final: 0.7049 (m-80)
REVERT: B   78 GLN cc_start: 0.8746 (mt0) cc_final: 0.7905 (mp10)
REVERT: B  100 LYS cc_start: 0.7618 (mptt) cc_final: 0.6557 (mmtt)
REVERT: C   11 ASP cc_start: 0.8868 (t0) cc_final: 0.8321 (t0)
REVERT: C   74 ILE cc_start: 0.8384 (mt) cc_final: 0.8156 (tp)
REVERT: C   78 GLN cc_start: 0.9148 (mt0) cc_final: 0.8764 (mm-40)
REVERT: C   89 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7475 (ptt-90)
REVERT: C  102 LEU cc_start: 0.8864 (tp) cc_final: 0.8624 (tp)
REVERT: C  103 LEU cc_start: 0.8887 (mp) cc_final: 0.8444 (mt)
REVERT: C  173 ASN cc_start: 0.8594 (t0) cc_final: 0.8305 (t0)
REVERT: C  178 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8043 (tm-30)
REVERT: C  182 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.7981 (mp)
REVERT: C  183 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8465 (mmmm)
REVERT: D   49 LYS cc_start: 0.8050 (mtpp) cc_final: 0.7767 (tptp)
REVERT: D   51 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7825 (mm-30)
REVERT: E   11 ASP cc_start: 0.8540 (t0) cc_final: 0.8318 (t0)
REVERT: E   77 ARG cc_start: 0.8670 (ttm170) cc_final: 0.8243 (ttm170)
REVERT: E   78 GLN cc_start: 0.9145 (mt0) cc_final: 0.8906 (mt0)
REVERT: E  138 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7846 (m-30)
REVERT: E  173 ASN cc_start: 0.8651 (t0) cc_final: 0.7845 (m110)
REVERT: E  185 ASP cc_start: 0.7977 (m-30) cc_final: 0.7703 (m-30)
REVERT: F   59 ILE cc_start: 0.8847 (mt) cc_final: 0.8471 (mm)
REVERT: F   60 GLU cc_start: 0.8127 (tp30) cc_final: 0.7900 (tp30)
  outliers start: 15
  outliers final: 8
  residues processed: 202
  average time/residue: 0.2472
  time to fit residues: 66.3858
Evaluate side-chains
  212 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 201
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain D residue   30 ASP
Chi-restraints excluded: chain D residue  183 LYS
Chi-restraints excluded: chain E residue   73 ASP
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  138 ASP
Chi-restraints excluded: chain F residue   31 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 42 optimal weight:    0.0060
   chunk 69 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.9598

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

Flipped N/Q/H residues before XYZ refinement:
B   6 ASN
F   6 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.133037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.107993 restraints weight = 11977.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 2.01
r_work: 0.2966 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2808 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.3469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8982  Z= 0.242
  Angle     :  0.486   7.447  12096  Z= 0.256
  Chirality :  0.037   0.191   1428
  Planarity :  0.003   0.051   1512
  Dihedral  :  3.314  14.509   1176
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.24 %
    Favored  : 83.23 %
  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:  2.33 (0.26), residues: 1092
  helix:  2.03 (0.19), residues: 768
  sheet:  None (None), residues: 0
  loop :  0.47 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C  47 
 HIS   0.003   0.001   HIS C 142 
 PHE   0.011   0.001   PHE B  20 
 TYR   0.013   0.002   TYR A  87 
 ARG   0.011   0.001   ARG B  52 

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 205
  time to evaluate  : 1.094 
Fit side-chains
REVERT: A   11 ASP cc_start: 0.8734 (t0) cc_final: 0.8484 (t0)
REVERT: A   60 GLU cc_start: 0.8899 (tp30) cc_final: 0.8560 (tp30)
REVERT: A  127 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8434 (tt)
REVERT: A  134 ILE cc_start: 0.8796 (mt) cc_final: 0.8492 (mt)
REVERT: B   60 GLU cc_start: 0.8601 (tp30) cc_final: 0.8052 (tp30)
REVERT: B   61 TYR cc_start: 0.8132 (m-80) cc_final: 0.7035 (m-80)
REVERT: B  100 LYS cc_start: 0.7683 (mptt) cc_final: 0.6606 (mmtt)
REVERT: B  159 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8032 (mt-10)
REVERT: C   11 ASP cc_start: 0.8885 (t0) cc_final: 0.8121 (t0)
REVERT: C   74 ILE cc_start: 0.8330 (mt) cc_final: 0.8110 (tp)
REVERT: C   78 GLN cc_start: 0.9158 (mt0) cc_final: 0.8672 (mm-40)
REVERT: C   89 ARG cc_start: 0.8106 (ttp-110) cc_final: 0.7487 (ptt-90)
REVERT: C  102 LEU cc_start: 0.8902 (tp) cc_final: 0.8670 (tp)
REVERT: C  103 LEU cc_start: 0.8973 (mp) cc_final: 0.8528 (mt)
REVERT: C  173 ASN cc_start: 0.8608 (t0) cc_final: 0.8340 (t0)
REVERT: C  178 GLN cc_start: 0.9198 (tm-30) cc_final: 0.7967 (tm-30)
REVERT: C  182 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.7849 (mp)
REVERT: C  183 LYS cc_start: 0.9004 (mmmt) cc_final: 0.8455 (mmmm)
REVERT: D   49 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7785 (tptp)
REVERT: D   51 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7858 (mm-30)
REVERT: E   11 ASP cc_start: 0.8547 (t0) cc_final: 0.8324 (t0)
REVERT: E   59 ILE cc_start: 0.9252 (mt) cc_final: 0.9006 (mp)
REVERT: E   77 ARG cc_start: 0.8714 (ttm170) cc_final: 0.8286 (ttm170)
REVERT: E   78 GLN cc_start: 0.9159 (mt0) cc_final: 0.8924 (mt0)
REVERT: E  138 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7976 (m-30)
REVERT: E  173 ASN cc_start: 0.8647 (t0) cc_final: 0.7826 (m110)
REVERT: E  185 ASP cc_start: 0.8103 (m-30) cc_final: 0.7789 (m-30)
REVERT: F   59 ILE cc_start: 0.8872 (mt) cc_final: 0.8574 (mm)
REVERT: F   60 GLU cc_start: 0.8194 (tp30) cc_final: 0.7923 (tp30)
  outliers start: 15
  outliers final: 8
  residues processed: 211
  average time/residue: 0.2398
  time to fit residues: 66.8484
Evaluate side-chains
  193 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 182
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain B residue    6 ASN
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain D residue  183 LYS
Chi-restraints excluded: chain E residue   73 ASP
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  138 ASP
Chi-restraints excluded: chain F residue   31 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 14 optimal weight:    0.0050
   chunk 62 optimal weight:    2.9990
   chunk 73 optimal weight:    0.3980
   chunk 95 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 103 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
D  29 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.136305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.111352 restraints weight = 12046.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 2.02
r_work: 0.3027 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.3457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051   8982  Z= 0.162
  Angle     :  0.458   7.276  12096  Z= 0.243
  Chirality :  0.036   0.197   1428
  Planarity :  0.003   0.049   1512
  Dihedral  :  3.226  13.680   1176
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 16.36 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.49 (0.26), residues: 1092
  helix:  2.16 (0.19), residues: 768
  sheet:  None (None), residues: 0
  loop :  0.50 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C  47 
 HIS   0.002   0.000   HIS B 142 
 PHE   0.006   0.001   PHE C  66 
 TYR   0.013   0.002   TYR E  61 
 ARG   0.011   0.001   ARG B  52 

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 196
  time to evaluate  : 1.098 
Fit side-chains
REVERT: A   11 ASP cc_start: 0.8731 (t0) cc_final: 0.8451 (t0)
REVERT: A   60 GLU cc_start: 0.8903 (tp30) cc_final: 0.8563 (tp30)
REVERT: A  127 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8380 (tt)
REVERT: A  134 ILE cc_start: 0.8757 (mt) cc_final: 0.8443 (mt)
REVERT: B   60 GLU cc_start: 0.8538 (tp30) cc_final: 0.8023 (tp30)
REVERT: B   61 TYR cc_start: 0.8046 (m-80) cc_final: 0.7069 (m-80)
REVERT: B   78 GLN cc_start: 0.8819 (mt0) cc_final: 0.7801 (mp10)
REVERT: B  100 LYS cc_start: 0.7656 (mptt) cc_final: 0.6542 (mmtp)
REVERT: C   11 ASP cc_start: 0.8872 (t0) cc_final: 0.8127 (t0)
REVERT: C   74 ILE cc_start: 0.8267 (mt) cc_final: 0.8043 (tp)
REVERT: C   78 GLN cc_start: 0.9035 (mt0) cc_final: 0.8564 (mm-40)
REVERT: C   89 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.7517 (ptt-90)
REVERT: C  103 LEU cc_start: 0.8962 (mp) cc_final: 0.8523 (mt)
REVERT: C  173 ASN cc_start: 0.8562 (t0) cc_final: 0.8307 (t0)
REVERT: C  178 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8170 (tm-30)
REVERT: C  183 LYS cc_start: 0.8933 (mmmt) cc_final: 0.8418 (mmmm)
REVERT: D   49 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7742 (tptp)
REVERT: D   51 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7781 (mm-30)
REVERT: E    6 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.8020 (m-40)
REVERT: E   11 ASP cc_start: 0.8539 (t0) cc_final: 0.8322 (t0)
REVERT: E   77 ARG cc_start: 0.8648 (ttm170) cc_final: 0.8187 (ttm170)
REVERT: E   78 GLN cc_start: 0.9091 (mt0) cc_final: 0.8854 (mt0)
REVERT: E  138 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8007 (m-30)
REVERT: E  173 ASN cc_start: 0.8628 (t0) cc_final: 0.7823 (m110)
REVERT: E  185 ASP cc_start: 0.8123 (m-30) cc_final: 0.7801 (m-30)
REVERT: F   59 ILE cc_start: 0.8842 (mt) cc_final: 0.8560 (mm)
REVERT: F   60 GLU cc_start: 0.8327 (tp30) cc_final: 0.7859 (tp30)
  outliers start: 14
  outliers final: 9
  residues processed: 204
  average time/residue: 0.2332
  time to fit residues: 63.8232
Evaluate side-chains
  195 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 183
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain D residue  183 LYS
Chi-restraints excluded: chain E residue    6 ASN
Chi-restraints excluded: chain E residue   73 ASP
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  138 ASP
Chi-restraints excluded: chain F residue    6 ASN
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain F residue   34 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 107 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 59 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B   6 ASN
D   6 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.134544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.109878 restraints weight = 12102.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 1.98
r_work: 0.2991 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2835 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.3606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8982  Z= 0.221
  Angle     :  0.497   6.999  12096  Z= 0.261
  Chirality :  0.037   0.198   1428
  Planarity :  0.003   0.053   1512
  Dihedral  :  3.254  13.942   1176
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 16.97 %
    Favored  : 81.40 %
  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:  2.41 (0.26), residues: 1092
  helix:  2.09 (0.19), residues: 768
  sheet:  None (None), residues: 0
  loop :  0.50 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C  47 
 HIS   0.004   0.001   HIS C 142 
 PHE   0.011   0.001   PHE B  20 
 TYR   0.016   0.002   TYR C  61 
 ARG   0.011   0.001   ARG B  52 

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 189
  time to evaluate  : 1.095 
Fit side-chains
REVERT: A   11 ASP cc_start: 0.8728 (t0) cc_final: 0.8461 (t0)
REVERT: A   60 GLU cc_start: 0.8902 (tp30) cc_final: 0.8562 (tp30)
REVERT: A  127 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8417 (tt)
REVERT: A  134 ILE cc_start: 0.8791 (mt) cc_final: 0.8486 (mt)
REVERT: B   60 GLU cc_start: 0.8601 (tp30) cc_final: 0.8059 (tp30)
REVERT: B   61 TYR cc_start: 0.8187 (m-80) cc_final: 0.7208 (m-80)
REVERT: B   78 GLN cc_start: 0.8835 (mt0) cc_final: 0.7795 (mp10)
REVERT: B  100 LYS cc_start: 0.7676 (mptt) cc_final: 0.6601 (mmtt)
REVERT: C   11 ASP cc_start: 0.8870 (t0) cc_final: 0.8107 (t0)
REVERT: C   74 ILE cc_start: 0.8319 (mt) cc_final: 0.8100 (tp)
REVERT: C   78 GLN cc_start: 0.9051 (mt0) cc_final: 0.8589 (mm-40)
REVERT: C   89 ARG cc_start: 0.8102 (ttp-110) cc_final: 0.7527 (ptt-90)
REVERT: C  103 LEU cc_start: 0.8970 (mp) cc_final: 0.8663 (mt)
REVERT: C  173 ASN cc_start: 0.8578 (t0) cc_final: 0.8324 (t0)
REVERT: C  178 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8016 (tm-30)
REVERT: C  182 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.7910 (mp)
REVERT: C  183 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8403 (mmmm)
REVERT: D   49 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7783 (tptp)
REVERT: D   51 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7854 (mm-30)
REVERT: E    6 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.8056 (m-40)
REVERT: E   11 ASP cc_start: 0.8532 (t0) cc_final: 0.8325 (t0)
REVERT: E   77 ARG cc_start: 0.8691 (ttm170) cc_final: 0.8262 (ttm170)
REVERT: E   78 GLN cc_start: 0.9141 (mt0) cc_final: 0.8907 (mt0)
REVERT: E  138 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8017 (m-30)
REVERT: E  173 ASN cc_start: 0.8637 (t0) cc_final: 0.7848 (m110)
REVERT: E  185 ASP cc_start: 0.8156 (m-30) cc_final: 0.7869 (m-30)
REVERT: F   60 GLU cc_start: 0.8327 (tp30) cc_final: 0.7857 (tp30)
  outliers start: 16
  outliers final: 10
  residues processed: 198
  average time/residue: 0.2367
  time to fit residues: 62.6623
Evaluate side-chains
  196 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 182
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain B residue    6 ASN
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  185 ASP
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain D residue  183 LYS
Chi-restraints excluded: chain E residue    6 ASN
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  138 ASP
Chi-restraints excluded: chain F residue    6 ASN
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain F residue   34 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0670
   chunk 59 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.6320

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

Flipped N/Q/H residues before XYZ refinement:
B   6 ASN
D  29 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.135860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.111009 restraints weight = 12040.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 2.01
r_work: 0.3007 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8982  Z= 0.193
  Angle     :  0.493   7.886  12096  Z= 0.259
  Chirality :  0.037   0.204   1428
  Planarity :  0.003   0.054   1512
  Dihedral  :  3.265  13.916   1176
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 17.28 %
    Favored  : 81.40 %
  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:  2.45 (0.26), residues: 1092
  helix:  2.11 (0.19), residues: 768
  sheet:  None (None), residues: 0
  loop :  0.54 (0.38), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C  47 
 HIS   0.002   0.001   HIS C 142 
 PHE   0.011   0.001   PHE B  20 
 TYR   0.019   0.002   TYR C  61 
 ARG   0.013   0.001   ARG B  52 

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 186
  time to evaluate  : 1.004 
Fit side-chains
REVERT: A   11 ASP cc_start: 0.8753 (t0) cc_final: 0.8532 (t0)
REVERT: A   60 GLU cc_start: 0.8906 (tp30) cc_final: 0.8539 (tp30)
REVERT: A  127 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8410 (tt)
REVERT: A  134 ILE cc_start: 0.8793 (mt) cc_final: 0.8492 (mt)
REVERT: B   60 GLU cc_start: 0.8611 (tp30) cc_final: 0.8077 (tp30)
REVERT: B   61 TYR cc_start: 0.8166 (m-80) cc_final: 0.7239 (m-80)
REVERT: B   78 GLN cc_start: 0.8805 (mt0) cc_final: 0.7772 (mp10)
REVERT: B  100 LYS cc_start: 0.7665 (mptt) cc_final: 0.6564 (mmtp)
REVERT: C   11 ASP cc_start: 0.8880 (t0) cc_final: 0.8106 (t0)
REVERT: C   74 ILE cc_start: 0.8314 (mt) cc_final: 0.8061 (tp)
REVERT: C   78 GLN cc_start: 0.9055 (mt0) cc_final: 0.8588 (mm-40)
REVERT: C   89 ARG cc_start: 0.8073 (ttp-110) cc_final: 0.7530 (ptt-90)
REVERT: C  103 LEU cc_start: 0.8988 (mp) cc_final: 0.8663 (mt)
REVERT: C  173 ASN cc_start: 0.8596 (t0) cc_final: 0.8358 (t0)
REVERT: C  178 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8175 (tm-30)
REVERT: C  183 LYS cc_start: 0.8938 (mmmt) cc_final: 0.8415 (mmmm)
REVERT: D    6 ASN cc_start: 0.8133 (t160) cc_final: 0.7918 (t0)
REVERT: D   51 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7802 (mm-30)
REVERT: E   11 ASP cc_start: 0.8525 (t0) cc_final: 0.8287 (t0)
REVERT: E   77 ARG cc_start: 0.8693 (ttm170) cc_final: 0.8264 (ttm170)
REVERT: E   78 GLN cc_start: 0.9083 (mt0) cc_final: 0.8838 (mt0)
REVERT: E  127 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8368 (tt)
REVERT: E  138 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8005 (m-30)
REVERT: E  173 ASN cc_start: 0.8636 (t0) cc_final: 0.7847 (m110)
REVERT: E  185 ASP cc_start: 0.8089 (m-30) cc_final: 0.7862 (m-30)
REVERT: F   60 GLU cc_start: 0.8237 (tp30) cc_final: 0.7874 (tp30)
  outliers start: 13
  outliers final: 10
  residues processed: 192
  average time/residue: 0.2501
  time to fit residues: 63.2021
Evaluate side-chains
  188 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 175
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain B residue    6 ASN
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain D residue  111 MET
Chi-restraints excluded: chain D residue  183 LYS
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  127 LEU
Chi-restraints excluded: chain E residue  138 ASP
Chi-restraints excluded: chain F residue    6 ASN
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain F residue   34 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 37 optimal weight:    0.3980
   chunk 56 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 96 optimal weight:    0.4980
   chunk 4 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B   6 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.135703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.110908 restraints weight = 11921.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.00
r_work: 0.2979 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.3689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8982  Z= 0.211
  Angle     :  0.508   7.630  12096  Z= 0.267
  Chirality :  0.038   0.209   1428
  Planarity :  0.003   0.057   1512
  Dihedral  :  3.270  13.792   1176
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 17.07 %
    Favored  : 81.40 %
  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:  2.41 (0.26), residues: 1092
  helix:  2.09 (0.19), residues: 768
  sheet:  None (None), residues: 0
  loop :  0.54 (0.38), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C  47 
 HIS   0.003   0.001   HIS C 142 
 PHE   0.011   0.001   PHE B  20 
 TYR   0.023   0.002   TYR C  61 
 ARG   0.013   0.001   ARG B  52 

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 193
  time to evaluate  : 1.029 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.8895 (tp30) cc_final: 0.8515 (tp30)
REVERT: A  127 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8421 (tt)
REVERT: A  134 ILE cc_start: 0.8815 (mt) cc_final: 0.8519 (mt)
REVERT: B   60 GLU cc_start: 0.8643 (tp30) cc_final: 0.8072 (tp30)
REVERT: B   61 TYR cc_start: 0.8192 (m-80) cc_final: 0.7228 (m-80)
REVERT: B   78 GLN cc_start: 0.8788 (mt0) cc_final: 0.7697 (mp10)
REVERT: B  100 LYS cc_start: 0.7694 (mptt) cc_final: 0.6571 (mmtp)
REVERT: C   11 ASP cc_start: 0.8881 (t0) cc_final: 0.8108 (t0)
REVERT: C   74 ILE cc_start: 0.8303 (mt) cc_final: 0.8061 (tp)
REVERT: C   78 GLN cc_start: 0.8970 (mt0) cc_final: 0.8515 (mm-40)
REVERT: C   89 ARG cc_start: 0.7930 (ttp-110) cc_final: 0.7392 (ptt-90)
REVERT: C  103 LEU cc_start: 0.8844 (mp) cc_final: 0.8505 (mt)
REVERT: C  173 ASN cc_start: 0.8591 (t0) cc_final: 0.8348 (t0)
REVERT: C  178 GLN cc_start: 0.9080 (tm-30) cc_final: 0.7991 (tm-30)
REVERT: C  182 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.7898 (mp)
REVERT: C  183 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8405 (mmmm)
REVERT: D    6 ASN cc_start: 0.8118 (t160) cc_final: 0.7876 (t0)
REVERT: D   51 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7826 (mm-30)
REVERT: E   11 ASP cc_start: 0.8506 (t0) cc_final: 0.8285 (t0)
REVERT: E   77 ARG cc_start: 0.8705 (ttm170) cc_final: 0.8269 (ttm170)
REVERT: E   78 GLN cc_start: 0.9096 (mt0) cc_final: 0.8852 (mt0)
REVERT: E  127 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8401 (tt)
REVERT: E  138 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8006 (m-30)
REVERT: E  173 ASN cc_start: 0.8662 (t0) cc_final: 0.7861 (m110)
REVERT: E  185 ASP cc_start: 0.8122 (m-30) cc_final: 0.7910 (m-30)
REVERT: F  102 LEU cc_start: 0.8794 (tt) cc_final: 0.8524 (tp)
  outliers start: 15
  outliers final: 11
  residues processed: 199
  average time/residue: 0.2525
  time to fit residues: 66.5884
Evaluate side-chains
  206 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 191
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain B residue    6 ASN
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  185 ASP
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain D residue  111 MET
Chi-restraints excluded: chain D residue  183 LYS
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  127 LEU
Chi-restraints excluded: chain E residue  138 ASP
Chi-restraints excluded: chain F residue    6 ASN
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain F residue   34 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 101 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0970
   chunk 62 optimal weight:    4.9990
   chunk 92 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 85 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0970
   overall best weight:    0.4376

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

Flipped N/Q/H residues before XYZ refinement:
B   6 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.137399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.113275 restraints weight = 11921.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.92
r_work: 0.3037 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.3645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8982  Z= 0.167
  Angle     :  0.495   7.825  12096  Z= 0.261
  Chirality :  0.037   0.207   1428
  Planarity :  0.003   0.056   1512
  Dihedral  :  3.222  14.376   1176
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 17.07 %
    Favored  : 81.50 %
  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:  2.51 (0.26), residues: 1092
  helix:  2.16 (0.19), residues: 768
  sheet:  None (None), residues: 0
  loop :  0.56 (0.38), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  47 
 HIS   0.002   0.000   HIS C 142 
 PHE   0.008   0.001   PHE B  20 
 TYR   0.023   0.002   TYR C  61 
 ARG   0.013   0.001   ARG B  52 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4939.29 seconds
wall clock time: 85 minutes 36.28 seconds (5136.28 seconds total)