Starting phenix.real_space_refine
on Wed Mar  4 02:06:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6skm_10228/03_2026/6skm_10228.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6skm_10228/03_2026/6skm_10228.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6skm_10228/03_2026/6skm_10228.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6skm_10228/03_2026/6skm_10228.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6skm_10228/03_2026/6skm_10228.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6skm_10228/03_2026/6skm_10228.map"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.007
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      78      5.16       5
     C    6508      2.51       5
     N    1800      2.21       5
     O    1950      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10336
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1728
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 220, 1720
          Classifications: {'peptide': 220}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203}
      Conformer: "B"
        Number of residues, atoms: 220, 1720
          Classifications: {'peptide': 220}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203}
          bond proxies already assigned to first conformer: 1749
    Chain: "B"
      Number of atoms: 1720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1720
          Classifications: {'peptide': 220}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203}
    Chain: "C"
      Number of atoms: 1720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1720
          Classifications: {'peptide': 220}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203}
    Chain: "D"
      Number of atoms: 1728
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 220, 1720
          Classifications: {'peptide': 220}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203}
      Conformer: "B"
        Number of residues, atoms: 220, 1720
          Classifications: {'peptide': 220}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203}
          bond proxies already assigned to first conformer: 1749
    Chain: "E"
      Number of atoms: 1720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1720
          Classifications: {'peptide': 220}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203}
    Chain: "F"
      Number of atoms: 1720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1720
          Classifications: {'peptide': 220}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203}
  Time building chain proxies: 3.28, per 1000 atoms: 0.32
  Number of scatterers: 10336
  At special positions: 0
  Unit cell: (115.9, 111.02, 84.18, 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      78     16.00
     O    1950      8.00
     N    1800      7.00
     C    6508      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 198 " - pdb=" SG  CYS A 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 198 " - pdb=" SG  CYS B 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 198 " - pdb=" SG  CYS C 218 " distance=1.53
    Simple disulfide: pdb=" SG  CYS D 198 " - pdb=" SG  CYS D 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 198 " - pdb=" SG  CYS E 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 198 " - pdb=" SG  CYS F 218 " distance=2.19

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 592.1 milliseconds
  

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2476

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 4 sheets defined
      67.0% alpha, 0.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 30
      removed outlier: 3.511A  pdb=" N   GLU A  28 " --> pdb=" O   VAL A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 44
    Processing helix  chain 'A' and resid 48 through 58
    Processing helix  chain 'A' and resid 62 through 84
    Processing helix  chain 'A' and resid 100 through 106
    Processing helix  chain 'A' and resid 110 through 119
    Processing helix  chain 'A' and resid 125 through 145
    Processing helix  chain 'A' and resid 160 through 175
    Processing helix  chain 'A' and resid 178 through 193
      removed outlier: 4.194A  pdb=" N   ASN A 183 " --> pdb=" O   GLN A 179 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   TRP A 184 " --> pdb=" O   GLU A 180 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   MET A 185 " --> pdb=" O   VAL A 181 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   THR A 186 " --> pdb=" O   LYS A 182 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   LEU A 190 " --> pdb=" O   THR A 186 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   VAL A 191 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 206
    Processing helix  chain 'A' and resid 210 through 220
    Processing helix  chain 'B' and resid 16 through 31
      removed outlier: 3.595A  pdb=" N   LYS B  30 " --> pdb=" O   VAL B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 44
    Processing helix  chain 'B' and resid 48 through 58
    Processing helix  chain 'B' and resid 62 through 84
    Processing helix  chain 'B' and resid 100 through 105
      removed outlier: 4.208A  pdb=" N   ALA B 105 " --> pdb=" O   GLY B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 119
      removed outlier: 3.586A  pdb=" N   GLN B 114 " --> pdb=" O   THR B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 145
      removed outlier: 3.524A  pdb=" N   ILE B 129 " --> pdb=" O   PRO B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 175
    Processing helix  chain 'B' and resid 178 through 191
      removed outlier: 3.578A  pdb=" N   LYS B 182 " --> pdb=" O   SER B 178 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ASN B 183 " --> pdb=" O   GLN B 179 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   TRP B 184 " --> pdb=" O   GLU B 180 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLU B 187 " --> pdb=" O   ASN B 183 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   VAL B 191 " --> pdb=" O   GLU B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 206
    Processing helix  chain 'B' and resid 210 through 218
      removed outlier: 3.956A  pdb=" N   MET B 214 " --> pdb=" O   THR B 210 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   CYS B 218 " --> pdb=" O   MET B 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 31
      removed outlier: 3.606A  pdb=" N   LEU C  20 " --> pdb=" O   SER C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 44
      removed outlier: 3.616A  pdb=" N   MET C  39 " --> pdb=" O   GLU C  35 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 58
    Processing helix  chain 'C' and resid 62 through 84
      removed outlier: 3.627A  pdb=" N   MET C  66 " --> pdb=" O   HIS C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 119
    Processing helix  chain 'C' and resid 125 through 145
    Processing helix  chain 'C' and resid 160 through 174
      removed outlier: 3.695A  pdb=" N   TYR C 164 " --> pdb=" O   PRO C 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 178 through 186
    Processing helix  chain 'C' and resid 188 through 193
    Processing helix  chain 'C' and resid 195 through 204
    Processing helix  chain 'C' and resid 210 through 219
      removed outlier: 3.625A  pdb=" N   GLN C 219 " --> pdb=" O   MET C 215 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 16 through 31
      removed outlier: 3.548A  pdb=" N   LEU D  20 " --> pdb=" O   SER D  16 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 35 through 44
    Processing helix  chain 'D' and resid 48 through 58
    Processing helix  chain 'D' and resid 62 through 84
    Processing helix  chain 'D' and resid 100 through 106
    Processing helix  chain 'D' and resid 110 through 119
      removed outlier: 3.718A  pdb=" N   GLN D 114 " --> pdb=" O   THR D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 125 through 146
    Processing helix  chain 'D' and resid 160 through 173
    Processing helix  chain 'D' and resid 178 through 193
      removed outlier: 3.703A  pdb=" N   TRP D 184 " --> pdb=" O   GLU D 180 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   LEU D 190 " --> pdb=" O   THR D 186 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   VAL D 191 " --> pdb=" O   GLU D 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 195 through 206
    Processing helix  chain 'D' and resid 210 through 220
      removed outlier: 3.533A  pdb=" N   GLY D 220 " --> pdb=" O   THR D 216 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 16 through 31
    Processing helix  chain 'E' and resid 35 through 44
      removed outlier: 3.634A  pdb=" N   MET E  39 " --> pdb=" O   GLU E  35 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 48 through 59
      removed outlier: 4.008A  pdb=" N   VAL E  59 " --> pdb=" O   MET E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 84
    Processing helix  chain 'E' and resid 100 through 105
      removed outlier: 4.176A  pdb=" N   ALA E 105 " --> pdb=" O   GLY E 101 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 110 through 119
      removed outlier: 3.648A  pdb=" N   GLN E 114 " --> pdb=" O   THR E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 125 through 145
    Processing helix  chain 'E' and resid 160 through 175
    Processing helix  chain 'E' and resid 178 through 191
      removed outlier: 4.188A  pdb=" N   TRP E 184 " --> pdb=" O   GLU E 180 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLU E 187 " --> pdb=" O   ASN E 183 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   VAL E 191 " --> pdb=" O   GLU E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 195 through 206
    Processing helix  chain 'E' and resid 210 through 218
      removed outlier: 3.970A  pdb=" N   MET E 214 " --> pdb=" O   THR E 210 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   CYS E 218 " --> pdb=" O   MET E 214 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 16 through 31
      removed outlier: 3.731A  pdb=" N   LEU F  20 " --> pdb=" O   SER F  16 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 35 through 44
    Processing helix  chain 'F' and resid 48 through 58
    Processing helix  chain 'F' and resid 62 through 84
      removed outlier: 3.546A  pdb=" N   MET F  66 " --> pdb=" O   HIS F  62 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 110 through 119
      removed outlier: 3.507A  pdb=" N   GLN F 114 " --> pdb=" O   THR F 110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 125 through 145
    Processing helix  chain 'F' and resid 160 through 174
      removed outlier: 3.554A  pdb=" N   TYR F 164 " --> pdb=" O   PRO F 160 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 178 through 186
    Processing helix  chain 'F' and resid 188 through 193
    Processing helix  chain 'F' and resid 195 through 206
      removed outlier: 3.617A  pdb=" N   GLY F 206 " --> pdb=" O   LEU F 202 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 210 through 219
      removed outlier: 3.717A  pdb=" N   GLN F 219 " --> pdb=" O   MET F 215 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4
      removed outlier: 3.569A  pdb=" N   VAL A   3 " --> pdb=" O   VAL A  11 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   VAL A  11 " --> pdb=" O   VAL A   3 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 2 through 3
      removed outlier: 4.465A  pdb=" N   VAL C   3 " --> pdb=" O   VAL C  11 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   VAL C  11 " --> pdb=" O   VAL C   3 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'D' and resid 2 through 4
      removed outlier: 3.794A  pdb=" N   VAL D   3 " --> pdb=" O   VAL D  11 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   VAL D  11 " --> pdb=" O   VAL D   3 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'F' and resid 2 through 3
      removed outlier: 4.588A  pdb=" N   VAL F   3 " --> pdb=" O   VAL F  11 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   VAL F  11 " --> pdb=" O   VAL F   3 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    577 hydrogen bonds defined for protein.
    1731 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.46

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2958
        1.34 -     1.45: 1564
        1.45 -     1.57: 5900
        1.57 -     1.69: 0
        1.69 -     1.81: 144
  Bond restraints: 10566
  Sorted by residual:
  bond pdb=" N   PRO D  38 "
       pdb=" CD  PRO D  38 "
    ideal  model  delta    sigma   weight residual
    1.473  1.535 -0.062 1.40e-02 5.10e+03 1.98e+01
  bond pdb=" N   PRO A  38 "
       pdb=" CD  PRO A  38 "
    ideal  model  delta    sigma   weight residual
    1.473  1.532 -0.059 1.40e-02 5.10e+03 1.78e+01
  bond pdb=" N   PRO A  34 "
       pdb=" CD  PRO A  34 "
    ideal  model  delta    sigma   weight residual
    1.473  1.532 -0.059 1.40e-02 5.10e+03 1.77e+01
  bond pdb=" C   SER A  33 "
       pdb=" N   PRO A  34 "
    ideal  model  delta    sigma   weight residual
    1.335  1.388 -0.053 1.28e-02 6.10e+03 1.74e+01
  bond pdb=" N   PRO E  34 "
       pdb=" CD  PRO E  34 "
    ideal  model  delta    sigma   weight residual
    1.473  1.531 -0.058 1.40e-02 5.10e+03 1.73e+01
  ... (remaining 10561 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.64: 14192
        2.64 -     5.27: 158
        5.27 -     7.91: 12
        7.91 -    10.54: 0
       10.54 -    13.18: 4
  Bond angle restraints: 14366
  Sorted by residual:
  angle pdb=" CA  ILE D  37 "
        pdb=" C   ILE D  37 "
        pdb=" N   PRO D  38 "
      ideal   model   delta    sigma   weight residual
     121.00  114.88    6.12 8.30e-01 1.45e+00 5.44e+01
  angle pdb=" N   GLU C  29 "
        pdb=" CA  GLU C  29 "
        pdb=" C   GLU C  29 "
      ideal   model   delta    sigma   weight residual
     111.36  118.39   -7.03 1.09e+00 8.42e-01 4.15e+01
  angle pdb=" N   GLU B  29 "
        pdb=" CA  GLU B  29 "
        pdb=" C   GLU B  29 "
      ideal   model   delta    sigma   weight residual
     111.36  118.26   -6.90 1.09e+00 8.42e-01 4.00e+01
  angle pdb=" C   ILE E  37 "
        pdb=" CA  ILE E  37 "
        pdb=" CB  ILE E  37 "
      ideal   model   delta    sigma   weight residual
     114.35  107.81    6.54 1.06e+00 8.90e-01 3.80e+01
  angle pdb=" O   ILE D  37 "
        pdb=" C   ILE D  37 "
        pdb=" N   PRO D  38 "
      ideal   model   delta    sigma   weight residual
     120.07  124.08   -4.01 7.10e-01 1.98e+00 3.18e+01
  ... (remaining 14361 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 6209
       17.91 -    35.83: 276
       35.83 -    53.74: 31
       53.74 -    71.66: 2
       71.66 -    89.57: 4
  Dihedral angle restraints: 6522
    sinusoidal: 2704
      harmonic: 3818
  Sorted by residual:
  dihedral pdb=" CB  CYS C 198 "
           pdb=" SG  CYS C 198 "
           pdb=" SG  CYS C 218 "
           pdb=" CB  CYS C 218 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -13.10  -72.90     1      1.00e+01 1.00e-02 6.78e+01
  dihedral pdb=" CB  CYS F 198 "
           pdb=" SG  CYS F 198 "
           pdb=" SG  CYS F 218 "
           pdb=" CB  CYS F 218 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.93   31.93     1      1.00e+01 1.00e-02 1.45e+01
  dihedral pdb=" C   PHE E  32 "
           pdb=" N   PHE E  32 "
           pdb=" CA  PHE E  32 "
           pdb=" CB  PHE E  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.69    8.09     0      2.50e+00 1.60e-01 1.05e+01
  ... (remaining 6519 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1234
       0.045 -    0.090: 270
       0.090 -    0.135: 79
       0.135 -    0.180: 15
       0.180 -    0.225: 6
  Chirality restraints: 1604
  Sorted by residual:
  chirality pdb=" CA  GLU B  29 "
            pdb=" N   GLU B  29 "
            pdb=" C   GLU B  29 "
            pdb=" CB  GLU B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  LYS C  30 "
            pdb=" N   LYS C  30 "
            pdb=" C   LYS C  30 "
            pdb=" CB  LYS C  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  VAL F  27 "
            pdb=" N   VAL F  27 "
            pdb=" C   VAL F  27 "
            pdb=" CB  VAL F  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 1601 not shown)

  Planarity restraints: 1882
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E  37 "   -0.047 5.00e-02 4.00e+02   6.98e-02 7.79e+00
        pdb=" N   PRO E  38 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO E  38 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO E  38 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU F  35 "    0.010 2.00e-02 2.50e+03   2.05e-02 4.19e+00
        pdb=" C   GLU F  35 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   GLU F  35 "    0.013 2.00e-02 2.50e+03
        pdb=" N   VAL F  36 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR E  19 "   -0.008 2.00e-02 2.50e+03   1.58e-02 2.50e+00
        pdb=" C   THR E  19 "    0.027 2.00e-02 2.50e+03
        pdb=" O   THR E  19 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LEU E  20 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1879 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.14: 2
        2.14 -     2.83: 3178
        2.83 -     3.52: 14574
        3.52 -     4.21: 22221
        4.21 -     4.90: 38333
  Nonbonded interactions: 78308
  Sorted by model distance:
  nonbonded pdb=" O   THR D  58 "
            pdb=" OE2 GLU E  35 "
     model   vdw
     1.449 3.040
  nonbonded pdb=" O   PRO F  17 "
            pdb=" OD1 ASN F  21 "
     model   vdw
     2.029 3.040
  nonbonded pdb=" NZ  LYS C  30 "
            pdb=" OE2 GLU C  35 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" O   PRO F  17 "
            pdb=" CG  ASN F  21 "
     model   vdw
     2.204 3.270
  nonbonded pdb=" OH  TYR D 145 "
            pdb=" NH2 ARG E 162 "
     model   vdw
     2.308 3.120
  ... (remaining 78303 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 17 or resid 19 through 220))
  selection = (chain 'B' and (resid 1 through 17 or resid 19 through 220))
  selection = (chain 'C' and (resid 1 through 17 or resid 19 through 220))
  selection = (chain 'D' and (resid 1 through 17 or resid 19 through 220))
  selection = (chain 'E' and (resid 1 through 17 or resid 19 through 220))
  selection = (chain 'F' and (resid 1 through 17 or resid 19 through 220))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.110
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.300
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
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      :  0.006   0.505  10572  Z= 0.358
  Angle     :  0.753  44.143  14378  Z= 0.462
  Chirality :  0.044   0.225   1604
  Planarity :  0.004   0.070   1882
  Dihedral  :  9.229  89.573   4028
  Min Nonbonded Distance : 1.449

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  5.13 %
    Favored  : 94.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.21), residues: 1310
  helix: -0.14 (0.17), residues: 814
  sheet:  None (None), residues: 0
  loop : -1.47 (0.24), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  82 
 TYR   0.004   0.001   TYR C 164 
 PHE   0.011   0.001   PHE E  32 
 TRP   0.003   0.000   TRP E 184 
 HIS   0.001   0.000   HIS F  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (10566)
  covalent geometry    : angle       0.63811 (14366)
  SS BOND              : bond        0.21559 (    6)
  SS BOND              : angle      13.84335 (   12)
  hydrogen bonds       : bond        0.13360 (  577)
  hydrogen bonds       : angle       4.66128 ( 1731)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  630 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 628
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7758 (tptm)
REVERT: A   79 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8554 (tp30)
REVERT: A   87 HIS cc_start: 0.7892 (m-70) cc_final: 0.7412 (t-90)
REVERT: A  100 ARG cc_start: 0.8498 (ttt180) cc_final: 0.7971 (tmm-80)
REVERT: A  103 ASP cc_start: 0.7931 (m-30) cc_final: 0.7158 (m-30)
REVERT: A  128 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7956 (tm-30)
REVERT: A  129 ILE cc_start: 0.8753 (mt) cc_final: 0.8366 (tt)
REVERT: A  149 SER cc_start: 0.8961 (t) cc_final: 0.8650 (p)
REVERT: A  152 ASP cc_start: 0.8821 (m-30) cc_final: 0.8569 (m-30)
REVERT: A  187 GLU cc_start: 0.9322 (mt-10) cc_final: 0.9107 (pt0)
REVERT: A  202 LEU cc_start: 0.9520 (mt) cc_final: 0.9318 (mm)
REVERT: A  212 GLU cc_start: 0.8848 (mt-10) cc_final: 0.7898 (pm20)
REVERT: B   39 MET cc_start: 0.9070 (tpp) cc_final: 0.8530 (tpt)
REVERT: B   40 PHE cc_start: 0.8539 (t80) cc_final: 0.8257 (t80)
REVERT: B   45 GLU cc_start: 0.8133 (tp30) cc_final: 0.7827 (tm-30)
REVERT: B   51 ASP cc_start: 0.8583 (t0) cc_final: 0.8359 (t0)
REVERT: B   68 MET cc_start: 0.8936 (mtp) cc_final: 0.8417 (tpp)
REVERT: B   84 HIS cc_start: 0.8830 (m90) cc_final: 0.8428 (t-90)
REVERT: B   86 VAL cc_start: 0.7380 (p) cc_final: 0.7008 (m)
REVERT: B  103 ASP cc_start: 0.9097 (m-30) cc_final: 0.8584 (m-30)
REVERT: B  128 GLU cc_start: 0.9299 (mp0) cc_final: 0.8763 (pp20)
REVERT: B  131 LYS cc_start: 0.8533 (mtpt) cc_final: 0.7833 (mtpt)
REVERT: B  141 ILE cc_start: 0.9141 (mt) cc_final: 0.8572 (mt)
REVERT: B  142 VAL cc_start: 0.9447 (m) cc_final: 0.9240 (p)
REVERT: B  144 MET cc_start: 0.8669 (tmm) cc_final: 0.7710 (tmm)
REVERT: B  166 ASP cc_start: 0.8372 (t0) cc_final: 0.8028 (t0)
REVERT: C    5 ASN cc_start: 0.7693 (t0) cc_final: 0.7048 (p0)
REVERT: C   24 VAL cc_start: 0.8744 (t) cc_final: 0.8484 (p)
REVERT: C   52 LEU cc_start: 0.9751 (mp) cc_final: 0.9539 (mp)
REVERT: C   68 MET cc_start: 0.9313 (mtp) cc_final: 0.8909 (mtt)
REVERT: C  103 ASP cc_start: 0.8661 (m-30) cc_final: 0.7833 (t0)
REVERT: C  104 ILE cc_start: 0.8501 (tt) cc_final: 0.8086 (pt)
REVERT: C  113 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8100 (mm-30)
REVERT: C  158 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8760 (mmmm)
REVERT: D   30 LYS cc_start: 0.8436 (mttm) cc_final: 0.8169 (tptp)
REVERT: D   40 PHE cc_start: 0.9006 (t80) cc_final: 0.8794 (t80)
REVERT: D   51 ASP cc_start: 0.8542 (m-30) cc_final: 0.8214 (m-30)
REVERT: D   54 THR cc_start: 0.9115 (p) cc_final: 0.8914 (p)
REVERT: D   55 MET cc_start: 0.9223 (ttm) cc_final: 0.8922 (ttm)
REVERT: D   71 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8193 (mt-10)
REVERT: D  115 ILE cc_start: 0.8841 (mm) cc_final: 0.8619 (mm)
REVERT: D  128 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7790 (tm-30)
REVERT: D  129 ILE cc_start: 0.8819 (mt) cc_final: 0.8539 (tt)
REVERT: D  131 LYS cc_start: 0.9363 (tttt) cc_final: 0.9139 (ptpt)
REVERT: D  141 ILE cc_start: 0.9617 (mm) cc_final: 0.9300 (tp)
REVERT: D  148 THR cc_start: 0.8567 (m) cc_final: 0.7210 (m)
REVERT: D  149 SER cc_start: 0.8749 (t) cc_final: 0.8142 (p)
REVERT: D  171 THR cc_start: 0.9275 (p) cc_final: 0.9013 (p)
REVERT: E   30 LYS cc_start: 0.9054 (mmtt) cc_final: 0.7345 (mppt)
REVERT: E   68 MET cc_start: 0.8820 (mtp) cc_final: 0.8435 (mmm)
REVERT: E   79 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7678 (mm-30)
REVERT: E   84 HIS cc_start: 0.8672 (m90) cc_final: 0.8452 (t-90)
REVERT: E   86 VAL cc_start: 0.6692 (p) cc_final: 0.6453 (m)
REVERT: E  103 ASP cc_start: 0.8880 (m-30) cc_final: 0.8363 (m-30)
REVERT: E  140 LYS cc_start: 0.9253 (mttt) cc_final: 0.8759 (mtpt)
REVERT: E  141 ILE cc_start: 0.9157 (mt) cc_final: 0.8307 (mt)
REVERT: E  211 LEU cc_start: 0.8774 (tt) cc_final: 0.8482 (tt)
REVERT: F   25 LYS cc_start: 0.9659 (mttt) cc_final: 0.9308 (mtmm)
REVERT: F   52 LEU cc_start: 0.9748 (mp) cc_final: 0.9307 (mp)
REVERT: F   53 ASN cc_start: 0.8889 (m-40) cc_final: 0.8669 (m110)
REVERT: F   62 HIS cc_start: 0.8691 (m-70) cc_final: 0.8393 (m90)
REVERT: F   68 MET cc_start: 0.9413 (mtp) cc_final: 0.8723 (mtt)
REVERT: F   72 THR cc_start: 0.9112 (m) cc_final: 0.8908 (p)
REVERT: F  103 ASP cc_start: 0.8555 (m-30) cc_final: 0.7470 (t70)
REVERT: F  115 ILE cc_start: 0.9191 (mt) cc_final: 0.8876 (pt)
REVERT: F  135 ILE cc_start: 0.9178 (mt) cc_final: 0.8762 (tt)
REVERT: F  138 LEU cc_start: 0.9642 (mt) cc_final: 0.9372 (mt)
REVERT: F  159 GLU cc_start: 0.8983 (mp0) cc_final: 0.8762 (pt0)
REVERT: F  164 TYR cc_start: 0.8694 (t80) cc_final: 0.7817 (t80)
REVERT: F  184 TRP cc_start: 0.8472 (t60) cc_final: 0.8191 (t60)
REVERT: F  190 LEU cc_start: 0.9313 (mt) cc_final: 0.8955 (mt)
  outliers start: 2
  outliers final: 1
  residues processed: 629
  average time/residue: 0.1307
  time to fit residues: 107.4392
Evaluate side-chains
  382 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 381
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:   30.0000
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    0.1980
   chunk 55 optimal weight:    7.9990
   overall best weight:    4.8186

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

Flipped N/Q/H residues before XYZ refinement:
A   4 GLN
A   7 GLN
A   9 GLN
A  53 ASN
** A  84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 219 GLN
** B  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   4 GLN
C   5 ASN
C  67 GLN
C  95 GLN
C 192 GLN
D   4 GLN
D   9 GLN
D  53 ASN
** D  84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 192 GLN
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  53 ASN
E  95 GLN
E 139 ASN
E 176 GLN
F   4 GLN
F  95 GLN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.090495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.062326 restraints weight = 86793.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.066168 restraints weight = 44413.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.069009 restraints weight = 28895.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.071087 restraints weight = 21069.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.072711 restraints weight = 16583.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3158
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3158 r_free = 0.3158    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3158 r_free = 0.3158    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3158
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.4584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10572  Z= 0.192
  Angle     :  0.682   7.268  14378  Z= 0.357
  Chirality :  0.046   0.283   1604
  Planarity :  0.006   0.055   1882
  Dihedral  :  3.475  22.507   1404
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.48 %
    Favored  : 97.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.22), residues: 1310
  helix:  0.54 (0.17), residues: 840
  sheet:  None (None), residues: 0
  loop : -0.92 (0.25), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 173 
 TYR   0.012   0.002   TYR B 169 
 PHE   0.040   0.004   PHE C 161 
 TRP   0.030   0.002   TRP F 184 
 HIS   0.004   0.001   HIS D  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (10566)
  covalent geometry    : angle       0.67875 (14366)
  SS BOND              : bond        0.01107 (    6)
  SS BOND              : angle       2.54820 (   12)
  hydrogen bonds       : bond        0.04359 (  577)
  hydrogen bonds       : angle       3.92087 ( 1731)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  471 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 470
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.6965 (mmp) cc_final: 0.6140 (tpp)
REVERT: A   30 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7775 (tptm)
REVERT: A   40 PHE cc_start: 0.9090 (t80) cc_final: 0.8531 (t80)
REVERT: A   53 ASN cc_start: 0.8624 (m-40) cc_final: 0.8369 (m-40)
REVERT: A   55 MET cc_start: 0.8726 (mtp) cc_final: 0.8308 (mtp)
REVERT: A   71 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8598 (mt-10)
REVERT: A   87 HIS cc_start: 0.8204 (m-70) cc_final: 0.7553 (t-90)
REVERT: A  100 ARG cc_start: 0.8642 (ttt180) cc_final: 0.8383 (tmm-80)
REVERT: A  114 GLN cc_start: 0.9013 (pp30) cc_final: 0.8475 (pp30)
REVERT: A  126 VAL cc_start: 0.6312 (t) cc_final: 0.5757 (p)
REVERT: A  128 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7721 (tm-30)
REVERT: A  129 ILE cc_start: 0.8926 (mt) cc_final: 0.8564 (tt)
REVERT: A  136 LEU cc_start: 0.9615 (tt) cc_final: 0.8995 (tt)
REVERT: A  141 ILE cc_start: 0.9413 (mt) cc_final: 0.9066 (mt)
REVERT: A  149 SER cc_start: 0.8982 (t) cc_final: 0.8629 (p)
REVERT: A  150 ILE cc_start: 0.8808 (tp) cc_final: 0.8598 (tp)
REVERT: A  168 PHE cc_start: 0.9101 (t80) cc_final: 0.8900 (t80)
REVERT: A  190 LEU cc_start: 0.8567 (tp) cc_final: 0.8272 (tp)
REVERT: A  212 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8658 (pm20)
REVERT: B   39 MET cc_start: 0.9542 (tpp) cc_final: 0.9036 (tpt)
REVERT: B   51 ASP cc_start: 0.9141 (t0) cc_final: 0.8908 (t0)
REVERT: B   55 MET cc_start: 0.8852 (mtm) cc_final: 0.8358 (mtm)
REVERT: B   68 MET cc_start: 0.9021 (mtp) cc_final: 0.8761 (mtp)
REVERT: B   84 HIS cc_start: 0.9259 (m90) cc_final: 0.8620 (t-90)
REVERT: B   96 MET cc_start: 0.8781 (mmp) cc_final: 0.8498 (mmp)
REVERT: B  103 ASP cc_start: 0.9117 (m-30) cc_final: 0.8812 (m-30)
REVERT: B  115 ILE cc_start: 0.9474 (mt) cc_final: 0.9227 (mm)
REVERT: B  128 GLU cc_start: 0.9569 (mp0) cc_final: 0.9306 (mp0)
REVERT: B  135 ILE cc_start: 0.9303 (pt) cc_final: 0.8987 (pt)
REVERT: B  182 LYS cc_start: 0.9418 (ptpt) cc_final: 0.9207 (ptpt)
REVERT: B  215 MET cc_start: 0.8848 (mtm) cc_final: 0.8621 (ptp)
REVERT: C    3 VAL cc_start: 0.7843 (p) cc_final: 0.7631 (p)
REVERT: C   68 MET cc_start: 0.9419 (mtp) cc_final: 0.8898 (mtt)
REVERT: C  103 ASP cc_start: 0.9206 (m-30) cc_final: 0.8020 (t0)
REVERT: C  104 ILE cc_start: 0.8705 (tt) cc_final: 0.8206 (pt)
REVERT: C  113 GLU cc_start: 0.9402 (mt-10) cc_final: 0.8525 (mm-30)
REVERT: C  152 ASP cc_start: 0.9096 (m-30) cc_final: 0.8877 (m-30)
REVERT: C  158 LYS cc_start: 0.9209 (mmmt) cc_final: 0.8871 (mmmm)
REVERT: C  168 PHE cc_start: 0.9532 (t80) cc_final: 0.9253 (t80)
REVERT: D   10 MET cc_start: 0.6498 (mmp) cc_final: 0.5784 (tpp)
REVERT: D   30 LYS cc_start: 0.8499 (mttm) cc_final: 0.8296 (tptp)
REVERT: D   40 PHE cc_start: 0.8986 (t80) cc_final: 0.8665 (t80)
REVERT: D   53 ASN cc_start: 0.8486 (m-40) cc_final: 0.8197 (m110)
REVERT: D   55 MET cc_start: 0.9662 (ttm) cc_final: 0.9417 (ttt)
REVERT: D   68 MET cc_start: 0.9177 (mtp) cc_final: 0.8964 (mtp)
REVERT: D  100 ARG cc_start: 0.9119 (ttt180) cc_final: 0.8427 (tmm-80)
REVERT: D  103 ASP cc_start: 0.9176 (m-30) cc_final: 0.8276 (m-30)
REVERT: D  126 VAL cc_start: 0.6893 (t) cc_final: 0.6639 (p)
REVERT: D  129 ILE cc_start: 0.9058 (mt) cc_final: 0.8777 (tt)
REVERT: D  164 TYR cc_start: 0.8297 (t80) cc_final: 0.7941 (t80)
REVERT: D  169 TYR cc_start: 0.9126 (m-80) cc_final: 0.8588 (m-80)
REVERT: D  212 GLU cc_start: 0.8993 (pt0) cc_final: 0.8566 (pm20)
REVERT: E   68 MET cc_start: 0.8844 (mtp) cc_final: 0.8394 (tpp)
REVERT: E   84 HIS cc_start: 0.9342 (m90) cc_final: 0.8729 (t-90)
REVERT: E   96 MET cc_start: 0.8371 (mmp) cc_final: 0.7893 (mmp)
REVERT: E  115 ILE cc_start: 0.9800 (mm) cc_final: 0.9351 (mm)
REVERT: E  140 LYS cc_start: 0.9260 (mttt) cc_final: 0.8904 (mtpt)
REVERT: E  141 ILE cc_start: 0.8993 (mt) cc_final: 0.8637 (mt)
REVERT: E  144 MET cc_start: 0.8383 (ppp) cc_final: 0.8129 (ppp)
REVERT: E  211 LEU cc_start: 0.9436 (tt) cc_final: 0.8980 (tt)
REVERT: E  215 MET cc_start: 0.8961 (mmp) cc_final: 0.8714 (mmp)
REVERT: F   62 HIS cc_start: 0.8670 (m-70) cc_final: 0.8376 (m90)
REVERT: F   68 MET cc_start: 0.9426 (mtp) cc_final: 0.9021 (mtt)
REVERT: F  103 ASP cc_start: 0.9091 (m-30) cc_final: 0.7941 (t0)
REVERT: F  104 ILE cc_start: 0.8693 (tt) cc_final: 0.8368 (pt)
REVERT: F  118 MET cc_start: 0.7651 (mmp) cc_final: 0.7364 (mmp)
REVERT: F  164 TYR cc_start: 0.8560 (t80) cc_final: 0.7713 (t80)
REVERT: F  167 ARG cc_start: 0.9226 (ptp90) cc_final: 0.8397 (ptp90)
REVERT: F  168 PHE cc_start: 0.9405 (t80) cc_final: 0.9038 (t80)
REVERT: F  185 MET cc_start: 0.8899 (mmp) cc_final: 0.8656 (mmm)
REVERT: F  190 LEU cc_start: 0.9422 (mt) cc_final: 0.8836 (mp)
  outliers start: 1
  outliers final: 0
  residues processed: 471
  average time/residue: 0.1212
  time to fit residues: 76.1716
Evaluate side-chains
  346 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 346
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 80 optimal weight:   10.0000
   chunk 21 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 60 optimal weight:   10.0000
   chunk 124 optimal weight:    3.9990
   chunk 23 optimal weight:   20.0000
   chunk 110 optimal weight:   20.0000
   chunk 131 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 130 optimal weight:    0.0870
   overall best weight:    2.0164

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

Flipped N/Q/H residues before XYZ refinement:
A  84 HIS
A  95 GLN
** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  95 GLN
D  74 ASN
D  84 HIS
D  95 GLN
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  95 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.091492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.063262 restraints weight = 74024.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.066991 restraints weight = 40817.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.069780 restraints weight = 27360.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.071809 restraints weight = 20216.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.073341 restraints weight = 16057.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.5138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10572  Z= 0.128
  Angle     :  0.624   6.945  14378  Z= 0.321
  Chirality :  0.046   0.288   1604
  Planarity :  0.005   0.045   1882
  Dihedral  :  3.744  19.068   1404
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.95 %
    Favored  : 97.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.22), residues: 1310
  helix:  0.76 (0.18), residues: 838
  sheet:  None (None), residues: 0
  loop : -0.70 (0.26), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 173 
 TYR   0.015   0.002   TYR E 169 
 PHE   0.030   0.003   PHE C 161 
 TRP   0.016   0.001   TRP D  23 
 HIS   0.003   0.001   HIS A  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (10566)
  covalent geometry    : angle       0.62203 (14366)
  SS BOND              : bond        0.00710 (    6)
  SS BOND              : angle       1.82362 (   12)
  hydrogen bonds       : bond        0.03638 (  577)
  hydrogen bonds       : angle       3.81504 ( 1731)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  460 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 458
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.6901 (mmp) cc_final: 0.6154 (tpp)
REVERT: A   29 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7928 (pt0)
REVERT: A   30 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7693 (tptm)
REVERT: A   40 PHE cc_start: 0.9038 (t80) cc_final: 0.8520 (t80)
REVERT: A   53 ASN cc_start: 0.8594 (m-40) cc_final: 0.8201 (m110)
REVERT: A   87 HIS cc_start: 0.8200 (m-70) cc_final: 0.7739 (t70)
REVERT: A  100 ARG cc_start: 0.8805 (ttt180) cc_final: 0.8481 (tmm-80)
REVERT: A  114 GLN cc_start: 0.8877 (pp30) cc_final: 0.8576 (pp30)
REVERT: A  149 SER cc_start: 0.9021 (t) cc_final: 0.8537 (p)
REVERT: A  152 ASP cc_start: 0.8919 (m-30) cc_final: 0.8658 (m-30)
REVERT: A  167 ARG cc_start: 0.9419 (mpp80) cc_final: 0.8956 (ptt-90)
REVERT: A  212 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8480 (pm20)
REVERT: B   24 VAL cc_start: 0.9258 (p) cc_final: 0.8802 (p)
REVERT: B   39 MET cc_start: 0.9529 (tpp) cc_final: 0.8913 (tpt)
REVERT: B   51 ASP cc_start: 0.9098 (t0) cc_final: 0.8751 (t0)
REVERT: B   55 MET cc_start: 0.8801 (mtm) cc_final: 0.8293 (mtm)
REVERT: B   68 MET cc_start: 0.8990 (mtp) cc_final: 0.8729 (mtp)
REVERT: B   84 HIS cc_start: 0.9257 (m90) cc_final: 0.8617 (t-90)
REVERT: B   96 MET cc_start: 0.8837 (mmp) cc_final: 0.8176 (mpp)
REVERT: B  103 ASP cc_start: 0.9075 (m-30) cc_final: 0.8597 (m-30)
REVERT: B  112 GLN cc_start: 0.9731 (tp40) cc_final: 0.9334 (tp-100)
REVERT: B  135 ILE cc_start: 0.9266 (pt) cc_final: 0.9017 (pt)
REVERT: C   52 LEU cc_start: 0.9618 (mp) cc_final: 0.9331 (mp)
REVERT: C   53 ASN cc_start: 0.9096 (m-40) cc_final: 0.8863 (m110)
REVERT: C   68 MET cc_start: 0.9345 (mtp) cc_final: 0.9024 (mtt)
REVERT: C  103 ASP cc_start: 0.9147 (m-30) cc_final: 0.8229 (t0)
REVERT: C  104 ILE cc_start: 0.8588 (tt) cc_final: 0.8066 (pt)
REVERT: C  113 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9062 (tt0)
REVERT: C  124 ILE cc_start: 0.9135 (mm) cc_final: 0.8914 (tp)
REVERT: C  129 ILE cc_start: 0.9257 (mt) cc_final: 0.8927 (mm)
REVERT: C  138 LEU cc_start: 0.9722 (mt) cc_final: 0.9517 (mt)
REVERT: C  151 LEU cc_start: 0.9305 (mm) cc_final: 0.9103 (mm)
REVERT: C  158 LYS cc_start: 0.9111 (mmmt) cc_final: 0.8792 (mmmm)
REVERT: D   10 MET cc_start: 0.6706 (mmp) cc_final: 0.5911 (tpp)
REVERT: D   30 LYS cc_start: 0.8673 (mttm) cc_final: 0.8109 (tptp)
REVERT: D   40 PHE cc_start: 0.9103 (t80) cc_final: 0.8187 (t80)
REVERT: D   53 ASN cc_start: 0.8454 (m-40) cc_final: 0.8093 (m110)
REVERT: D  100 ARG cc_start: 0.8961 (ttt180) cc_final: 0.8595 (tmm-80)
REVERT: D  114 GLN cc_start: 0.9461 (pt0) cc_final: 0.9091 (pp30)
REVERT: D  131 LYS cc_start: 0.9481 (tttt) cc_final: 0.9200 (tttt)
REVERT: D  164 TYR cc_start: 0.8335 (t80) cc_final: 0.8014 (t80)
REVERT: D  169 TYR cc_start: 0.9093 (m-80) cc_final: 0.8500 (m-80)
REVERT: D  212 GLU cc_start: 0.9124 (pt0) cc_final: 0.8533 (pm20)
REVERT: E   28 GLU cc_start: 0.8905 (pt0) cc_final: 0.8455 (pp20)
REVERT: E   35 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7884 (tm-30)
REVERT: E   68 MET cc_start: 0.8822 (mtp) cc_final: 0.8446 (tpp)
REVERT: E   84 HIS cc_start: 0.9372 (m90) cc_final: 0.8740 (t-90)
REVERT: E   96 MET cc_start: 0.8349 (mmp) cc_final: 0.7936 (mmp)
REVERT: E  103 ASP cc_start: 0.8871 (m-30) cc_final: 0.8467 (m-30)
REVERT: E  124 ILE cc_start: 0.8502 (mp) cc_final: 0.7665 (mp)
REVERT: E  140 LYS cc_start: 0.9275 (mttt) cc_final: 0.8912 (mtpt)
REVERT: E  141 ILE cc_start: 0.8962 (mt) cc_final: 0.8513 (mt)
REVERT: E  144 MET cc_start: 0.8274 (ppp) cc_final: 0.7907 (ppp)
REVERT: E  145 TYR cc_start: 0.8283 (t80) cc_final: 0.8051 (t80)
REVERT: E  211 LEU cc_start: 0.9192 (tt) cc_final: 0.8965 (tt)
REVERT: E  215 MET cc_start: 0.8946 (mmp) cc_final: 0.8648 (mmp)
REVERT: F   52 LEU cc_start: 0.9808 (mp) cc_final: 0.9548 (mp)
REVERT: F   68 MET cc_start: 0.9333 (mtp) cc_final: 0.8940 (mtt)
REVERT: F  103 ASP cc_start: 0.9048 (m-30) cc_final: 0.8025 (t70)
REVERT: F  104 ILE cc_start: 0.8774 (tt) cc_final: 0.8464 (pt)
REVERT: F  164 TYR cc_start: 0.8506 (t80) cc_final: 0.7737 (t80)
REVERT: F  167 ARG cc_start: 0.9238 (ptp90) cc_final: 0.8425 (ptp90)
REVERT: F  168 PHE cc_start: 0.9435 (t80) cc_final: 0.9018 (t80)
REVERT: F  190 LEU cc_start: 0.9379 (mt) cc_final: 0.8709 (mt)
REVERT: F  213 GLU cc_start: 0.8921 (pt0) cc_final: 0.8694 (pt0)
  outliers start: 2
  outliers final: 0
  residues processed: 460
  average time/residue: 0.1109
  time to fit residues: 69.4174
Evaluate side-chains
  331 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 331
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 127 optimal weight:   10.0000
   chunk 10 optimal weight:   30.0000
   chunk 43 optimal weight:    0.7980
   chunk 31 optimal weight:    0.4980
   chunk 117 optimal weight:   20.0000
   chunk 79 optimal weight:    9.9990
   chunk 97 optimal weight:    2.9990
   chunk 89 optimal weight:    9.9990
   chunk 70 optimal weight:    7.9990
   chunk 119 optimal weight:   10.0000
   chunk 63 optimal weight:    5.9990
   overall best weight:    3.6586

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

Flipped N/Q/H residues before XYZ refinement:
A  12 HIS
A  74 ASN
A  95 GLN
D  95 GLN
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 219 GLN
** E  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  95 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.088979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.061589 restraints weight = 71424.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.065062 restraints weight = 40386.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.067682 restraints weight = 27481.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.069590 restraints weight = 20554.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.070995 restraints weight = 16430.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3130
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3130
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.5760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10572  Z= 0.147
  Angle     :  0.634   6.090  14378  Z= 0.330
  Chirality :  0.045   0.171   1604
  Planarity :  0.005   0.045   1882
  Dihedral  :  3.881  15.385   1404
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.30 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.22), residues: 1310
  helix:  0.79 (0.18), residues: 836
  sheet:  None (None), residues: 0
  loop : -0.55 (0.26), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  82 
 TYR   0.012   0.002   TYR B 169 
 PHE   0.024   0.003   PHE C 161 
 TRP   0.022   0.002   TRP D  23 
 HIS   0.003   0.001   HIS C  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (10566)
  covalent geometry    : angle       0.63338 (14366)
  SS BOND              : bond        0.00274 (    6)
  SS BOND              : angle       1.10061 (   12)
  hydrogen bonds       : bond        0.03738 (  577)
  hydrogen bonds       : angle       3.95033 ( 1731)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  423 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 421
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7944 (pt0)
REVERT: A   30 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7743 (tptm)
REVERT: A   40 PHE cc_start: 0.9074 (t80) cc_final: 0.8563 (t80)
REVERT: A   53 ASN cc_start: 0.8574 (m-40) cc_final: 0.8226 (m110)
REVERT: A   68 MET cc_start: 0.9212 (ppp) cc_final: 0.8831 (ppp)
REVERT: A   71 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8516 (mt-10)
REVERT: A   87 HIS cc_start: 0.8193 (m-70) cc_final: 0.7846 (t70)
REVERT: A  100 ARG cc_start: 0.8601 (ttt180) cc_final: 0.8363 (tmm-80)
REVERT: A  149 SER cc_start: 0.9073 (t) cc_final: 0.8613 (p)
REVERT: A  152 ASP cc_start: 0.8934 (m-30) cc_final: 0.8675 (m-30)
REVERT: A  203 LYS cc_start: 0.9290 (mttt) cc_final: 0.8953 (mttt)
REVERT: A  212 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8437 (pm20)
REVERT: B   51 ASP cc_start: 0.9166 (t0) cc_final: 0.8753 (t0)
REVERT: B   55 MET cc_start: 0.8968 (mtm) cc_final: 0.8249 (mtm)
REVERT: B   68 MET cc_start: 0.8963 (mtp) cc_final: 0.8509 (tpp)
REVERT: B   84 HIS cc_start: 0.9324 (m90) cc_final: 0.8698 (t-90)
REVERT: B   96 MET cc_start: 0.9004 (mmp) cc_final: 0.8415 (mpp)
REVERT: B  103 ASP cc_start: 0.9242 (m-30) cc_final: 0.8871 (m-30)
REVERT: B  135 ILE cc_start: 0.9344 (pt) cc_final: 0.9118 (pt)
REVERT: B  215 MET cc_start: 0.8806 (ptp) cc_final: 0.8364 (ptt)
REVERT: C   52 LEU cc_start: 0.9697 (mp) cc_final: 0.9454 (mp)
REVERT: C   68 MET cc_start: 0.9339 (mtp) cc_final: 0.8971 (mtt)
REVERT: C  103 ASP cc_start: 0.9104 (m-30) cc_final: 0.8115 (t0)
REVERT: C  104 ILE cc_start: 0.8609 (tt) cc_final: 0.8090 (pt)
REVERT: C  113 GLU cc_start: 0.9436 (mt-10) cc_final: 0.8430 (mm-30)
REVERT: C  124 ILE cc_start: 0.8955 (mm) cc_final: 0.8599 (tp)
REVERT: C  158 LYS cc_start: 0.9159 (mmmt) cc_final: 0.8861 (mmmm)
REVERT: C  167 ARG cc_start: 0.9433 (ptp90) cc_final: 0.9200 (ptp90)
REVERT: C  168 PHE cc_start: 0.9409 (t80) cc_final: 0.9149 (t80)
REVERT: D   40 PHE cc_start: 0.8862 (t80) cc_final: 0.8443 (t80)
REVERT: D   53 ASN cc_start: 0.8614 (m-40) cc_final: 0.8263 (m110)
REVERT: D   71 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8515 (mt-10)
REVERT: D  114 GLN cc_start: 0.9453 (pt0) cc_final: 0.9194 (pp30)
REVERT: D  131 LYS cc_start: 0.9499 (tttt) cc_final: 0.9298 (tttt)
REVERT: D  164 TYR cc_start: 0.8650 (t80) cc_final: 0.8071 (t80)
REVERT: D  212 GLU cc_start: 0.9105 (pt0) cc_final: 0.8512 (pm20)
REVERT: E   35 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8113 (tm-30)
REVERT: E   55 MET cc_start: 0.9629 (ttt) cc_final: 0.9234 (ttp)
REVERT: E   68 MET cc_start: 0.8843 (mtp) cc_final: 0.8527 (tpp)
REVERT: E   84 HIS cc_start: 0.9410 (m90) cc_final: 0.8805 (t-90)
REVERT: E   96 MET cc_start: 0.8450 (mmp) cc_final: 0.7104 (mpp)
REVERT: E  140 LYS cc_start: 0.9322 (mttt) cc_final: 0.8989 (mtpt)
REVERT: E  141 ILE cc_start: 0.9069 (mt) cc_final: 0.8664 (mt)
REVERT: E  144 MET cc_start: 0.8406 (ppp) cc_final: 0.7989 (ppp)
REVERT: E  211 LEU cc_start: 0.9357 (tt) cc_final: 0.8821 (tt)
REVERT: E  215 MET cc_start: 0.8889 (mmp) cc_final: 0.8655 (mmp)
REVERT: F   52 LEU cc_start: 0.9808 (mp) cc_final: 0.9561 (mp)
REVERT: F   68 MET cc_start: 0.9235 (mtp) cc_final: 0.8942 (mtt)
REVERT: F  118 MET cc_start: 0.7613 (mmp) cc_final: 0.7111 (mmm)
REVERT: F  164 TYR cc_start: 0.8646 (t80) cc_final: 0.7712 (t80)
REVERT: F  167 ARG cc_start: 0.9260 (ptp90) cc_final: 0.8410 (ptp90)
REVERT: F  168 PHE cc_start: 0.9473 (t80) cc_final: 0.9053 (t80)
REVERT: F  185 MET cc_start: 0.8822 (mmp) cc_final: 0.8608 (mmm)
REVERT: F  190 LEU cc_start: 0.9427 (mt) cc_final: 0.8818 (mt)
REVERT: F  213 GLU cc_start: 0.8950 (pt0) cc_final: 0.8697 (pt0)
  outliers start: 2
  outliers final: 0
  residues processed: 423
  average time/residue: 0.1160
  time to fit residues: 66.4762
Evaluate side-chains
  323 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 323
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 8 optimal weight:   20.0000
   chunk 64 optimal weight:    0.0670
   chunk 113 optimal weight:    0.7980
   chunk 126 optimal weight:    5.9990
   chunk 1 optimal weight:   20.0000
   chunk 19 optimal weight:    8.9990
   chunk 61 optimal weight:    8.9990
   chunk 101 optimal weight:    6.9990
   chunk 45 optimal weight:    0.4980
   chunk 23 optimal weight:   10.0000
   overall best weight:    2.6722

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
D  95 GLN
D 192 GLN
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.089203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.062869 restraints weight = 60344.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.066079 restraints weight = 36240.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.068494 restraints weight = 25423.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.070264 restraints weight = 19362.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.071639 restraints weight = 15702.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3137
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3137
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.6056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10572  Z= 0.130
  Angle     :  0.636  10.299  14378  Z= 0.326
  Chirality :  0.046   0.290   1604
  Planarity :  0.005   0.045   1882
  Dihedral  :  3.924  15.310   1404
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.77 %
    Favored  : 98.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.22), residues: 1310
  helix:  0.79 (0.18), residues: 836
  sheet:  None (None), residues: 0
  loop : -0.49 (0.26), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  82 
 TYR   0.041   0.002   TYR D 145 
 PHE   0.015   0.002   PHE A 168 
 TRP   0.017   0.001   TRP D  23 
 HIS   0.003   0.001   HIS A  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (10566)
  covalent geometry    : angle       0.63476 (14366)
  SS BOND              : bond        0.00411 (    6)
  SS BOND              : angle       1.57444 (   12)
  hydrogen bonds       : bond        0.03635 (  577)
  hydrogen bonds       : angle       3.98115 ( 1731)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  408 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 406
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7867 (mt-10)
REVERT: A   30 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7754 (tptm)
REVERT: A   40 PHE cc_start: 0.9034 (t80) cc_final: 0.8532 (t80)
REVERT: A   53 ASN cc_start: 0.8624 (m-40) cc_final: 0.8278 (m110)
REVERT: A   68 MET cc_start: 0.9285 (ppp) cc_final: 0.8831 (ppp)
REVERT: A   71 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8498 (mt-10)
REVERT: A   87 HIS cc_start: 0.8158 (m-70) cc_final: 0.7865 (t70)
REVERT: A  100 ARG cc_start: 0.8592 (ttt180) cc_final: 0.8360 (tmm-80)
REVERT: A  132 ARG cc_start: 0.9293 (tmt-80) cc_final: 0.8896 (tpt90)
REVERT: A  136 LEU cc_start: 0.9531 (tt) cc_final: 0.9085 (tt)
REVERT: A  149 SER cc_start: 0.9089 (t) cc_final: 0.8634 (p)
REVERT: A  152 ASP cc_start: 0.8956 (m-30) cc_final: 0.8677 (m-30)
REVERT: A  212 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8401 (pm20)
REVERT: B   24 VAL cc_start: 0.9159 (p) cc_final: 0.8909 (p)
REVERT: B   39 MET cc_start: 0.9555 (tpp) cc_final: 0.9129 (tmm)
REVERT: B   51 ASP cc_start: 0.9093 (t0) cc_final: 0.8654 (t0)
REVERT: B   55 MET cc_start: 0.9261 (mtm) cc_final: 0.8219 (mtm)
REVERT: B   84 HIS cc_start: 0.9329 (m90) cc_final: 0.8701 (t-90)
REVERT: B   96 MET cc_start: 0.9005 (mmp) cc_final: 0.8479 (mpp)
REVERT: B  103 ASP cc_start: 0.9202 (m-30) cc_final: 0.8809 (m-30)
REVERT: B  135 ILE cc_start: 0.9374 (pt) cc_final: 0.9151 (pt)
REVERT: B  215 MET cc_start: 0.8800 (ptp) cc_final: 0.8409 (ptp)
REVERT: C   52 LEU cc_start: 0.9627 (mp) cc_final: 0.9368 (mp)
REVERT: C   68 MET cc_start: 0.9360 (mtp) cc_final: 0.8967 (mtt)
REVERT: C  103 ASP cc_start: 0.9064 (m-30) cc_final: 0.8503 (m-30)
REVERT: C  104 ILE cc_start: 0.8636 (tt) cc_final: 0.8146 (pt)
REVERT: C  140 LYS cc_start: 0.9423 (mtpp) cc_final: 0.9148 (mtpp)
REVERT: C  158 LYS cc_start: 0.9163 (mmmt) cc_final: 0.8794 (mmmm)
REVERT: C  167 ARG cc_start: 0.9396 (ptp90) cc_final: 0.9175 (ptp90)
REVERT: C  168 PHE cc_start: 0.9416 (t80) cc_final: 0.9128 (t80)
REVERT: D   10 MET cc_start: 0.6819 (mmp) cc_final: 0.5864 (tpp)
REVERT: D   39 MET cc_start: 0.9085 (mtp) cc_final: 0.8671 (mmm)
REVERT: D   40 PHE cc_start: 0.9082 (t80) cc_final: 0.8212 (t80)
REVERT: D   53 ASN cc_start: 0.8548 (m-40) cc_final: 0.8239 (m110)
REVERT: D   68 MET cc_start: 0.9288 (ptp) cc_final: 0.9067 (ptm)
REVERT: D   71 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8518 (mt-10)
REVERT: D  114 GLN cc_start: 0.9351 (pt0) cc_final: 0.9127 (pp30)
REVERT: D  131 LYS cc_start: 0.9518 (tttt) cc_final: 0.9249 (tttt)
REVERT: D  164 TYR cc_start: 0.8618 (t80) cc_final: 0.8042 (t80)
REVERT: D  212 GLU cc_start: 0.8973 (pt0) cc_final: 0.8374 (pm20)
REVERT: E   28 GLU cc_start: 0.8967 (pt0) cc_final: 0.8415 (pp20)
REVERT: E   35 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8083 (tm-30)
REVERT: E   68 MET cc_start: 0.8811 (mtp) cc_final: 0.8596 (tpp)
REVERT: E   84 HIS cc_start: 0.9417 (m90) cc_final: 0.8802 (t-90)
REVERT: E   96 MET cc_start: 0.8572 (mmp) cc_final: 0.7347 (mpp)
REVERT: E  140 LYS cc_start: 0.9344 (mttt) cc_final: 0.8952 (tttt)
REVERT: E  141 ILE cc_start: 0.9043 (mt) cc_final: 0.8716 (mt)
REVERT: E  144 MET cc_start: 0.8381 (ppp) cc_final: 0.7973 (ppp)
REVERT: E  170 LYS cc_start: 0.9091 (pttt) cc_final: 0.8832 (pttm)
REVERT: E  211 LEU cc_start: 0.9285 (tt) cc_final: 0.8889 (tt)
REVERT: E  215 MET cc_start: 0.9173 (mmp) cc_final: 0.8639 (mmp)
REVERT: F   52 LEU cc_start: 0.9795 (mp) cc_final: 0.9552 (mp)
REVERT: F   68 MET cc_start: 0.9261 (mtp) cc_final: 0.8959 (mtt)
REVERT: F  164 TYR cc_start: 0.8612 (t80) cc_final: 0.8147 (t80)
REVERT: F  168 PHE cc_start: 0.9484 (t80) cc_final: 0.9004 (t80)
REVERT: F  190 LEU cc_start: 0.9354 (mt) cc_final: 0.8708 (mt)
  outliers start: 2
  outliers final: 0
  residues processed: 408
  average time/residue: 0.1026
  time to fit residues: 57.6525
Evaluate side-chains
  316 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 316
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 117 optimal weight:    6.9990
   chunk 64 optimal weight:   20.0000
   chunk 55 optimal weight:    9.9990
   chunk 120 optimal weight:    0.0070
   chunk 42 optimal weight:   10.0000
   chunk 73 optimal weight:    1.9990
   chunk 115 optimal weight:   10.0000
   chunk 80 optimal weight:    9.9990
   chunk 124 optimal weight:    0.0970
   chunk 50 optimal weight:    8.9990
   chunk 85 optimal weight:    0.6980
   overall best weight:    1.9600

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
D  95 GLN
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  50 GLN
F  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.089138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.061062 restraints weight = 93773.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.065014 restraints weight = 46636.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.067909 restraints weight = 29932.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.070013 restraints weight = 21560.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.071681 restraints weight = 16799.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3140
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.6282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10572  Z= 0.124
  Angle     :  0.624   7.716  14378  Z= 0.322
  Chirality :  0.045   0.178   1604
  Planarity :  0.005   0.054   1882
  Dihedral  :  3.968  18.649   1404
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.88 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.22), residues: 1310
  helix:  0.73 (0.18), residues: 850
  sheet:  None (None), residues: 0
  loop : -0.48 (0.26), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F 100 
 TYR   0.014   0.001   TYR D 145 
 PHE   0.017   0.002   PHE B  40 
 TRP   0.020   0.001   TRP D  23 
 HIS   0.003   0.001   HIS A  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (10566)
  covalent geometry    : angle       0.62326 (14366)
  SS BOND              : bond        0.00249 (    6)
  SS BOND              : angle       1.36299 (   12)
  hydrogen bonds       : bond        0.03520 (  577)
  hydrogen bonds       : angle       3.99613 ( 1731)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  403 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 401
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.6957 (mmp) cc_final: 0.6163 (tpp)
REVERT: A   29 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7824 (mt-10)
REVERT: A   30 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7718 (tptm)
REVERT: A   40 PHE cc_start: 0.9001 (t80) cc_final: 0.8491 (t80)
REVERT: A   53 ASN cc_start: 0.8648 (m-40) cc_final: 0.8298 (m110)
REVERT: A   68 MET cc_start: 0.9241 (ppp) cc_final: 0.8911 (ppp)
REVERT: A   71 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8568 (mt-10)
REVERT: A   87 HIS cc_start: 0.8139 (m-70) cc_final: 0.7867 (t70)
REVERT: A  100 ARG cc_start: 0.8713 (ttt180) cc_final: 0.8501 (tmm-80)
REVERT: A  132 ARG cc_start: 0.9320 (tmt-80) cc_final: 0.8917 (tpt90)
REVERT: A  136 LEU cc_start: 0.9523 (tt) cc_final: 0.9093 (tt)
REVERT: A  152 ASP cc_start: 0.8999 (m-30) cc_final: 0.8742 (m-30)
REVERT: A  171 THR cc_start: 0.9364 (p) cc_final: 0.8917 (p)
REVERT: A  187 GLU cc_start: 0.9458 (mt-10) cc_final: 0.9193 (pt0)
REVERT: A  192 GLN cc_start: 0.9231 (mp10) cc_final: 0.8956 (mp10)
REVERT: A  212 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8437 (pm20)
REVERT: B   39 MET cc_start: 0.9565 (tpp) cc_final: 0.9086 (tmm)
REVERT: B   51 ASP cc_start: 0.9167 (t0) cc_final: 0.8692 (t0)
REVERT: B   55 MET cc_start: 0.9243 (mtm) cc_final: 0.8342 (mtm)
REVERT: B   68 MET cc_start: 0.9041 (ttm) cc_final: 0.8690 (tpp)
REVERT: B   84 HIS cc_start: 0.9366 (m90) cc_final: 0.8685 (t-90)
REVERT: B   96 MET cc_start: 0.9008 (mmp) cc_final: 0.8551 (mpp)
REVERT: B  103 ASP cc_start: 0.9217 (m-30) cc_final: 0.8832 (m-30)
REVERT: B  118 MET cc_start: 0.8580 (mmt) cc_final: 0.8316 (ptm)
REVERT: B  135 ILE cc_start: 0.9429 (pt) cc_final: 0.9212 (pt)
REVERT: B  215 MET cc_start: 0.8784 (ptp) cc_final: 0.8374 (ptp)
REVERT: C   52 LEU cc_start: 0.9643 (mp) cc_final: 0.9377 (mp)
REVERT: C   68 MET cc_start: 0.9355 (mtp) cc_final: 0.9004 (mtt)
REVERT: C  103 ASP cc_start: 0.9034 (m-30) cc_final: 0.8153 (t70)
REVERT: C  104 ILE cc_start: 0.8612 (tt) cc_final: 0.8088 (pt)
REVERT: C  110 THR cc_start: 0.9423 (m) cc_final: 0.9169 (p)
REVERT: C  128 GLU cc_start: 0.9575 (mp0) cc_final: 0.9302 (mp0)
REVERT: C  140 LYS cc_start: 0.9436 (mtpp) cc_final: 0.9178 (mtpp)
REVERT: C  152 ASP cc_start: 0.9070 (m-30) cc_final: 0.8870 (m-30)
REVERT: C  158 LYS cc_start: 0.9179 (mmmt) cc_final: 0.8827 (mmmm)
REVERT: C  167 ARG cc_start: 0.9380 (ptp90) cc_final: 0.9155 (ptp90)
REVERT: C  168 PHE cc_start: 0.9388 (t80) cc_final: 0.9104 (t80)
REVERT: D   10 MET cc_start: 0.6851 (mmp) cc_final: 0.5789 (tpp)
REVERT: D   39 MET cc_start: 0.9060 (mtp) cc_final: 0.8482 (mmm)
REVERT: D   40 PHE cc_start: 0.8992 (t80) cc_final: 0.8619 (t80)
REVERT: D   53 ASN cc_start: 0.8595 (m-40) cc_final: 0.8260 (m110)
REVERT: D   55 MET cc_start: 0.9238 (ttt) cc_final: 0.8958 (tpt)
REVERT: D   68 MET cc_start: 0.9265 (ptp) cc_final: 0.8916 (ptm)
REVERT: D   71 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8502 (mt-10)
REVERT: D  131 LYS cc_start: 0.9535 (tttt) cc_final: 0.9283 (tttt)
REVERT: D  164 TYR cc_start: 0.8655 (t80) cc_final: 0.8110 (t80)
REVERT: D  212 GLU cc_start: 0.8958 (pt0) cc_final: 0.8754 (pm20)
REVERT: D  215 MET cc_start: 0.8808 (ptm) cc_final: 0.8536 (ppp)
REVERT: E   25 LYS cc_start: 0.9335 (mtmm) cc_final: 0.8896 (mttp)
REVERT: E   28 GLU cc_start: 0.8972 (pt0) cc_final: 0.8483 (pp20)
REVERT: E   30 LYS cc_start: 0.9183 (tptp) cc_final: 0.8982 (tptp)
REVERT: E   35 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7986 (tm-30)
REVERT: E   68 MET cc_start: 0.8732 (mtp) cc_final: 0.8524 (tpp)
REVERT: E   84 HIS cc_start: 0.9427 (m90) cc_final: 0.8798 (t-90)
REVERT: E   96 MET cc_start: 0.8595 (mmp) cc_final: 0.7519 (mpp)
REVERT: E  139 ASN cc_start: 0.9676 (m110) cc_final: 0.9461 (m-40)
REVERT: E  140 LYS cc_start: 0.9361 (mttt) cc_final: 0.9048 (tttm)
REVERT: E  141 ILE cc_start: 0.9002 (mt) cc_final: 0.8699 (mt)
REVERT: E  144 MET cc_start: 0.8420 (ppp) cc_final: 0.7978 (ppp)
REVERT: E  211 LEU cc_start: 0.9307 (tt) cc_final: 0.8938 (tt)
REVERT: E  215 MET cc_start: 0.9187 (mmp) cc_final: 0.8599 (mmp)
REVERT: F   52 LEU cc_start: 0.9797 (mp) cc_final: 0.9548 (mp)
REVERT: F   68 MET cc_start: 0.9223 (mtp) cc_final: 0.8972 (mtt)
REVERT: F   70 LYS cc_start: 0.9435 (pttm) cc_final: 0.9182 (pttp)
REVERT: F  104 ILE cc_start: 0.8996 (tt) cc_final: 0.8638 (pt)
REVERT: F  164 TYR cc_start: 0.8584 (t80) cc_final: 0.7825 (t80)
REVERT: F  167 ARG cc_start: 0.9344 (ptp90) cc_final: 0.8558 (ptp90)
REVERT: F  168 PHE cc_start: 0.9497 (t80) cc_final: 0.9038 (t80)
REVERT: F  185 MET cc_start: 0.8798 (mmp) cc_final: 0.8554 (mmm)
REVERT: F  190 LEU cc_start: 0.9357 (mt) cc_final: 0.8778 (mt)
REVERT: F  213 GLU cc_start: 0.9079 (pt0) cc_final: 0.8871 (pt0)
  outliers start: 2
  outliers final: 0
  residues processed: 403
  average time/residue: 0.1077
  time to fit residues: 59.4227
Evaluate side-chains
  325 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 325
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 20 optimal weight:   20.0000
   chunk 37 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 59 optimal weight:    0.3980
   chunk 70 optimal weight:    0.0030
   chunk 3 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 31 optimal weight:   20.0000
   chunk 50 optimal weight:    6.9990
   chunk 110 optimal weight:   10.0000
   overall best weight:    0.8592

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
D  95 GLN
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 183 ASN
F  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.091067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.063510 restraints weight = 68933.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.067104 restraints weight = 39403.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.069799 restraints weight = 26750.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.071816 restraints weight = 19912.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.073353 restraints weight = 15811.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.6408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10572  Z= 0.121
  Angle     :  0.626   6.678  14378  Z= 0.322
  Chirality :  0.045   0.190   1604
  Planarity :  0.005   0.048   1882
  Dihedral  :  3.929  15.094   1404
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.15 %
    Favored  : 98.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.22), residues: 1310
  helix:  0.81 (0.18), residues: 848
  sheet:  None (None), residues: 0
  loop : -0.55 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F 100 
 TYR   0.034   0.002   TYR A 169 
 PHE   0.017   0.002   PHE B 168 
 TRP   0.036   0.001   TRP C 117 
 HIS   0.002   0.000   HIS D  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (10566)
  covalent geometry    : angle       0.62574 (14366)
  SS BOND              : bond        0.00228 (    6)
  SS BOND              : angle       1.06381 (   12)
  hydrogen bonds       : bond        0.03467 (  577)
  hydrogen bonds       : angle       4.06436 ( 1731)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  407 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 405
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.6878 (mmp) cc_final: 0.6153 (tpp)
REVERT: A   29 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7749 (mt-10)
REVERT: A   30 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7696 (tptm)
REVERT: A   40 PHE cc_start: 0.8971 (t80) cc_final: 0.8493 (t80)
REVERT: A   53 ASN cc_start: 0.8576 (m-40) cc_final: 0.8197 (m110)
REVERT: A   68 MET cc_start: 0.9236 (ppp) cc_final: 0.8909 (ppp)
REVERT: A   71 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8533 (mt-10)
REVERT: A  100 ARG cc_start: 0.8717 (ttt180) cc_final: 0.8460 (tmm-80)
REVERT: A  132 ARG cc_start: 0.9304 (tmt-80) cc_final: 0.8905 (tpt90)
REVERT: A  136 LEU cc_start: 0.9523 (tt) cc_final: 0.9074 (tt)
REVERT: A  150 ILE cc_start: 0.9187 (tp) cc_final: 0.8875 (tp)
REVERT: A  192 GLN cc_start: 0.9199 (mp10) cc_final: 0.8993 (mp10)
REVERT: A  212 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8510 (pm20)
REVERT: B   39 MET cc_start: 0.9555 (tpp) cc_final: 0.9072 (tmm)
REVERT: B   51 ASP cc_start: 0.8988 (t0) cc_final: 0.8549 (t0)
REVERT: B   55 MET cc_start: 0.8965 (mtm) cc_final: 0.8184 (mtm)
REVERT: B   68 MET cc_start: 0.9010 (ttm) cc_final: 0.8465 (tpp)
REVERT: B   84 HIS cc_start: 0.9341 (m90) cc_final: 0.8649 (t-90)
REVERT: B   96 MET cc_start: 0.8994 (mmp) cc_final: 0.8562 (mpp)
REVERT: B  103 ASP cc_start: 0.9185 (m-30) cc_final: 0.8812 (m-30)
REVERT: B  135 ILE cc_start: 0.9460 (pt) cc_final: 0.9237 (pt)
REVERT: B  215 MET cc_start: 0.8790 (ptp) cc_final: 0.8435 (ptp)
REVERT: C   52 LEU cc_start: 0.9635 (mp) cc_final: 0.9371 (mp)
REVERT: C   68 MET cc_start: 0.9343 (mtp) cc_final: 0.8884 (mtt)
REVERT: C  103 ASP cc_start: 0.9013 (m-30) cc_final: 0.8360 (m-30)
REVERT: C  104 ILE cc_start: 0.8660 (tt) cc_final: 0.8167 (pt)
REVERT: C  110 THR cc_start: 0.9479 (m) cc_final: 0.9251 (p)
REVERT: C  128 GLU cc_start: 0.9515 (mp0) cc_final: 0.9174 (mp0)
REVERT: C  140 LYS cc_start: 0.9430 (mtpp) cc_final: 0.9177 (mtpp)
REVERT: C  158 LYS cc_start: 0.9186 (mmmt) cc_final: 0.8821 (mmmm)
REVERT: C  167 ARG cc_start: 0.9369 (ptp90) cc_final: 0.9136 (ptp90)
REVERT: C  168 PHE cc_start: 0.9368 (t80) cc_final: 0.9100 (t80)
REVERT: C  182 LYS cc_start: 0.8444 (ptpt) cc_final: 0.8142 (ptpt)
REVERT: D   10 MET cc_start: 0.6781 (mmp) cc_final: 0.5796 (tpp)
REVERT: D   40 PHE cc_start: 0.8944 (t80) cc_final: 0.8521 (t80)
REVERT: D   53 ASN cc_start: 0.8557 (m-40) cc_final: 0.8187 (m110)
REVERT: D   55 MET cc_start: 0.9251 (ttt) cc_final: 0.8955 (tpt)
REVERT: D   68 MET cc_start: 0.9213 (ptp) cc_final: 0.8911 (ptm)
REVERT: D   71 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8491 (mt-10)
REVERT: D  131 LYS cc_start: 0.9467 (tttt) cc_final: 0.9208 (tttt)
REVERT: D  145 TYR cc_start: 0.8173 (m-80) cc_final: 0.6879 (m-80)
REVERT: D  164 TYR cc_start: 0.8695 (t80) cc_final: 0.7986 (t80)
REVERT: D  212 GLU cc_start: 0.8899 (pt0) cc_final: 0.8664 (pm20)
REVERT: D  215 MET cc_start: 0.8718 (ptm) cc_final: 0.8471 (ppp)
REVERT: E   25 LYS cc_start: 0.9354 (mtmm) cc_final: 0.8912 (mttp)
REVERT: E   28 GLU cc_start: 0.8941 (pt0) cc_final: 0.8456 (pp20)
REVERT: E   35 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7971 (tm-30)
REVERT: E   55 MET cc_start: 0.9531 (ttt) cc_final: 0.9166 (ttm)
REVERT: E   68 MET cc_start: 0.8731 (mtp) cc_final: 0.8481 (tpp)
REVERT: E   84 HIS cc_start: 0.9398 (m90) cc_final: 0.8772 (t-90)
REVERT: E   96 MET cc_start: 0.8586 (mmp) cc_final: 0.7549 (mpp)
REVERT: E  140 LYS cc_start: 0.9327 (mttt) cc_final: 0.9015 (tttm)
REVERT: E  141 ILE cc_start: 0.8891 (mt) cc_final: 0.8582 (mt)
REVERT: E  144 MET cc_start: 0.8359 (ppp) cc_final: 0.7897 (ppp)
REVERT: E  170 LYS cc_start: 0.9064 (pttt) cc_final: 0.8829 (pttm)
REVERT: E  210 THR cc_start: 0.9406 (t) cc_final: 0.8991 (t)
REVERT: E  211 LEU cc_start: 0.9385 (tt) cc_final: 0.9128 (tt)
REVERT: E  215 MET cc_start: 0.9213 (mmp) cc_final: 0.8510 (mmp)
REVERT: F   52 LEU cc_start: 0.9794 (mp) cc_final: 0.9582 (mp)
REVERT: F   68 MET cc_start: 0.9227 (mtp) cc_final: 0.8794 (mtt)
REVERT: F  104 ILE cc_start: 0.8991 (tt) cc_final: 0.8637 (pt)
REVERT: F  159 GLU cc_start: 0.8772 (pt0) cc_final: 0.7951 (mp0)
REVERT: F  164 TYR cc_start: 0.8577 (t80) cc_final: 0.7745 (t80)
REVERT: F  167 ARG cc_start: 0.9339 (ptp90) cc_final: 0.8455 (ptp90)
REVERT: F  168 PHE cc_start: 0.9495 (t80) cc_final: 0.9032 (t80)
REVERT: F  190 LEU cc_start: 0.9293 (mt) cc_final: 0.8909 (mt)
  outliers start: 2
  outliers final: 0
  residues processed: 407
  average time/residue: 0.1054
  time to fit residues: 59.3004
Evaluate side-chains
  328 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 328
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 58 optimal weight:    0.5980
   chunk 63 optimal weight:    5.9990
   chunk 125 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 115 optimal weight:    5.9990
   chunk 81 optimal weight:    0.0470
   chunk 57 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.0882

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
D  95 GLN
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  95 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.091091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.062001 restraints weight = 90746.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.065970 restraints weight = 46976.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.068884 restraints weight = 30744.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.071061 restraints weight = 22406.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.072736 restraints weight = 17540.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.6551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10572  Z= 0.129
  Angle     :  0.655   8.921  14378  Z= 0.336
  Chirality :  0.046   0.222   1604
  Planarity :  0.005   0.046   1882
  Dihedral  :  4.050  24.571   1404
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.71 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.22), residues: 1310
  helix:  0.80 (0.18), residues: 850
  sheet:  None (None), residues: 0
  loop : -0.59 (0.26), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F 100 
 TYR   0.033   0.002   TYR E 145 
 PHE   0.021   0.002   PHE B  40 
 TRP   0.026   0.001   TRP C 117 
 HIS   0.002   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (10566)
  covalent geometry    : angle       0.65362 (14366)
  SS BOND              : bond        0.00312 (    6)
  SS BOND              : angle       1.73121 (   12)
  hydrogen bonds       : bond        0.03596 (  577)
  hydrogen bonds       : angle       4.10493 ( 1731)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  401 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 399
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.6873 (mmp) cc_final: 0.6162 (tpp)
REVERT: A   29 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7766 (mt-10)
REVERT: A   30 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7693 (tptm)
REVERT: A   40 PHE cc_start: 0.9001 (t80) cc_final: 0.8535 (t80)
REVERT: A   53 ASN cc_start: 0.8564 (m-40) cc_final: 0.8215 (m110)
REVERT: A   68 MET cc_start: 0.9218 (ppp) cc_final: 0.8903 (ppp)
REVERT: A   71 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8538 (mt-10)
REVERT: A  100 ARG cc_start: 0.8769 (ttt180) cc_final: 0.8127 (tmm-80)
REVERT: A  103 ASP cc_start: 0.9184 (m-30) cc_final: 0.8277 (m-30)
REVERT: A  128 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7706 (tm-30)
REVERT: A  129 ILE cc_start: 0.8777 (tt) cc_final: 0.8170 (tt)
REVERT: A  131 LYS cc_start: 0.9534 (ptmt) cc_final: 0.9075 (pttt)
REVERT: A  132 ARG cc_start: 0.9322 (tmt-80) cc_final: 0.8941 (tpt90)
REVERT: A  136 LEU cc_start: 0.9520 (tt) cc_final: 0.9103 (tt)
REVERT: A  164 TYR cc_start: 0.8575 (t80) cc_final: 0.8080 (t80)
REVERT: A  192 GLN cc_start: 0.9054 (mp10) cc_final: 0.8843 (tm-30)
REVERT: A  212 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8713 (pm20)
REVERT: A  215 MET cc_start: 0.8826 (ptm) cc_final: 0.8522 (ppp)
REVERT: B   39 MET cc_start: 0.9535 (tpp) cc_final: 0.9035 (tmm)
REVERT: B   51 ASP cc_start: 0.8919 (t0) cc_final: 0.8504 (t0)
REVERT: B   55 MET cc_start: 0.9009 (mtm) cc_final: 0.8268 (mtm)
REVERT: B   68 MET cc_start: 0.8939 (ttm) cc_final: 0.8376 (tpp)
REVERT: B   96 MET cc_start: 0.9015 (mmp) cc_final: 0.8609 (mpp)
REVERT: B  103 ASP cc_start: 0.9203 (m-30) cc_final: 0.8881 (m-30)
REVERT: B  215 MET cc_start: 0.8832 (ptp) cc_final: 0.8481 (ptp)
REVERT: C   52 LEU cc_start: 0.9583 (mp) cc_final: 0.9368 (mp)
REVERT: C   68 MET cc_start: 0.9335 (mtp) cc_final: 0.8918 (mtt)
REVERT: C  103 ASP cc_start: 0.8898 (m-30) cc_final: 0.8067 (t70)
REVERT: C  104 ILE cc_start: 0.8703 (tt) cc_final: 0.8258 (pt)
REVERT: C  110 THR cc_start: 0.9442 (m) cc_final: 0.9222 (p)
REVERT: C  124 ILE cc_start: 0.8867 (mm) cc_final: 0.8462 (tp)
REVERT: C  128 GLU cc_start: 0.9466 (mp0) cc_final: 0.9106 (mp0)
REVERT: C  140 LYS cc_start: 0.9453 (mtpp) cc_final: 0.9195 (mtpp)
REVERT: C  158 LYS cc_start: 0.9186 (mmmt) cc_final: 0.8814 (mmmm)
REVERT: C  167 ARG cc_start: 0.9368 (ptp90) cc_final: 0.9140 (ptp90)
REVERT: C  168 PHE cc_start: 0.9354 (t80) cc_final: 0.9104 (t80)
REVERT: C  182 LYS cc_start: 0.8485 (ptpt) cc_final: 0.8174 (ptpt)
REVERT: D   10 MET cc_start: 0.6773 (mmp) cc_final: 0.5807 (tpp)
REVERT: D   39 MET cc_start: 0.8778 (mmm) cc_final: 0.8480 (mmm)
REVERT: D   40 PHE cc_start: 0.8865 (t80) cc_final: 0.8526 (t80)
REVERT: D   53 ASN cc_start: 0.8581 (m-40) cc_final: 0.8207 (m110)
REVERT: D   68 MET cc_start: 0.9168 (ptp) cc_final: 0.8890 (ptm)
REVERT: D   71 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8534 (mt-10)
REVERT: D  131 LYS cc_start: 0.9443 (tttt) cc_final: 0.9239 (tttt)
REVERT: D  145 TYR cc_start: 0.7578 (m-80) cc_final: 0.7135 (m-80)
REVERT: D  164 TYR cc_start: 0.8295 (t80) cc_final: 0.7887 (t80)
REVERT: D  212 GLU cc_start: 0.8888 (pt0) cc_final: 0.8282 (pm20)
REVERT: D  214 MET cc_start: 0.8632 (mmp) cc_final: 0.8341 (mmm)
REVERT: E   35 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7970 (tm-30)
REVERT: E   55 MET cc_start: 0.9512 (ttt) cc_final: 0.9210 (ttm)
REVERT: E   68 MET cc_start: 0.8715 (mtp) cc_final: 0.8466 (tpp)
REVERT: E   84 HIS cc_start: 0.9389 (m90) cc_final: 0.8744 (t-90)
REVERT: E   96 MET cc_start: 0.8627 (mmp) cc_final: 0.7594 (mpp)
REVERT: E  128 GLU cc_start: 0.9315 (pm20) cc_final: 0.9065 (pm20)
REVERT: E  140 LYS cc_start: 0.9328 (mttt) cc_final: 0.9087 (mtpt)
REVERT: E  141 ILE cc_start: 0.8866 (mt) cc_final: 0.8544 (mt)
REVERT: E  144 MET cc_start: 0.8434 (ppp) cc_final: 0.7917 (ppp)
REVERT: E  170 LYS cc_start: 0.9033 (pttt) cc_final: 0.8791 (pttm)
REVERT: E  211 LEU cc_start: 0.9360 (tt) cc_final: 0.8909 (tt)
REVERT: E  215 MET cc_start: 0.9134 (mmp) cc_final: 0.8502 (mmp)
REVERT: F   52 LEU cc_start: 0.9798 (mp) cc_final: 0.9507 (mp)
REVERT: F   68 MET cc_start: 0.9116 (mtp) cc_final: 0.8833 (mtp)
REVERT: F  104 ILE cc_start: 0.8987 (tt) cc_final: 0.8675 (pt)
REVERT: F  164 TYR cc_start: 0.8585 (t80) cc_final: 0.7718 (t80)
REVERT: F  167 ARG cc_start: 0.9357 (ptp90) cc_final: 0.8487 (ptp90)
REVERT: F  168 PHE cc_start: 0.9503 (t80) cc_final: 0.8950 (t80)
REVERT: F  190 LEU cc_start: 0.9246 (mt) cc_final: 0.8871 (mt)
REVERT: F  213 GLU cc_start: 0.9105 (pt0) cc_final: 0.8871 (pt0)
  outliers start: 2
  outliers final: 0
  residues processed: 401
  average time/residue: 0.1041
  time to fit residues: 57.5060
Evaluate side-chains
  327 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 327
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 74 optimal weight:    5.9990
   chunk 117 optimal weight:    0.8980
   chunk 129 optimal weight:    0.9990
   chunk 120 optimal weight:   30.0000
   chunk 91 optimal weight:    4.9990
   chunk 105 optimal weight:    9.9990
   chunk 30 optimal weight:    7.9990
   chunk 25 optimal weight:    0.5980
   chunk 123 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   overall best weight:    2.6986

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

Flipped N/Q/H residues before XYZ refinement:
A  12 HIS
A  95 GLN
B  84 HIS
C  67 GLN
D  95 GLN
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  95 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.089000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.062782 restraints weight = 58235.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.065979 restraints weight = 35443.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.068360 restraints weight = 24993.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.070176 restraints weight = 19142.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.071539 restraints weight = 15529.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3137
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3137
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.6746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10572  Z= 0.133
  Angle     :  0.648   6.753  14378  Z= 0.335
  Chirality :  0.045   0.158   1604
  Planarity :  0.005   0.044   1882
  Dihedral  :  4.056  20.316   1404
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.80 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.22), residues: 1310
  helix:  0.81 (0.18), residues: 860
  sheet:  None (None), residues: 0
  loop : -0.57 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG F 100 
 TYR   0.040   0.002   TYR E 145 
 PHE   0.015   0.002   PHE E 168 
 TRP   0.022   0.002   TRP E  23 
 HIS   0.003   0.001   HIS A  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (10566)
  covalent geometry    : angle       0.64673 (14366)
  SS BOND              : bond        0.00452 (    6)
  SS BOND              : angle       1.52148 (   12)
  hydrogen bonds       : bond        0.03542 (  577)
  hydrogen bonds       : angle       4.08707 ( 1731)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  399 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 397
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.7093 (mmp) cc_final: 0.6305 (tpp)
REVERT: A   29 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7822 (mt-10)
REVERT: A   30 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7819 (tptm)
REVERT: A   40 PHE cc_start: 0.9063 (t80) cc_final: 0.8632 (t80)
REVERT: A   53 ASN cc_start: 0.8661 (m-40) cc_final: 0.8320 (m110)
REVERT: A   68 MET cc_start: 0.9236 (ppp) cc_final: 0.8893 (ppp)
REVERT: A   71 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8575 (mt-10)
REVERT: A   96 MET cc_start: 0.0400 (mmt) cc_final: 0.0151 (mpp)
REVERT: A  100 ARG cc_start: 0.8781 (ttt180) cc_final: 0.8232 (tmm-80)
REVERT: A  103 ASP cc_start: 0.9163 (m-30) cc_final: 0.8301 (m-30)
REVERT: A  128 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7732 (tm-30)
REVERT: A  129 ILE cc_start: 0.8818 (tt) cc_final: 0.8194 (tt)
REVERT: A  131 LYS cc_start: 0.9536 (ptmt) cc_final: 0.9083 (pttt)
REVERT: A  132 ARG cc_start: 0.9339 (tmt-80) cc_final: 0.8928 (tpt90)
REVERT: A  136 LEU cc_start: 0.9521 (tt) cc_final: 0.9067 (tt)
REVERT: A  164 TYR cc_start: 0.8531 (t80) cc_final: 0.8015 (t80)
REVERT: A  203 LYS cc_start: 0.9255 (mttt) cc_final: 0.9019 (mttt)
REVERT: B   39 MET cc_start: 0.9599 (tpp) cc_final: 0.9065 (tmm)
REVERT: B   51 ASP cc_start: 0.9193 (t0) cc_final: 0.8664 (t0)
REVERT: B   55 MET cc_start: 0.8958 (mtm) cc_final: 0.8317 (mtm)
REVERT: B   68 MET cc_start: 0.8939 (ttm) cc_final: 0.8428 (tpp)
REVERT: B   84 HIS cc_start: 0.9332 (m90) cc_final: 0.9041 (m-70)
REVERT: B   96 MET cc_start: 0.9070 (mmp) cc_final: 0.8701 (mpp)
REVERT: B  103 ASP cc_start: 0.9276 (m-30) cc_final: 0.8903 (m-30)
REVERT: B  170 LYS cc_start: 0.9268 (ptmm) cc_final: 0.8984 (pttt)
REVERT: B  215 MET cc_start: 0.8773 (ptp) cc_final: 0.8355 (ptp)
REVERT: C   52 LEU cc_start: 0.9583 (mp) cc_final: 0.9359 (mp)
REVERT: C   68 MET cc_start: 0.9363 (mtp) cc_final: 0.8987 (mtt)
REVERT: C  103 ASP cc_start: 0.8948 (m-30) cc_final: 0.8108 (t70)
REVERT: C  104 ILE cc_start: 0.8707 (tt) cc_final: 0.8261 (pt)
REVERT: C  110 THR cc_start: 0.9463 (m) cc_final: 0.9182 (p)
REVERT: C  124 ILE cc_start: 0.8971 (mm) cc_final: 0.8660 (tp)
REVERT: C  128 GLU cc_start: 0.9464 (mp0) cc_final: 0.9108 (mp0)
REVERT: C  140 LYS cc_start: 0.9468 (mtpp) cc_final: 0.9213 (mtpp)
REVERT: C  158 LYS cc_start: 0.9196 (mmmt) cc_final: 0.8835 (mmmm)
REVERT: C  167 ARG cc_start: 0.9399 (ptp90) cc_final: 0.9166 (ptp90)
REVERT: C  168 PHE cc_start: 0.9368 (t80) cc_final: 0.9134 (t80)
REVERT: C  182 LYS cc_start: 0.8550 (ptpt) cc_final: 0.8237 (ptpt)
REVERT: D   53 ASN cc_start: 0.8610 (m-40) cc_final: 0.8216 (m110)
REVERT: D   68 MET cc_start: 0.9117 (ptp) cc_final: 0.8844 (ptm)
REVERT: D   71 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8549 (mt-10)
REVERT: D  100 ARG cc_start: 0.8654 (ttt180) cc_final: 0.8341 (ptm160)
REVERT: D  103 ASP cc_start: 0.9112 (m-30) cc_final: 0.8782 (m-30)
REVERT: D  145 TYR cc_start: 0.7747 (m-80) cc_final: 0.7246 (m-80)
REVERT: D  164 TYR cc_start: 0.8257 (t80) cc_final: 0.7920 (t80)
REVERT: D  212 GLU cc_start: 0.8930 (pt0) cc_final: 0.8667 (pm20)
REVERT: D  215 MET cc_start: 0.8733 (ptm) cc_final: 0.8514 (ppp)
REVERT: E   35 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8100 (tm-30)
REVERT: E   39 MET cc_start: 0.9248 (tpp) cc_final: 0.8876 (tpt)
REVERT: E   84 HIS cc_start: 0.9414 (m90) cc_final: 0.8804 (t-90)
REVERT: E   96 MET cc_start: 0.8782 (mmp) cc_final: 0.7935 (mpp)
REVERT: E  132 ARG cc_start: 0.8970 (ptp-170) cc_final: 0.8543 (ptp-170)
REVERT: E  140 LYS cc_start: 0.9351 (mttt) cc_final: 0.9123 (mtpt)
REVERT: E  141 ILE cc_start: 0.8921 (mt) cc_final: 0.8640 (mt)
REVERT: E  144 MET cc_start: 0.8424 (ppp) cc_final: 0.7923 (ppp)
REVERT: E  170 LYS cc_start: 0.9033 (pttt) cc_final: 0.8621 (pttt)
REVERT: E  210 THR cc_start: 0.9323 (t) cc_final: 0.9029 (t)
REVERT: E  211 LEU cc_start: 0.9435 (tt) cc_final: 0.9099 (tt)
REVERT: E  215 MET cc_start: 0.9168 (mmp) cc_final: 0.8536 (mmp)
REVERT: F   52 LEU cc_start: 0.9831 (mp) cc_final: 0.9450 (mp)
REVERT: F   68 MET cc_start: 0.9121 (mtp) cc_final: 0.8839 (mtt)
REVERT: F  103 ASP cc_start: 0.8885 (m-30) cc_final: 0.7948 (t70)
REVERT: F  104 ILE cc_start: 0.9046 (tt) cc_final: 0.8760 (pt)
REVERT: F  159 GLU cc_start: 0.8815 (pt0) cc_final: 0.7935 (mp0)
REVERT: F  164 TYR cc_start: 0.8632 (t80) cc_final: 0.8310 (t80)
REVERT: F  168 PHE cc_start: 0.9537 (t80) cc_final: 0.8959 (t80)
REVERT: F  185 MET cc_start: 0.8712 (mmp) cc_final: 0.8450 (mmm)
REVERT: F  190 LEU cc_start: 0.9219 (mt) cc_final: 0.8904 (mt)
REVERT: F  213 GLU cc_start: 0.9194 (pt0) cc_final: 0.8959 (pt0)
  outliers start: 2
  outliers final: 0
  residues processed: 399
  average time/residue: 0.1025
  time to fit residues: 56.0695
Evaluate side-chains
  318 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 318
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 64 optimal weight:    8.9990
   chunk 56 optimal weight:    4.9990
   chunk 0 optimal weight:   40.0000
   chunk 102 optimal weight:    0.0870
   chunk 4 optimal weight:    3.9990
   chunk 115 optimal weight:    9.9990
   chunk 48 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   chunk 107 optimal weight:    8.9990
   chunk 100 optimal weight:    0.0010
   overall best weight:    1.8170

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 192 GLN
C 139 ASN
D  95 GLN
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  95 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.089703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.061999 restraints weight = 76748.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.065685 restraints weight = 42482.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.068378 restraints weight = 28486.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.070435 restraints weight = 21193.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.072012 restraints weight = 16752.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3147
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3147 r_free = 0.3147    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3147 r_free = 0.3147    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3147
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.6950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10572  Z= 0.127
  Angle     :  0.676   7.829  14378  Z= 0.345
  Chirality :  0.046   0.187   1604
  Planarity :  0.005   0.046   1882
  Dihedral  :  4.174  20.699   1404
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.35 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.22), residues: 1310
  helix:  0.77 (0.18), residues: 862
  sheet:  None (None), residues: 0
  loop : -0.60 (0.26), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG F 100 
 TYR   0.037   0.002   TYR E 145 
 PHE   0.022   0.002   PHE B 168 
 TRP   0.040   0.002   TRP F 117 
 HIS   0.003   0.001   HIS A  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (10566)
  covalent geometry    : angle       0.67540 (14366)
  SS BOND              : bond        0.00343 (    6)
  SS BOND              : angle       1.49685 (   12)
  hydrogen bonds       : bond        0.03624 (  577)
  hydrogen bonds       : angle       4.15819 ( 1731)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  391 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 389
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.7080 (mmp) cc_final: 0.6280 (tpp)
REVERT: A   29 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7828 (mt-10)
REVERT: A   30 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7855 (tptm)
REVERT: A   40 PHE cc_start: 0.9045 (t80) cc_final: 0.8569 (t80)
REVERT: A   53 ASN cc_start: 0.8654 (m-40) cc_final: 0.8300 (m110)
REVERT: A   68 MET cc_start: 0.9230 (ppp) cc_final: 0.8955 (ppp)
REVERT: A   71 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8561 (mt-10)
REVERT: A  100 ARG cc_start: 0.8782 (ttt180) cc_final: 0.8180 (tmm-80)
REVERT: A  103 ASP cc_start: 0.9064 (m-30) cc_final: 0.8276 (m-30)
REVERT: A  128 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7687 (tm-30)
REVERT: A  129 ILE cc_start: 0.8803 (tt) cc_final: 0.8171 (tt)
REVERT: A  131 LYS cc_start: 0.9525 (ptmt) cc_final: 0.9034 (pttt)
REVERT: A  132 ARG cc_start: 0.9348 (tmt-80) cc_final: 0.8945 (tpt90)
REVERT: A  136 LEU cc_start: 0.9507 (tt) cc_final: 0.9049 (tt)
REVERT: A  164 TYR cc_start: 0.8565 (t80) cc_final: 0.8033 (t80)
REVERT: A  168 PHE cc_start: 0.8895 (t80) cc_final: 0.8659 (t80)
REVERT: A  203 LYS cc_start: 0.9253 (mttt) cc_final: 0.9012 (mttt)
REVERT: A  212 GLU cc_start: 0.9233 (pt0) cc_final: 0.8493 (pm20)
REVERT: B   28 GLU cc_start: 0.8723 (pt0) cc_final: 0.8506 (pt0)
REVERT: B   39 MET cc_start: 0.9555 (tpp) cc_final: 0.9065 (tmm)
REVERT: B   51 ASP cc_start: 0.8936 (t0) cc_final: 0.8422 (t0)
REVERT: B   55 MET cc_start: 0.8891 (mtm) cc_final: 0.8238 (mtm)
REVERT: B   68 MET cc_start: 0.8959 (ttm) cc_final: 0.8355 (tpp)
REVERT: B   84 HIS cc_start: 0.9332 (m90) cc_final: 0.9047 (m-70)
REVERT: B   96 MET cc_start: 0.9094 (mmp) cc_final: 0.8738 (mpp)
REVERT: B  103 ASP cc_start: 0.9193 (m-30) cc_final: 0.8856 (m-30)
REVERT: B  170 LYS cc_start: 0.9277 (ptmm) cc_final: 0.8992 (pttt)
REVERT: B  215 MET cc_start: 0.8807 (ptp) cc_final: 0.8518 (ptt)
REVERT: C   52 LEU cc_start: 0.9591 (mp) cc_final: 0.9354 (mp)
REVERT: C   68 MET cc_start: 0.9346 (mtp) cc_final: 0.8884 (mtt)
REVERT: C  103 ASP cc_start: 0.8895 (m-30) cc_final: 0.8007 (t70)
REVERT: C  104 ILE cc_start: 0.8780 (tt) cc_final: 0.8349 (pt)
REVERT: C  117 TRP cc_start: 0.8240 (m-10) cc_final: 0.8034 (m-10)
REVERT: C  128 GLU cc_start: 0.9422 (mp0) cc_final: 0.9030 (mp0)
REVERT: C  140 LYS cc_start: 0.9465 (mtpp) cc_final: 0.9209 (mtpp)
REVERT: C  158 LYS cc_start: 0.9193 (mmmt) cc_final: 0.8779 (mmmm)
REVERT: C  167 ARG cc_start: 0.9387 (ptp90) cc_final: 0.9162 (ptp90)
REVERT: C  168 PHE cc_start: 0.9367 (t80) cc_final: 0.9118 (t80)
REVERT: D   39 MET cc_start: 0.8827 (mmm) cc_final: 0.8522 (mmm)
REVERT: D   53 ASN cc_start: 0.8609 (m-40) cc_final: 0.8200 (m110)
REVERT: D   68 MET cc_start: 0.9327 (ptp) cc_final: 0.8885 (ptp)
REVERT: D   71 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8536 (mt-10)
REVERT: D  100 ARG cc_start: 0.8718 (ttt180) cc_final: 0.8029 (ttm-80)
REVERT: D  145 TYR cc_start: 0.7762 (m-80) cc_final: 0.7336 (m-80)
REVERT: D  164 TYR cc_start: 0.8516 (t80) cc_final: 0.7727 (t80)
REVERT: D  212 GLU cc_start: 0.8879 (pt0) cc_final: 0.8653 (pm20)
REVERT: D  215 MET cc_start: 0.8718 (ptm) cc_final: 0.8486 (ppp)
REVERT: E   35 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7944 (tm-30)
REVERT: E   39 MET cc_start: 0.9294 (tpp) cc_final: 0.8881 (tpt)
REVERT: E   84 HIS cc_start: 0.9359 (m90) cc_final: 0.8739 (t-90)
REVERT: E   96 MET cc_start: 0.8754 (mmp) cc_final: 0.7968 (mpp)
REVERT: E  140 LYS cc_start: 0.9368 (mttt) cc_final: 0.9094 (mtpt)
REVERT: E  141 ILE cc_start: 0.8864 (mt) cc_final: 0.8627 (mt)
REVERT: E  144 MET cc_start: 0.8375 (ppp) cc_final: 0.7918 (ppp)
REVERT: E  170 LYS cc_start: 0.9069 (pttt) cc_final: 0.8597 (pttt)
REVERT: E  210 THR cc_start: 0.9368 (t) cc_final: 0.9133 (t)
REVERT: E  211 LEU cc_start: 0.9441 (tt) cc_final: 0.9114 (tt)
REVERT: E  215 MET cc_start: 0.9170 (mmp) cc_final: 0.8524 (mmp)
REVERT: F   55 MET cc_start: 0.7821 (ttt) cc_final: 0.7207 (ppp)
REVERT: F   68 MET cc_start: 0.9194 (mtp) cc_final: 0.8838 (mtp)
REVERT: F  103 ASP cc_start: 0.8469 (m-30) cc_final: 0.7843 (p0)
REVERT: F  104 ILE cc_start: 0.9158 (tt) cc_final: 0.8902 (pt)
REVERT: F  159 GLU cc_start: 0.8818 (pt0) cc_final: 0.7936 (mp0)
REVERT: F  164 TYR cc_start: 0.8586 (t80) cc_final: 0.8283 (t80)
REVERT: F  168 PHE cc_start: 0.9526 (t80) cc_final: 0.8891 (t80)
REVERT: F  190 LEU cc_start: 0.9220 (mt) cc_final: 0.8899 (mt)
  outliers start: 2
  outliers final: 0
  residues processed: 391
  average time/residue: 0.1068
  time to fit residues: 56.6136
Evaluate side-chains
  313 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 313
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 97 optimal weight:    5.9990
   chunk 3 optimal weight:    0.3980
   chunk 99 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0970
   chunk 32 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   chunk 121 optimal weight:    0.0770
   chunk 8 optimal weight:    9.9990
   chunk 105 optimal weight:   10.0000
   overall best weight:    2.1140

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

Flipped N/Q/H residues before XYZ refinement:
A  12 HIS
A  95 GLN
D  95 GLN
** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.089083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.060252 restraints weight = 90600.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.064085 restraints weight = 46614.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.066959 restraints weight = 30646.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.069068 restraints weight = 22405.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.070638 restraints weight = 17628.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3119
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3119
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.7016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10572  Z= 0.125
  Angle     :  0.660   7.178  14378  Z= 0.339
  Chirality :  0.046   0.176   1604
  Planarity :  0.005   0.048   1882
  Dihedral  :  4.167  23.026   1404
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.27 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.22), residues: 1310
  helix:  0.81 (0.18), residues: 852
  sheet:  None (None), residues: 0
  loop : -0.53 (0.26), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F 100 
 TYR   0.036   0.002   TYR E 145 
 PHE   0.018   0.002   PHE D  40 
 TRP   0.034   0.002   TRP F 117 
 HIS   0.003   0.001   HIS A  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (10566)
  covalent geometry    : angle       0.65878 (14366)
  SS BOND              : bond        0.00374 (    6)
  SS BOND              : angle       1.43482 (   12)
  hydrogen bonds       : bond        0.03502 (  577)
  hydrogen bonds       : angle       4.12364 ( 1731)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1986.28 seconds
wall clock time: 34 minutes 56.63 seconds (2096.63 seconds total)