Starting phenix.real_space_refine
on Tue Jul 29 20:53:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zra_60394/07_2025/8zra_60394.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zra_60394/07_2025/8zra_60394.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zra_60394/07_2025/8zra_60394.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zra_60394/07_2025/8zra_60394.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zra_60394/07_2025/8zra_60394.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zra_60394/07_2025/8zra_60394.cif"
  }
  resolution = 3.32
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.029
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      36      5.16       5
     C    7614      2.51       5
     N    1890      2.21       5
     O    2232      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11772
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 654
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 2, 'TRANS': 76}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, R
  Time building chain proxies: 3.15, per 1000 atoms: 0.27
  Number of scatterers: 11772
  At special positions: 0
  Unit cell: (97.65, 97.65, 86.1, 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      36     16.00
     O    2232      8.00
     N    1890      7.00
     C    7614      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.66
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2700

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 18 sheets defined
      21.5% alpha, 27.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 93 through 97
      removed outlier: 3.730A  pdb=" N   GLU A  96 " --> pdb=" O   PRO A  93 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER A  97 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 93 through 97'
    Processing helix  chain 'A' and resid 98 through 106
    Processing helix  chain 'A' and resid 154 through 156
      No H-bonds generated for 'chain 'A' and resid 154 through 156'
    Processing helix  chain 'B' and resid 93 through 97
      removed outlier: 3.730A  pdb=" N   GLU B  96 " --> pdb=" O   PRO B  93 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER B  97 " --> pdb=" O   ILE B  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 93 through 97'
    Processing helix  chain 'B' and resid 98 through 106
    Processing helix  chain 'B' and resid 154 through 156
      No H-bonds generated for 'chain 'B' and resid 154 through 156'
    Processing helix  chain 'C' and resid 93 through 97
      removed outlier: 3.730A  pdb=" N   GLU C  96 " --> pdb=" O   PRO C  93 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER C  97 " --> pdb=" O   ILE C  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 93 through 97'
    Processing helix  chain 'C' and resid 98 through 106
    Processing helix  chain 'C' and resid 154 through 156
      No H-bonds generated for 'chain 'C' and resid 154 through 156'
    Processing helix  chain 'D' and resid 93 through 97
      removed outlier: 3.730A  pdb=" N   GLU D  96 " --> pdb=" O   PRO D  93 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER D  97 " --> pdb=" O   ILE D  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 93 through 97'
    Processing helix  chain 'D' and resid 98 through 106
    Processing helix  chain 'D' and resid 154 through 156
      No H-bonds generated for 'chain 'D' and resid 154 through 156'
    Processing helix  chain 'E' and resid 93 through 97
      removed outlier: 3.730A  pdb=" N   GLU E  96 " --> pdb=" O   PRO E  93 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER E  97 " --> pdb=" O   ILE E  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 93 through 97'
    Processing helix  chain 'E' and resid 98 through 106
    Processing helix  chain 'E' and resid 154 through 156
      No H-bonds generated for 'chain 'E' and resid 154 through 156'
    Processing helix  chain 'F' and resid 93 through 97
      removed outlier: 3.730A  pdb=" N   GLU F  96 " --> pdb=" O   PRO F  93 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER F  97 " --> pdb=" O   ILE F  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 93 through 97'
    Processing helix  chain 'F' and resid 98 through 106
    Processing helix  chain 'F' and resid 154 through 156
      No H-bonds generated for 'chain 'F' and resid 154 through 156'
    Processing helix  chain 'G' and resid 93 through 97
      removed outlier: 3.730A  pdb=" N   GLU G  96 " --> pdb=" O   PRO G  93 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER G  97 " --> pdb=" O   ILE G  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 93 through 97'
    Processing helix  chain 'G' and resid 98 through 106
    Processing helix  chain 'G' and resid 154 through 156
      No H-bonds generated for 'chain 'G' and resid 154 through 156'
    Processing helix  chain 'H' and resid 93 through 97
      removed outlier: 3.730A  pdb=" N   GLU H  96 " --> pdb=" O   PRO H  93 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER H  97 " --> pdb=" O   ILE H  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 93 through 97'
    Processing helix  chain 'H' and resid 98 through 106
    Processing helix  chain 'H' and resid 154 through 156
      No H-bonds generated for 'chain 'H' and resid 154 through 156'
    Processing helix  chain 'I' and resid 93 through 97
      removed outlier: 3.731A  pdb=" N   GLU I  96 " --> pdb=" O   PRO I  93 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER I  97 " --> pdb=" O   ILE I  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 93 through 97'
    Processing helix  chain 'I' and resid 98 through 106
    Processing helix  chain 'I' and resid 154 through 156
      No H-bonds generated for 'chain 'I' and resid 154 through 156'
    Processing helix  chain 'J' and resid 93 through 97
      removed outlier: 3.731A  pdb=" N   GLU J  96 " --> pdb=" O   PRO J  93 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER J  97 " --> pdb=" O   ILE J  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 93 through 97'
    Processing helix  chain 'J' and resid 98 through 106
    Processing helix  chain 'J' and resid 154 through 156
      No H-bonds generated for 'chain 'J' and resid 154 through 156'
    Processing helix  chain 'K' and resid 93 through 97
      removed outlier: 3.730A  pdb=" N   GLU K  96 " --> pdb=" O   PRO K  93 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER K  97 " --> pdb=" O   ILE K  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 93 through 97'
    Processing helix  chain 'K' and resid 98 through 106
    Processing helix  chain 'K' and resid 154 through 156
      No H-bonds generated for 'chain 'K' and resid 154 through 156'
    Processing helix  chain 'L' and resid 93 through 97
      removed outlier: 3.731A  pdb=" N   GLU L  96 " --> pdb=" O   PRO L  93 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER L  97 " --> pdb=" O   ILE L  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 93 through 97'
    Processing helix  chain 'L' and resid 98 through 106
    Processing helix  chain 'L' and resid 154 through 156
      No H-bonds generated for 'chain 'L' and resid 154 through 156'
    Processing helix  chain 'M' and resid 93 through 97
      removed outlier: 3.730A  pdb=" N   GLU M  96 " --> pdb=" O   PRO M  93 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER M  97 " --> pdb=" O   ILE M  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'M' and resid 93 through 97'
    Processing helix  chain 'M' and resid 98 through 106
    Processing helix  chain 'M' and resid 154 through 156
      No H-bonds generated for 'chain 'M' and resid 154 through 156'
    Processing helix  chain 'N' and resid 93 through 97
      removed outlier: 3.731A  pdb=" N   GLU N  96 " --> pdb=" O   PRO N  93 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER N  97 " --> pdb=" O   ILE N  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 93 through 97'
    Processing helix  chain 'N' and resid 98 through 106
    Processing helix  chain 'N' and resid 154 through 156
      No H-bonds generated for 'chain 'N' and resid 154 through 156'
    Processing helix  chain 'O' and resid 93 through 97
      removed outlier: 3.731A  pdb=" N   GLU O  96 " --> pdb=" O   PRO O  93 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER O  97 " --> pdb=" O   ILE O  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 93 through 97'
    Processing helix  chain 'O' and resid 98 through 106
    Processing helix  chain 'O' and resid 154 through 156
      No H-bonds generated for 'chain 'O' and resid 154 through 156'
    Processing helix  chain 'P' and resid 93 through 97
      removed outlier: 3.730A  pdb=" N   GLU P  96 " --> pdb=" O   PRO P  93 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER P  97 " --> pdb=" O   ILE P  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 93 through 97'
    Processing helix  chain 'P' and resid 98 through 106
    Processing helix  chain 'P' and resid 154 through 156
      No H-bonds generated for 'chain 'P' and resid 154 through 156'
    Processing helix  chain 'Q' and resid 93 through 97
      removed outlier: 3.730A  pdb=" N   GLU Q  96 " --> pdb=" O   PRO Q  93 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER Q  97 " --> pdb=" O   ILE Q  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Q' and resid 93 through 97'
    Processing helix  chain 'Q' and resid 98 through 106
    Processing helix  chain 'Q' and resid 154 through 156
      No H-bonds generated for 'chain 'Q' and resid 154 through 156'
    Processing helix  chain 'R' and resid 93 through 97
      removed outlier: 3.730A  pdb=" N   GLU R  96 " --> pdb=" O   PRO R  93 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER R  97 " --> pdb=" O   ILE R  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 93 through 97'
    Processing helix  chain 'R' and resid 98 through 106
    Processing helix  chain 'R' and resid 154 through 156
      No H-bonds generated for 'chain 'R' and resid 154 through 156'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 143
      removed outlier: 7.066A  pdb=" N   ILE A 141 " --> pdb=" O   GLU A 133 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 152
      removed outlier: 7.066A  pdb=" N   ILE B 141 " --> pdb=" O   GLU B 133 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 151 through 152
      removed outlier: 7.066A  pdb=" N   ILE C 141 " --> pdb=" O   GLU C 133 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 151 through 152
      removed outlier: 7.066A  pdb=" N   ILE D 141 " --> pdb=" O   GLU D 133 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 151 through 152
      removed outlier: 7.066A  pdb=" N   ILE E 141 " --> pdb=" O   GLU E 133 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 151 through 152
      removed outlier: 7.066A  pdb=" N   ILE F 141 " --> pdb=" O   GLU F 133 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 151 through 152
      removed outlier: 7.066A  pdb=" N   ILE G 141 " --> pdb=" O   GLU G 133 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 151 through 152
      removed outlier: 7.066A  pdb=" N   ILE H 141 " --> pdb=" O   GLU H 133 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 151 through 152
      removed outlier: 7.066A  pdb=" N   ILE J 141 " --> pdb=" O   GLU J 133 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'I' and resid 140 through 143
      removed outlier: 7.066A  pdb=" N   ILE I 141 " --> pdb=" O   GLU I 133 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'I' and resid 151 through 152
      removed outlier: 7.066A  pdb=" N   ILE K 141 " --> pdb=" O   GLU K 133 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 151 through 152
      removed outlier: 7.067A  pdb=" N   ILE L 141 " --> pdb=" O   GLU L 133 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 151 through 152
      removed outlier: 7.066A  pdb=" N   ILE M 141 " --> pdb=" O   GLU M 133 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'M' and resid 151 through 152
      removed outlier: 7.066A  pdb=" N   ILE N 141 " --> pdb=" O   GLU N 133 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'N' and resid 151 through 152
      removed outlier: 7.067A  pdb=" N   ILE O 141 " --> pdb=" O   GLU O 133 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'O' and resid 151 through 152
      removed outlier: 7.066A  pdb=" N   ILE P 141 " --> pdb=" O   GLU P 133 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'P' and resid 151 through 152
      removed outlier: 7.066A  pdb=" N   ILE Q 141 " --> pdb=" O   GLU Q 133 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'Q' and resid 151 through 152
      removed outlier: 7.066A  pdb=" N   ILE R 141 " --> pdb=" O   GLU R 133 " (cutoff:3.500A)

    360 hydrogen bonds defined for protein.
    1026 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: 3.23

  Time building geometry restraints manager: 3.21 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3690
        1.34 -     1.46: 2456
        1.46 -     1.57: 5788
        1.57 -     1.69: 0
        1.69 -     1.80: 72
  Bond restraints: 12006
  Sorted by residual:
  bond pdb=" N   PRO B  93 "
       pdb=" CA  PRO B  93 "
    ideal  model  delta    sigma   weight residual
    1.469  1.451  0.018 1.28e-02 6.10e+03 1.95e+00
  bond pdb=" N   PRO A  93 "
       pdb=" CA  PRO A  93 "
    ideal  model  delta    sigma   weight residual
    1.469  1.451  0.018 1.28e-02 6.10e+03 1.94e+00
  bond pdb=" N   PRO G  93 "
       pdb=" CA  PRO G  93 "
    ideal  model  delta    sigma   weight residual
    1.469  1.451  0.018 1.28e-02 6.10e+03 1.92e+00
  bond pdb=" N   PRO F  93 "
       pdb=" CA  PRO F  93 "
    ideal  model  delta    sigma   weight residual
    1.469  1.451  0.018 1.28e-02 6.10e+03 1.91e+00
  bond pdb=" N   PRO E  93 "
       pdb=" CA  PRO E  93 "
    ideal  model  delta    sigma   weight residual
    1.469  1.451  0.018 1.28e-02 6.10e+03 1.90e+00
  ... (remaining 12001 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.96: 14134
        0.96 -     1.93: 1517
        1.93 -     2.89: 402
        2.89 -     3.85: 93
        3.85 -     4.82: 90
  Bond angle restraints: 16236
  Sorted by residual:
  angle pdb=" C   ASP F 159 "
        pdb=" N   TYR F 160 "
        pdb=" CA  TYR F 160 "
      ideal   model   delta    sigma   weight residual
     121.63  116.90    4.73 1.92e+00 2.71e-01 6.07e+00
  angle pdb=" C   ASP O 159 "
        pdb=" N   TYR O 160 "
        pdb=" CA  TYR O 160 "
      ideal   model   delta    sigma   weight residual
     121.63  116.91    4.72 1.92e+00 2.71e-01 6.04e+00
  angle pdb=" C   ASP R 159 "
        pdb=" N   TYR R 160 "
        pdb=" CA  TYR R 160 "
      ideal   model   delta    sigma   weight residual
     121.63  116.91    4.72 1.92e+00 2.71e-01 6.04e+00
  angle pdb=" C   ASP K 159 "
        pdb=" N   TYR K 160 "
        pdb=" CA  TYR K 160 "
      ideal   model   delta    sigma   weight residual
     121.63  116.92    4.71 1.92e+00 2.71e-01 6.02e+00
  angle pdb=" C   ASP N 159 "
        pdb=" N   TYR N 160 "
        pdb=" CA  TYR N 160 "
      ideal   model   delta    sigma   weight residual
     121.63  116.93    4.70 1.92e+00 2.71e-01 6.00e+00
  ... (remaining 16231 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.34: 5958
       14.34 -    28.67: 864
       28.67 -    43.01: 270
       43.01 -    57.34: 72
       57.34 -    71.68: 18
  Dihedral angle restraints: 7182
    sinusoidal: 2970
      harmonic: 4212
  Sorted by residual:
  dihedral pdb=" CA  PHE I 117 "
           pdb=" C   PHE I 117 "
           pdb=" N   GLU I 118 "
           pdb=" CA  GLU I 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.26  -16.74     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  PHE J 117 "
           pdb=" C   PHE J 117 "
           pdb=" N   GLU J 118 "
           pdb=" CA  GLU J 118 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.29  -16.71     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  PHE G 117 "
           pdb=" C   PHE G 117 "
           pdb=" N   GLU G 118 "
           pdb=" CA  GLU G 118 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.30  -16.70     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 7179 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1063
       0.035 -    0.070: 439
       0.070 -    0.105: 173
       0.105 -    0.140: 143
       0.140 -    0.174: 18
  Chirality restraints: 1836
  Sorted by residual:
  chirality pdb=" CB  THR M 116 "
            pdb=" CA  THR M 116 "
            pdb=" OG1 THR M 116 "
            pdb=" CG2 THR M 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.61e-01
  chirality pdb=" CB  THR P 116 "
            pdb=" CA  THR P 116 "
            pdb=" OG1 THR P 116 "
            pdb=" CG2 THR P 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.54e-01
  chirality pdb=" CB  THR C 116 "
            pdb=" CA  THR C 116 "
            pdb=" OG1 THR C 116 "
            pdb=" CG2 THR C 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.52e-01
  ... (remaining 1833 not shown)

  Planarity restraints: 2016
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG J 129 "    0.157 9.50e-02 1.11e+02   7.06e-02 3.64e+00
        pdb=" NE  ARG J 129 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG J 129 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG J 129 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG J 129 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 129 "    0.157 9.50e-02 1.11e+02   7.06e-02 3.64e+00
        pdb=" NE  ARG C 129 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 129 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 129 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 129 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G 129 "    0.156 9.50e-02 1.11e+02   7.05e-02 3.63e+00
        pdb=" NE  ARG G 129 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG G 129 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG G 129 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG G 129 "    0.001 2.00e-02 2.50e+03
  ... (remaining 2013 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2702
        2.78 -     3.31: 10153
        3.31 -     3.84: 18013
        3.84 -     4.37: 21631
        4.37 -     4.90: 38953
  Nonbonded interactions: 91452
  Sorted by model distance:
  nonbonded pdb=" O   GLU M  96 "
            pdb=" ND2 ASN M 101 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" O   GLU H  96 "
            pdb=" ND2 ASN H 101 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" O   GLU L  96 "
            pdb=" ND2 ASN L 101 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" O   GLU N  96 "
            pdb=" ND2 ASN N 101 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" O   GLU P  96 "
            pdb=" ND2 ASN P 101 "
     model   vdw
     2.252 3.120
  ... (remaining 91447 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'L'
  selection = chain 'O'
  selection = chain 'N'
  selection = chain 'Q'
  selection = chain 'P'
  selection = chain 'R'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.400
  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:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     23.720
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
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   0.050  12006  Z= 0.266
  Angle     :  0.774   4.817  16236  Z= 0.415
  Chirality :  0.054   0.174   1836
  Planarity :  0.008   0.071   2016
  Dihedral  : 15.351  71.680   4482
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 16.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.39 %
    Favored  : 89.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.94 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.04 (0.20), residues: 1386
  helix: -1.47 (0.34), residues: 144
  sheet: -2.64 (0.22), residues: 450
  loop : -3.02 (0.20), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 123 
 HIS   0.003   0.002   HIS F 139 
 PHE   0.028   0.004   PHE R 117 
 TYR   0.013   0.002   TYR D 160 
 ARG   0.013   0.002   ARG J 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22412 (  360)
  hydrogen bonds       : angle      10.82741 ( 1026)
  covalent geometry    : bond        0.00587 (12006)
  covalent geometry    : angle       0.77389 (16236)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  409 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 409
  time to evaluate  : 1.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8194 (mmtp)
REVERT: A  115 MET cc_start: 0.8685 (mtp) cc_final: 0.8463 (ttm)
REVERT: A  124 ASN cc_start: 0.9260 (t0) cc_final: 0.9042 (t0)
REVERT: B  109 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8130 (mmtp)
REVERT: B  115 MET cc_start: 0.8857 (mtp) cc_final: 0.8565 (ttm)
REVERT: B  164 ASP cc_start: 0.8260 (t0) cc_final: 0.8026 (t0)
REVERT: C  109 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8251 (mmtp)
REVERT: C  126 LYS cc_start: 0.8362 (mmtt) cc_final: 0.7945 (mmmm)
REVERT: C  164 ASP cc_start: 0.8290 (t0) cc_final: 0.7982 (t0)
REVERT: D  109 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8189 (mmtp)
REVERT: D  164 ASP cc_start: 0.8381 (t0) cc_final: 0.8132 (t0)
REVERT: E  109 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8191 (mmtp)
REVERT: E  164 ASP cc_start: 0.8382 (t0) cc_final: 0.8167 (t0)
REVERT: F  109 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8255 (mmtp)
REVERT: G  109 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8198 (mmtm)
REVERT: H  109 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8164 (mmtp)
REVERT: I  107 ARG cc_start: 0.8711 (mtp-110) cc_final: 0.8479 (mtp85)
REVERT: J  126 LYS cc_start: 0.8419 (mmtt) cc_final: 0.8215 (mmmt)
REVERT: L  164 ASP cc_start: 0.8235 (t0) cc_final: 0.8022 (t0)
REVERT: O  126 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8253 (mmmm)
REVERT: O  151 TYR cc_start: 0.8662 (m-80) cc_final: 0.8388 (m-80)
REVERT: P  107 ARG cc_start: 0.8634 (mtp-110) cc_final: 0.8429 (mtm110)
REVERT: P  114 TYR cc_start: 0.8984 (m-80) cc_final: 0.8736 (m-80)
REVERT: Q  119 ASN cc_start: 0.7979 (m110) cc_final: 0.7658 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 409
  average time/residue: 0.3913
  time to fit residues: 200.4904
Evaluate side-chains
  378 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 378
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 64 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 98 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 73 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
C 124 ASN
J 124 ASN
K 106 ASN
L 106 ASN
M 106 ASN
O 106 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.124126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.107544 restraints weight = 14058.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.04
r_work: 0.3087 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12006  Z= 0.221
  Angle     :  0.636   4.785  16236  Z= 0.349
  Chirality :  0.053   0.172   1836
  Planarity :  0.005   0.033   2016
  Dihedral  :  4.696  21.595   1602
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 22.46 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.15 (0.20), residues: 1386
  helix: -1.01 (0.40), residues: 180
  sheet: -2.90 (0.18), residues: 684
  loop : -2.87 (0.21), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP M 123 
 HIS   0.005   0.002   HIS I 139 
 PHE   0.026   0.003   PHE M 117 
 TYR   0.015   0.002   TYR K 160 
 ARG   0.009   0.001   ARG H 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05836 (  360)
  hydrogen bonds       : angle       7.90526 ( 1026)
  covalent geometry    : bond        0.00513 (12006)
  covalent geometry    : angle       0.63562 (16236)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  421 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 374
  time to evaluate  : 1.395 
Fit side-chains
   revert: symmetry clash
REVERT: B  109 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8354 (mmtp)
REVERT: B  119 ASN cc_start: 0.8501 (m110) cc_final: 0.8249 (m-40)
REVERT: C  109 LYS cc_start: 0.8745 (mmtt) cc_final: 0.8493 (mmtp)
REVERT: D  164 ASP cc_start: 0.8666 (t0) cc_final: 0.8462 (t0)
REVERT: E  119 ASN cc_start: 0.8426 (m110) cc_final: 0.8154 (m-40)
REVERT: E  164 ASP cc_start: 0.8768 (t0) cc_final: 0.8338 (t0)
REVERT: F  137 ARG cc_start: 0.8902 (ptp-170) cc_final: 0.8658 (ptp-170)
REVERT: G   95 GLU cc_start: 0.8806 (mp0) cc_final: 0.8592 (mp0)
REVERT: H  109 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8442 (mmtp)
REVERT: H  119 ASN cc_start: 0.8463 (m110) cc_final: 0.8257 (m110)
REVERT: I   92 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8260 (mp)
REVERT: I  129 ARG cc_start: 0.8306 (ttm110) cc_final: 0.8100 (ttm110)
REVERT: K  119 ASN cc_start: 0.8487 (m110) cc_final: 0.8206 (m-40)
REVERT: N  119 ASN cc_start: 0.8609 (m110) cc_final: 0.8386 (m-40)
REVERT: Q  119 ASN cc_start: 0.8518 (m110) cc_final: 0.8297 (m-40)
REVERT: R  119 ASN cc_start: 0.8561 (m110) cc_final: 0.8318 (m110)
  outliers start: 47
  outliers final: 18
  residues processed: 414
  average time/residue: 0.4352
  time to fit residues: 237.2290
Evaluate side-chains
  379 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 360
  time to evaluate  : 1.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   92 LEU
Chi-restraints excluded: chain H residue  102 ILE
Chi-restraints excluded: chain I residue   92 LEU
Chi-restraints excluded: chain J residue   92 LEU
Chi-restraints excluded: chain J residue  102 ILE
Chi-restraints excluded: chain K residue  102 ILE
Chi-restraints excluded: chain K residue  105 LEU
Chi-restraints excluded: chain M residue  102 ILE
Chi-restraints excluded: chain N residue   92 LEU
Chi-restraints excluded: chain N residue  102 ILE
Chi-restraints excluded: chain Q residue   92 LEU
Chi-restraints excluded: chain Q residue  102 ILE
Chi-restraints excluded: chain Q residue  105 LEU
Chi-restraints excluded: chain R residue  105 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 83 optimal weight:    4.9990
   chunk 36 optimal weight:    6.9990
   chunk 94 optimal weight:    1.9990
   chunk 119 optimal weight:    0.0770
   chunk 47 optimal weight:    7.9990
   chunk 3 optimal weight:    6.9990
   chunk 76 optimal weight:    4.9990
   overall best weight:    2.8146

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

Flipped N/Q/H residues before XYZ refinement:
C 119 ASN
C 124 ASN
J 124 ASN
N 124 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.123002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.105764 restraints weight = 14292.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.15
r_work: 0.3073 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12006  Z= 0.222
  Angle     :  0.617   5.124  16236  Z= 0.340
  Chirality :  0.053   0.188   1836
  Planarity :  0.004   0.038   2016
  Dihedral  :  4.593  23.880   1602
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 25.98 %
    Favored  : 71.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.35 (0.21), residues: 1386
  helix: -1.00 (0.39), residues: 180
  sheet: -2.53 (0.19), residues: 594
  loop : -2.08 (0.24), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP N 123 
 HIS   0.004   0.002   HIS Q 139 
 PHE   0.022   0.003   PHE M 117 
 TYR   0.015   0.002   TYR K 160 
 ARG   0.008   0.001   ARG M 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05763 (  360)
  hydrogen bonds       : angle       7.37762 ( 1026)
  covalent geometry    : bond        0.00511 (12006)
  covalent geometry    : angle       0.61748 (16236)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  406 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 373
  time to evaluate  : 2.403 
Fit side-chains
   revert: symmetry clash
REVERT: B  109 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8336 (mmtp)
REVERT: C  109 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8410 (mmtp)
REVERT: C  122 GLU cc_start: 0.8391 (mp0) cc_final: 0.7939 (mp0)
REVERT: D  164 ASP cc_start: 0.8768 (t0) cc_final: 0.8520 (t0)
REVERT: E  119 ASN cc_start: 0.8495 (m110) cc_final: 0.8266 (m110)
REVERT: E  122 GLU cc_start: 0.8124 (mp0) cc_final: 0.7716 (mp0)
REVERT: E  164 ASP cc_start: 0.8780 (t0) cc_final: 0.8520 (t0)
REVERT: H  109 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8341 (mmtp)
REVERT: H  119 ASN cc_start: 0.8543 (m110) cc_final: 0.8317 (m110)
REVERT: H  159 ASP cc_start: 0.8844 (m-30) cc_final: 0.8641 (m-30)
REVERT: I   92 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8299 (mp)
REVERT: I  129 ARG cc_start: 0.8350 (ttm110) cc_final: 0.8142 (ttm110)
REVERT: J  122 GLU cc_start: 0.8454 (mp0) cc_final: 0.7979 (mp0)
REVERT: K  104 ARG cc_start: 0.7768 (mtt-85) cc_final: 0.7413 (mtp180)
REVERT: L   92 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8257 (mp)
REVERT: N  119 ASN cc_start: 0.8564 (m110) cc_final: 0.8279 (m-40)
REVERT: Q  119 ASN cc_start: 0.8509 (m110) cc_final: 0.8297 (m110)
REVERT: R  119 ASN cc_start: 0.8663 (m110) cc_final: 0.8318 (m110)
  outliers start: 33
  outliers final: 21
  residues processed: 398
  average time/residue: 0.4533
  time to fit residues: 237.3879
Evaluate side-chains
  392 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 369
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain F residue   92 LEU
Chi-restraints excluded: chain G residue   92 LEU
Chi-restraints excluded: chain G residue  105 LEU
Chi-restraints excluded: chain H residue  105 LEU
Chi-restraints excluded: chain I residue   92 LEU
Chi-restraints excluded: chain K residue   92 LEU
Chi-restraints excluded: chain K residue  105 LEU
Chi-restraints excluded: chain L residue   92 LEU
Chi-restraints excluded: chain L residue  102 ILE
Chi-restraints excluded: chain M residue   92 LEU
Chi-restraints excluded: chain P residue  102 ILE
Chi-restraints excluded: chain Q residue   92 LEU
Chi-restraints excluded: chain Q residue  105 LEU
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  105 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 31 optimal weight:    0.0040
   chunk 121 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9980
   chunk 104 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 67 optimal weight:    8.9990
   chunk 116 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    1.7998

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

Flipped N/Q/H residues before XYZ refinement:
A 124 ASN
C 106 ASN
C 119 ASN
C 124 ASN
F 106 ASN
G 106 ASN
J 124 ASN
Q 106 ASN
Q 124 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.125583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.108186 restraints weight = 14085.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.17
r_work: 0.3098 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12006  Z= 0.160
  Angle     :  0.572   5.098  16236  Z= 0.314
  Chirality :  0.051   0.187   1836
  Planarity :  0.004   0.041   2016
  Dihedral  :  4.391  22.037   1602
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 26.68 %
    Favored  : 69.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.06 (0.22), residues: 1386
  helix: -0.79 (0.39), residues: 180
  sheet: -2.24 (0.20), residues: 594
  loop : -2.02 (0.24), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP Q 123 
 HIS   0.005   0.002   HIS R 139 
 PHE   0.018   0.002   PHE M 117 
 TYR   0.012   0.001   TYR Q 160 
 ARG   0.009   0.001   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05257 (  360)
  hydrogen bonds       : angle       6.86471 ( 1026)
  covalent geometry    : bond        0.00364 (12006)
  covalent geometry    : angle       0.57246 (16236)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  415 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 365
  time to evaluate  : 1.410 
Fit side-chains
REVERT: A  129 ARG cc_start: 0.8215 (ttm110) cc_final: 0.8006 (ttm110)
REVERT: B  109 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8358 (mmtp)
REVERT: C  109 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8428 (mmtp)
REVERT: C  122 GLU cc_start: 0.8427 (mp0) cc_final: 0.7939 (mp0)
REVERT: D  164 ASP cc_start: 0.8825 (t0) cc_final: 0.8516 (t0)
REVERT: E  119 ASN cc_start: 0.8515 (m110) cc_final: 0.8240 (m110)
REVERT: E  122 GLU cc_start: 0.8141 (mp0) cc_final: 0.7735 (mp0)
REVERT: E  164 ASP cc_start: 0.8790 (t0) cc_final: 0.8472 (t0)
REVERT: H  109 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8300 (mmtp)
REVERT: H  119 ASN cc_start: 0.8575 (m110) cc_final: 0.8311 (m110)
REVERT: J  122 GLU cc_start: 0.8454 (mp0) cc_final: 0.8038 (mp0)
REVERT: L  110 THR cc_start: 0.8909 (m) cc_final: 0.8561 (p)
REVERT: L  121 LYS cc_start: 0.8369 (ttpt) cc_final: 0.7860 (pttm)
REVERT: N  119 ASN cc_start: 0.8559 (m110) cc_final: 0.8247 (m-40)
REVERT: N  121 LYS cc_start: 0.8255 (ttpt) cc_final: 0.7926 (ttpt)
REVERT: O  151 TYR cc_start: 0.9056 (m-80) cc_final: 0.8755 (m-80)
REVERT: Q  119 ASN cc_start: 0.8500 (m110) cc_final: 0.8268 (m110)
REVERT: Q  121 LYS cc_start: 0.8358 (ttpt) cc_final: 0.8032 (ttpt)
REVERT: R  104 ARG cc_start: 0.7727 (mtt-85) cc_final: 0.7493 (mtp180)
REVERT: R  119 ASN cc_start: 0.8548 (m110) cc_final: 0.8192 (m110)
  outliers start: 50
  outliers final: 31
  residues processed: 403
  average time/residue: 0.3193
  time to fit residues: 168.4555
Evaluate side-chains
  395 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 364
  time to evaluate  : 1.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  119 ASN
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  102 ILE
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   92 LEU
Chi-restraints excluded: chain H residue  102 ILE
Chi-restraints excluded: chain H residue  105 LEU
Chi-restraints excluded: chain J residue   92 LEU
Chi-restraints excluded: chain J residue  102 ILE
Chi-restraints excluded: chain J residue  105 LEU
Chi-restraints excluded: chain K residue   92 LEU
Chi-restraints excluded: chain K residue  102 ILE
Chi-restraints excluded: chain K residue  105 LEU
Chi-restraints excluded: chain L residue  102 ILE
Chi-restraints excluded: chain M residue  102 ILE
Chi-restraints excluded: chain N residue   92 LEU
Chi-restraints excluded: chain N residue  102 ILE
Chi-restraints excluded: chain O residue  102 ILE
Chi-restraints excluded: chain P residue  102 ILE
Chi-restraints excluded: chain Q residue  100 GLU
Chi-restraints excluded: chain Q residue  102 ILE
Chi-restraints excluded: chain Q residue  105 LEU
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  105 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   chunk 120 optimal weight:   10.0000
   chunk 118 optimal weight:    0.4980
   chunk 52 optimal weight:    1.9990
   chunk 111 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 112 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
A 124 ASN
C 119 ASN
C 124 ASN
D 124 ASN
E 106 ASN
** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 124 ASN
J 124 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.122005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.104331 restraints weight = 14868.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 2.37
r_work: 0.3051 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2890 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12006  Z= 0.189
  Angle     :  0.594   5.509  16236  Z= 0.325
  Chirality :  0.052   0.226   1836
  Planarity :  0.005   0.048   2016
  Dihedral  :  4.374  21.138   1602
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 25.90 %
    Favored  : 69.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.93 (0.22), residues: 1386
  helix: -0.65 (0.39), residues: 180
  sheet: -2.16 (0.20), residues: 594
  loop : -1.94 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP N 123 
 HIS   0.004   0.002   HIS R 139 
 PHE   0.019   0.002   PHE C 117 
 TYR   0.012   0.001   TYR M 160 
 ARG   0.010   0.001   ARG L 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05375 (  360)
  hydrogen bonds       : angle       6.80220 ( 1026)
  covalent geometry    : bond        0.00432 (12006)
  covalent geometry    : angle       0.59363 (16236)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  422 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 359
  time to evaluate  : 2.883 
Fit side-chains
REVERT: A  121 LYS cc_start: 0.8550 (tptp) cc_final: 0.8339 (ttpp)
REVERT: B  109 LYS cc_start: 0.8491 (mmtt) cc_final: 0.8233 (mmtp)
REVERT: C  109 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8282 (mmtp)
REVERT: C  122 GLU cc_start: 0.8476 (mp0) cc_final: 0.7954 (mp0)
REVERT: D  122 GLU cc_start: 0.8432 (mp0) cc_final: 0.7831 (mp0)
REVERT: E  115 MET cc_start: 0.9330 (mtp) cc_final: 0.9122 (mtm)
REVERT: E  122 GLU cc_start: 0.8278 (mp0) cc_final: 0.7752 (mp0)
REVERT: E  164 ASP cc_start: 0.8776 (t0) cc_final: 0.8479 (t0)
REVERT: F  153 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8843 (mt)
REVERT: G  122 GLU cc_start: 0.8385 (mp0) cc_final: 0.7963 (mp0)
REVERT: H  109 LYS cc_start: 0.8533 (mmtt) cc_final: 0.8179 (mmtp)
REVERT: H  119 ASN cc_start: 0.8619 (m110) cc_final: 0.8291 (m110)
REVERT: H  122 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7889 (mp0)
REVERT: H  153 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8968 (mt)
REVERT: I  107 ARG cc_start: 0.8834 (mtp85) cc_final: 0.8594 (mtp-110)
REVERT: I  110 THR cc_start: 0.8915 (m) cc_final: 0.8451 (p)
REVERT: J  122 GLU cc_start: 0.8498 (mp0) cc_final: 0.8103 (mp0)
REVERT: J  153 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9029 (mt)
REVERT: K  133 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7714 (mm-30)
REVERT: L  110 THR cc_start: 0.8954 (m) cc_final: 0.8605 (p)
REVERT: L  121 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8096 (ttpt)
REVERT: L  129 ARG cc_start: 0.8527 (ttm110) cc_final: 0.8321 (ttm110)
REVERT: N  119 ASN cc_start: 0.8685 (m110) cc_final: 0.8297 (m-40)
REVERT: N  121 LYS cc_start: 0.8321 (ttpt) cc_final: 0.8016 (ttpt)
REVERT: P  121 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8336 (mmtt)
REVERT: Q  119 ASN cc_start: 0.8669 (m110) cc_final: 0.8366 (m110)
REVERT: Q  121 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7996 (ttpt)
REVERT: R  110 THR cc_start: 0.8957 (m) cc_final: 0.8593 (p)
REVERT: R  119 ASN cc_start: 0.8595 (m110) cc_final: 0.8164 (m110)
  outliers start: 63
  outliers final: 33
  residues processed: 412
  average time/residue: 0.3969
  time to fit residues: 217.8359
Evaluate side-chains
  398 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 360
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  119 ASN
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  102 ILE
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  153 LEU
Chi-restraints excluded: chain G residue   92 LEU
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   92 LEU
Chi-restraints excluded: chain H residue  102 ILE
Chi-restraints excluded: chain H residue  105 LEU
Chi-restraints excluded: chain H residue  122 GLU
Chi-restraints excluded: chain H residue  153 LEU
Chi-restraints excluded: chain J residue   92 LEU
Chi-restraints excluded: chain J residue  102 ILE
Chi-restraints excluded: chain J residue  105 LEU
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain K residue   92 LEU
Chi-restraints excluded: chain K residue  102 ILE
Chi-restraints excluded: chain L residue  102 ILE
Chi-restraints excluded: chain M residue   92 LEU
Chi-restraints excluded: chain M residue  102 ILE
Chi-restraints excluded: chain N residue   92 LEU
Chi-restraints excluded: chain N residue  102 ILE
Chi-restraints excluded: chain O residue  102 ILE
Chi-restraints excluded: chain P residue  102 ILE
Chi-restraints excluded: chain P residue  121 LYS
Chi-restraints excluded: chain Q residue   92 LEU
Chi-restraints excluded: chain Q residue  102 ILE
Chi-restraints excluded: chain Q residue  105 LEU
Chi-restraints excluded: chain R residue   92 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 110 optimal weight:    9.9990
   chunk 52 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 57 optimal weight:    0.5980
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 124 ASN
C 124 ASN
H 124 ASN
J 124 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.123425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.105780 restraints weight = 14899.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 2.38
r_work: 0.3068 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12006  Z= 0.163
  Angle     :  0.582   5.420  16236  Z= 0.319
  Chirality :  0.052   0.208   1836
  Planarity :  0.005   0.050   2016
  Dihedral  :  4.308  20.656   1602
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 25.82 %
    Favored  : 68.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.82 (0.22), residues: 1386
  helix: -0.56 (0.39), residues: 180
  sheet: -2.08 (0.20), residues: 594
  loop : -1.87 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP N 123 
 HIS   0.003   0.001   HIS R 139 
 PHE   0.014   0.002   PHE P 117 
 TYR   0.011   0.001   TYR L 114 
 ARG   0.011   0.001   ARG H 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05286 (  360)
  hydrogen bonds       : angle       6.70116 ( 1026)
  covalent geometry    : bond        0.00374 (12006)
  covalent geometry    : angle       0.58183 (16236)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  426 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 357
  time to evaluate  : 1.246 
Fit side-chains
REVERT: A  121 LYS cc_start: 0.8536 (tptp) cc_final: 0.8316 (ttpp)
REVERT: B  109 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8253 (mmtp)
REVERT: B  122 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7818 (mp0)
REVERT: C  109 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8248 (mmtp)
REVERT: C  122 GLU cc_start: 0.8480 (mp0) cc_final: 0.7972 (mp0)
REVERT: D  122 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7810 (mp0)
REVERT: E  122 GLU cc_start: 0.8284 (mp0) cc_final: 0.7744 (mp0)
REVERT: E  153 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9000 (mt)
REVERT: E  164 ASP cc_start: 0.8791 (t0) cc_final: 0.8472 (t0)
REVERT: F  153 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8874 (mt)
REVERT: G  122 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7962 (mp0)
REVERT: H  109 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8207 (mmtp)
REVERT: H  119 ASN cc_start: 0.8596 (m110) cc_final: 0.8279 (m110)
REVERT: H  122 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7903 (mp0)
REVERT: H  153 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9010 (mt)
REVERT: I  107 ARG cc_start: 0.8800 (mtp85) cc_final: 0.8519 (mtp-110)
REVERT: I  110 THR cc_start: 0.8938 (m) cc_final: 0.8489 (p)
REVERT: I  121 LYS cc_start: 0.8380 (ttpt) cc_final: 0.7935 (ttpt)
REVERT: J  122 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8106 (mp0)
REVERT: J  153 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9000 (mt)
REVERT: L  110 THR cc_start: 0.8950 (m) cc_final: 0.8602 (p)
REVERT: L  121 LYS cc_start: 0.8428 (ttpt) cc_final: 0.8075 (ttpt)
REVERT: L  129 ARG cc_start: 0.8543 (ttm110) cc_final: 0.8285 (ttm110)
REVERT: N  119 ASN cc_start: 0.8614 (m110) cc_final: 0.8301 (m110)
REVERT: N  121 LYS cc_start: 0.8290 (ttpt) cc_final: 0.7958 (ttpt)
REVERT: O  151 TYR cc_start: 0.9030 (m-80) cc_final: 0.8796 (m-80)
REVERT: Q  106 ASN cc_start: 0.8179 (m-40) cc_final: 0.7958 (m110)
REVERT: Q  119 ASN cc_start: 0.8690 (m110) cc_final: 0.8375 (m110)
REVERT: Q  121 LYS cc_start: 0.8357 (ttpt) cc_final: 0.8025 (ttpt)
REVERT: R  110 THR cc_start: 0.8976 (m) cc_final: 0.8602 (p)
REVERT: R  119 ASN cc_start: 0.8624 (m110) cc_final: 0.8304 (m110)
  outliers start: 69
  outliers final: 36
  residues processed: 415
  average time/residue: 0.3035
  time to fit residues: 166.2346
Evaluate side-chains
  399 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 354
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  119 ASN
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  102 ILE
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain F residue   92 LEU
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  153 LEU
Chi-restraints excluded: chain G residue   92 LEU
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  105 LEU
Chi-restraints excluded: chain G residue  122 GLU
Chi-restraints excluded: chain H residue   92 LEU
Chi-restraints excluded: chain H residue  102 ILE
Chi-restraints excluded: chain H residue  105 LEU
Chi-restraints excluded: chain H residue  122 GLU
Chi-restraints excluded: chain H residue  153 LEU
Chi-restraints excluded: chain J residue   92 LEU
Chi-restraints excluded: chain J residue  102 ILE
Chi-restraints excluded: chain J residue  105 LEU
Chi-restraints excluded: chain J residue  122 GLU
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain K residue   92 LEU
Chi-restraints excluded: chain K residue  102 ILE
Chi-restraints excluded: chain L residue  102 ILE
Chi-restraints excluded: chain M residue  102 ILE
Chi-restraints excluded: chain N residue   92 LEU
Chi-restraints excluded: chain N residue  102 ILE
Chi-restraints excluded: chain N residue  105 LEU
Chi-restraints excluded: chain O residue  102 ILE
Chi-restraints excluded: chain P residue  102 ILE
Chi-restraints excluded: chain Q residue   92 LEU
Chi-restraints excluded: chain Q residue  102 ILE
Chi-restraints excluded: chain Q residue  105 LEU
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  153 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 102 optimal weight:   10.0000
   chunk 112 optimal weight:    5.9990
   chunk 93 optimal weight:    5.9990
   chunk 26 optimal weight:    9.9990
   chunk 47 optimal weight:    0.4980
   chunk 73 optimal weight:    0.4980
   chunk 14 optimal weight:    2.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 124 ASN
C 119 ASN
D 124 ASN
H 124 ASN
J 124 ASN
N 124 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.121188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.103329 restraints weight = 15020.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 2.40
r_work: 0.3035 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  12006  Z= 0.225
  Angle     :  0.625   5.487  16236  Z= 0.342
  Chirality :  0.054   0.221   1836
  Planarity :  0.005   0.057   2016
  Dihedral  :  4.413  20.443   1602
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 26.53 %
    Favored  : 68.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.22), residues: 1386
  helix: -0.78 (0.37), residues: 180
  sheet: -2.00 (0.20), residues: 594
  loop : -1.82 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP P 123 
 HIS   0.004   0.002   HIS G 139 
 PHE   0.018   0.002   PHE H 117 
 TYR   0.012   0.001   TYR L 114 
 ARG   0.012   0.001   ARG H 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05623 (  360)
  hydrogen bonds       : angle       6.78146 ( 1026)
  covalent geometry    : bond        0.00524 (12006)
  covalent geometry    : angle       0.62524 (16236)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  443 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 376
  time to evaluate  : 1.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.8538 (tptp) cc_final: 0.8276 (ttpp)
REVERT: A  164 ASP cc_start: 0.9043 (t0) cc_final: 0.8490 (t0)
REVERT: B  109 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8219 (mmtp)
REVERT: B  122 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7863 (mp0)
REVERT: B  153 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9052 (mt)
REVERT: C  109 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8273 (mmtp)
REVERT: C  122 GLU cc_start: 0.8490 (mp0) cc_final: 0.7981 (mp0)
REVERT: D  122 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7813 (mp0)
REVERT: E  122 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7721 (mp0)
REVERT: E  164 ASP cc_start: 0.8823 (t0) cc_final: 0.8531 (t0)
REVERT: F  121 LYS cc_start: 0.8528 (tptp) cc_final: 0.8139 (ttpt)
REVERT: F  122 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7416 (mp0)
REVERT: F  153 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8820 (mt)
REVERT: G  122 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7991 (mp0)
REVERT: H  109 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8142 (mmtp)
REVERT: H  122 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7921 (mp0)
REVERT: H  153 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9010 (mt)
REVERT: I  110 THR cc_start: 0.8950 (m) cc_final: 0.8504 (p)
REVERT: I  121 LYS cc_start: 0.8458 (ttpt) cc_final: 0.7959 (ttpt)
REVERT: J  122 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8137 (mp0)
REVERT: J  153 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9033 (mt)
REVERT: K  104 ARG cc_start: 0.7677 (mtt-85) cc_final: 0.7273 (mtp180)
REVERT: K  110 THR cc_start: 0.9030 (m) cc_final: 0.8698 (p)
REVERT: K  121 LYS cc_start: 0.8455 (tptp) cc_final: 0.8235 (ttpp)
REVERT: L  110 THR cc_start: 0.8960 (m) cc_final: 0.8608 (p)
REVERT: L  121 LYS cc_start: 0.8426 (ttpt) cc_final: 0.7926 (ttpp)
REVERT: M  110 THR cc_start: 0.8977 (m) cc_final: 0.8670 (p)
REVERT: N  119 ASN cc_start: 0.8657 (m110) cc_final: 0.8325 (m110)
REVERT: N  121 LYS cc_start: 0.8329 (ttpt) cc_final: 0.7959 (ttpt)
REVERT: P  164 ASP cc_start: 0.8947 (t0) cc_final: 0.8639 (t0)
REVERT: Q  106 ASN cc_start: 0.8265 (m-40) cc_final: 0.7993 (m110)
REVERT: Q  119 ASN cc_start: 0.8615 (m110) cc_final: 0.8277 (m110)
REVERT: Q  121 LYS cc_start: 0.8422 (ttpt) cc_final: 0.8091 (ttpt)
REVERT: R  110 THR cc_start: 0.8984 (m) cc_final: 0.8600 (p)
REVERT: R  119 ASN cc_start: 0.8625 (m110) cc_final: 0.8321 (m110)
REVERT: R  164 ASP cc_start: 0.8624 (t0) cc_final: 0.8377 (t0)
  outliers start: 67
  outliers final: 36
  residues processed: 433
  average time/residue: 0.3245
  time to fit residues: 182.9852
Evaluate side-chains
  418 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 371
  time to evaluate  : 1.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  119 ASN
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  122 GLU
Chi-restraints excluded: chain F residue   92 LEU
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  122 GLU
Chi-restraints excluded: chain F residue  153 LEU
Chi-restraints excluded: chain G residue   92 LEU
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  122 GLU
Chi-restraints excluded: chain H residue   92 LEU
Chi-restraints excluded: chain H residue  102 ILE
Chi-restraints excluded: chain H residue  105 LEU
Chi-restraints excluded: chain H residue  122 GLU
Chi-restraints excluded: chain H residue  153 LEU
Chi-restraints excluded: chain I residue  100 GLU
Chi-restraints excluded: chain J residue   92 LEU
Chi-restraints excluded: chain J residue  102 ILE
Chi-restraints excluded: chain J residue  122 GLU
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain K residue   92 LEU
Chi-restraints excluded: chain K residue  102 ILE
Chi-restraints excluded: chain L residue  102 ILE
Chi-restraints excluded: chain L residue  122 GLU
Chi-restraints excluded: chain M residue   92 LEU
Chi-restraints excluded: chain M residue  102 ILE
Chi-restraints excluded: chain N residue   92 LEU
Chi-restraints excluded: chain N residue  102 ILE
Chi-restraints excluded: chain O residue  102 ILE
Chi-restraints excluded: chain P residue  102 ILE
Chi-restraints excluded: chain Q residue   92 LEU
Chi-restraints excluded: chain Q residue  100 GLU
Chi-restraints excluded: chain Q residue  102 ILE
Chi-restraints excluded: chain Q residue  105 LEU
Chi-restraints excluded: chain R residue   92 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 123 optimal weight:    5.9990
   chunk 87 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 102 optimal weight:    9.9990
   chunk 106 optimal weight:    1.9990
   chunk 64 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 115 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
C 124 ASN
H 124 ASN
J 124 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.122777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.105040 restraints weight = 14941.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 2.42
r_work: 0.3057 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.3266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12006  Z= 0.188
  Angle     :  0.619   5.619  16236  Z= 0.338
  Chirality :  0.054   0.217   1836
  Planarity :  0.006   0.059   2016
  Dihedral  :  4.419  20.386   1602
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 26.29 %
    Favored  : 68.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.76 (0.22), residues: 1386
  helix: -0.83 (0.37), residues: 180
  sheet: -1.98 (0.20), residues: 594
  loop : -1.81 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP N 123 
 HIS   0.004   0.001   HIS Q 139 
 PHE   0.016   0.002   PHE C 117 
 TYR   0.013   0.001   TYR J 151 
 ARG   0.013   0.002   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05484 (  360)
  hydrogen bonds       : angle       6.67251 ( 1026)
  covalent geometry    : bond        0.00441 (12006)
  covalent geometry    : angle       0.61920 (16236)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  429 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 366
  time to evaluate  : 1.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.8520 (tptp) cc_final: 0.8264 (ttpp)
REVERT: B   95 GLU cc_start: 0.8958 (mp0) cc_final: 0.8213 (mp0)
REVERT: B  109 LYS cc_start: 0.8468 (mmtt) cc_final: 0.8202 (mmtp)
REVERT: B  122 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7848 (mp0)
REVERT: B  153 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8943 (mt)
REVERT: C  109 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8308 (mmtp)
REVERT: C  121 LYS cc_start: 0.9003 (mtmm) cc_final: 0.8566 (mmtt)
REVERT: C  122 GLU cc_start: 0.8487 (mp0) cc_final: 0.7992 (mp0)
REVERT: D   95 GLU cc_start: 0.8873 (mp0) cc_final: 0.7955 (mp0)
REVERT: D  122 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7847 (mp0)
REVERT: E  122 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7733 (mp0)
REVERT: E  164 ASP cc_start: 0.8780 (t0) cc_final: 0.8466 (t0)
REVERT: F  121 LYS cc_start: 0.8502 (tptp) cc_final: 0.8265 (ttpt)
REVERT: F  122 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7418 (mp0)
REVERT: F  153 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8899 (mt)
REVERT: G  122 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7983 (mp0)
REVERT: H  109 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8172 (mmtp)
REVERT: H  122 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7902 (mp0)
REVERT: I  110 THR cc_start: 0.8919 (m) cc_final: 0.8478 (p)
REVERT: I  121 LYS cc_start: 0.8458 (ttpt) cc_final: 0.7935 (ttpt)
REVERT: I  150 ARG cc_start: 0.8672 (mtt90) cc_final: 0.8427 (mpt-90)
REVERT: J  122 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8033 (mp0)
REVERT: J  153 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9051 (mt)
REVERT: K  110 THR cc_start: 0.9015 (m) cc_final: 0.8663 (p)
REVERT: K  121 LYS cc_start: 0.8482 (tptp) cc_final: 0.8247 (ttpp)
REVERT: L  110 THR cc_start: 0.8951 (m) cc_final: 0.8580 (p)
REVERT: L  121 LYS cc_start: 0.8398 (ttpt) cc_final: 0.8118 (ttpt)
REVERT: M  110 THR cc_start: 0.8955 (m) cc_final: 0.8659 (p)
REVERT: N  119 ASN cc_start: 0.8609 (m110) cc_final: 0.8281 (m110)
REVERT: N  121 LYS cc_start: 0.8324 (ttpt) cc_final: 0.7972 (ttpt)
REVERT: O  121 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8051 (ttpp)
REVERT: O  151 TYR cc_start: 0.9052 (m-80) cc_final: 0.8811 (m-80)
REVERT: P  164 ASP cc_start: 0.8911 (t0) cc_final: 0.8582 (t0)
REVERT: Q  106 ASN cc_start: 0.8283 (m-40) cc_final: 0.7980 (m110)
REVERT: Q  119 ASN cc_start: 0.8670 (m110) cc_final: 0.8317 (m110)
REVERT: Q  121 LYS cc_start: 0.8427 (ttpt) cc_final: 0.8049 (ttpt)
REVERT: R  110 THR cc_start: 0.8998 (m) cc_final: 0.8600 (p)
REVERT: R  119 ASN cc_start: 0.8570 (m110) cc_final: 0.8294 (m110)
REVERT: R  164 ASP cc_start: 0.8571 (t0) cc_final: 0.8296 (t0)
  outliers start: 63
  outliers final: 36
  residues processed: 415
  average time/residue: 0.3293
  time to fit residues: 178.3501
Evaluate side-chains
  409 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 363
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  122 GLU
Chi-restraints excluded: chain F residue   92 LEU
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  122 GLU
Chi-restraints excluded: chain F residue  153 LEU
Chi-restraints excluded: chain G residue   92 LEU
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  122 GLU
Chi-restraints excluded: chain H residue   92 LEU
Chi-restraints excluded: chain H residue  102 ILE
Chi-restraints excluded: chain H residue  105 LEU
Chi-restraints excluded: chain H residue  122 GLU
Chi-restraints excluded: chain I residue  100 GLU
Chi-restraints excluded: chain J residue   92 LEU
Chi-restraints excluded: chain J residue  102 ILE
Chi-restraints excluded: chain J residue  105 LEU
Chi-restraints excluded: chain J residue  122 GLU
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain K residue   92 LEU
Chi-restraints excluded: chain K residue  102 ILE
Chi-restraints excluded: chain L residue  102 ILE
Chi-restraints excluded: chain L residue  122 GLU
Chi-restraints excluded: chain M residue  102 ILE
Chi-restraints excluded: chain M residue  119 ASN
Chi-restraints excluded: chain N residue   92 LEU
Chi-restraints excluded: chain N residue  102 ILE
Chi-restraints excluded: chain O residue  102 ILE
Chi-restraints excluded: chain P residue  102 ILE
Chi-restraints excluded: chain P residue  153 LEU
Chi-restraints excluded: chain Q residue   92 LEU
Chi-restraints excluded: chain Q residue  102 ILE
Chi-restraints excluded: chain Q residue  105 LEU
Chi-restraints excluded: chain R residue   92 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 105 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 59 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 125 optimal weight:    6.9990
   chunk 107 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
C 119 ASN
D 124 ASN
H 124 ASN
J 124 ASN
N 124 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.123568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.105921 restraints weight = 14791.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 2.39
r_work: 0.3074 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12006  Z= 0.168
  Angle     :  0.615   6.179  16236  Z= 0.335
  Chirality :  0.053   0.218   1836
  Planarity :  0.006   0.063   2016
  Dihedral  :  4.384  19.570   1602
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 26.60 %
    Favored  : 68.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.68 (0.22), residues: 1386
  helix: -0.75 (0.37), residues: 180
  sheet: -1.93 (0.19), residues: 594
  loop : -1.74 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP K 123 
 HIS   0.004   0.001   HIS Q 139 
 PHE   0.015   0.002   PHE P 117 
 TYR   0.013   0.001   TYR J 151 
 ARG   0.014   0.002   ARG H 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05365 (  360)
  hydrogen bonds       : angle       6.59430 ( 1026)
  covalent geometry    : bond        0.00393 (12006)
  covalent geometry    : angle       0.61503 (16236)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  409 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 349
  time to evaluate  : 1.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.8525 (tptp) cc_final: 0.8276 (ttpp)
REVERT: B   95 GLU cc_start: 0.8975 (mp0) cc_final: 0.8180 (mp0)
REVERT: B  109 LYS cc_start: 0.8461 (mmtt) cc_final: 0.8195 (mmtp)
REVERT: B  122 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7832 (mp0)
REVERT: B  153 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9035 (mt)
REVERT: C  109 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8308 (mmtp)
REVERT: C  122 GLU cc_start: 0.8512 (mp0) cc_final: 0.8016 (mp0)
REVERT: D   95 GLU cc_start: 0.8897 (mp0) cc_final: 0.8094 (mp0)
REVERT: D  122 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7871 (mp0)
REVERT: E  122 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7704 (mp0)
REVERT: F   95 GLU cc_start: 0.8842 (mp0) cc_final: 0.8555 (mp0)
REVERT: F  121 LYS cc_start: 0.8494 (tptp) cc_final: 0.8151 (ttpt)
REVERT: F  122 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7407 (mp0)
REVERT: F  153 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8855 (mt)
REVERT: G   95 GLU cc_start: 0.8897 (mp0) cc_final: 0.8558 (mp0)
REVERT: G  122 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7961 (mp0)
REVERT: H  104 ARG cc_start: 0.7118 (mtp180) cc_final: 0.6865 (mtp180)
REVERT: H  109 LYS cc_start: 0.8556 (mmtt) cc_final: 0.8220 (mmtp)
REVERT: H  122 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7794 (mp0)
REVERT: I  110 THR cc_start: 0.8929 (m) cc_final: 0.8488 (p)
REVERT: I  121 LYS cc_start: 0.8357 (ttpt) cc_final: 0.7909 (ttpp)
REVERT: J  122 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8031 (mp0)
REVERT: J  153 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8940 (mt)
REVERT: L  110 THR cc_start: 0.8934 (m) cc_final: 0.8556 (p)
REVERT: L  121 LYS cc_start: 0.8369 (ttpt) cc_final: 0.8118 (ttpt)
REVERT: M  110 THR cc_start: 0.8973 (m) cc_final: 0.8653 (p)
REVERT: N  121 LYS cc_start: 0.8339 (ttpt) cc_final: 0.7992 (ttpt)
REVERT: O  121 LYS cc_start: 0.8483 (ttpt) cc_final: 0.7993 (ttpp)
REVERT: P  164 ASP cc_start: 0.8840 (t0) cc_final: 0.8496 (t0)
REVERT: Q  106 ASN cc_start: 0.8373 (m-40) cc_final: 0.8147 (m110)
REVERT: Q  119 ASN cc_start: 0.8611 (m110) cc_final: 0.8253 (m110)
REVERT: Q  121 LYS cc_start: 0.8388 (ttpt) cc_final: 0.7734 (ttpt)
REVERT: Q  122 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7085 (mp0)
REVERT: R  110 THR cc_start: 0.9000 (m) cc_final: 0.8605 (p)
REVERT: R  119 ASN cc_start: 0.8512 (m110) cc_final: 0.8247 (m110)
REVERT: R  164 ASP cc_start: 0.8513 (t0) cc_final: 0.8215 (t0)
  outliers start: 60
  outliers final: 41
  residues processed: 398
  average time/residue: 0.3328
  time to fit residues: 172.8682
Evaluate side-chains
  396 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 344
  time to evaluate  : 1.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  119 ASN
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  122 GLU
Chi-restraints excluded: chain F residue   92 LEU
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  122 GLU
Chi-restraints excluded: chain F residue  153 LEU
Chi-restraints excluded: chain G residue   92 LEU
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  122 GLU
Chi-restraints excluded: chain H residue   92 LEU
Chi-restraints excluded: chain H residue  102 ILE
Chi-restraints excluded: chain H residue  105 LEU
Chi-restraints excluded: chain H residue  122 GLU
Chi-restraints excluded: chain I residue  100 GLU
Chi-restraints excluded: chain J residue   92 LEU
Chi-restraints excluded: chain J residue  102 ILE
Chi-restraints excluded: chain J residue  105 LEU
Chi-restraints excluded: chain J residue  106 ASN
Chi-restraints excluded: chain J residue  110 THR
Chi-restraints excluded: chain J residue  122 GLU
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain K residue   92 LEU
Chi-restraints excluded: chain K residue  102 ILE
Chi-restraints excluded: chain L residue  102 ILE
Chi-restraints excluded: chain L residue  122 GLU
Chi-restraints excluded: chain M residue   92 LEU
Chi-restraints excluded: chain M residue  102 ILE
Chi-restraints excluded: chain N residue  102 ILE
Chi-restraints excluded: chain N residue  153 LEU
Chi-restraints excluded: chain O residue  102 ILE
Chi-restraints excluded: chain P residue  102 ILE
Chi-restraints excluded: chain P residue  153 LEU
Chi-restraints excluded: chain Q residue   92 LEU
Chi-restraints excluded: chain Q residue  100 GLU
Chi-restraints excluded: chain Q residue  102 ILE
Chi-restraints excluded: chain Q residue  105 LEU
Chi-restraints excluded: chain Q residue  122 GLU
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  102 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 89 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 87 optimal weight:    0.9980
   chunk 124 optimal weight:    4.9990
   chunk 85 optimal weight:    6.9990
   chunk 14 optimal weight:    0.6980
   chunk 104 optimal weight:    1.9990
   chunk 116 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0970
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
H 124 ASN
J 124 ASN
N 124 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.125260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.107820 restraints weight = 14667.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.36
r_work: 0.3099 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.3504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12006  Z= 0.146
  Angle     :  0.604   6.142  16236  Z= 0.328
  Chirality :  0.052   0.211   1836
  Planarity :  0.006   0.064   2016
  Dihedral  :  4.323  18.111   1602
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 26.84 %
    Favored  : 68.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.22), residues: 1386
  helix: -0.63 (0.38), residues: 180
  sheet: -1.93 (0.19), residues: 594
  loop : -1.65 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D 123 
 HIS   0.004   0.001   HIS Q 139 
 PHE   0.013   0.002   PHE P 117 
 TYR   0.012   0.001   TYR E 114 
 ARG   0.014   0.002   ARG H 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05268 (  360)
  hydrogen bonds       : angle       6.49762 ( 1026)
  covalent geometry    : bond        0.00339 (12006)
  covalent geometry    : angle       0.60432 (16236)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  394 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 336
  time to evaluate  : 1.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.8509 (tptp) cc_final: 0.8293 (ttpp)
REVERT: B   95 GLU cc_start: 0.8942 (mp0) cc_final: 0.8168 (mp0)
REVERT: B  109 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8242 (mmtp)
REVERT: B  122 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7815 (mp0)
REVERT: B  153 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8890 (mt)
REVERT: C  109 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8345 (mmtp)
REVERT: C  122 GLU cc_start: 0.8491 (mp0) cc_final: 0.8039 (mp0)
REVERT: D   95 GLU cc_start: 0.8780 (mp0) cc_final: 0.8003 (mp0)
REVERT: D  122 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7877 (mp0)
REVERT: E  122 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7815 (mp0)
REVERT: F   95 GLU cc_start: 0.8813 (mp0) cc_final: 0.8580 (mp0)
REVERT: F  121 LYS cc_start: 0.8433 (tptp) cc_final: 0.8142 (ttpt)
REVERT: F  122 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7398 (mp0)
REVERT: F  153 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8861 (mt)
REVERT: G   95 GLU cc_start: 0.8911 (mp0) cc_final: 0.8499 (mp0)
REVERT: G  105 LEU cc_start: 0.8902 (mm) cc_final: 0.8616 (mm)
REVERT: G  122 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7928 (mp0)
REVERT: H  109 LYS cc_start: 0.8561 (mmtt) cc_final: 0.8245 (mmtp)
REVERT: H  122 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7835 (mp0)
REVERT: I  110 THR cc_start: 0.8918 (m) cc_final: 0.8475 (p)
REVERT: I  121 LYS cc_start: 0.8320 (ttpt) cc_final: 0.7857 (ttpp)
REVERT: J  122 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8057 (mp0)
REVERT: J  153 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8982 (mt)
REVERT: L  110 THR cc_start: 0.8921 (m) cc_final: 0.8550 (p)
REVERT: L  121 LYS cc_start: 0.8345 (ttpt) cc_final: 0.8090 (ttpt)
REVERT: M  110 THR cc_start: 0.8960 (m) cc_final: 0.8645 (p)
REVERT: N  121 LYS cc_start: 0.8341 (ttpt) cc_final: 0.8025 (ttpt)
REVERT: Q  106 ASN cc_start: 0.8369 (m-40) cc_final: 0.8149 (m110)
REVERT: Q  119 ASN cc_start: 0.8561 (m110) cc_final: 0.8218 (m110)
REVERT: Q  121 LYS cc_start: 0.8355 (ttpt) cc_final: 0.7685 (ttpt)
REVERT: Q  122 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7065 (mp0)
REVERT: Q  138 ASP cc_start: 0.8770 (t0) cc_final: 0.8382 (t0)
REVERT: R  110 THR cc_start: 0.8992 (m) cc_final: 0.8604 (p)
REVERT: R  119 ASN cc_start: 0.8407 (m110) cc_final: 0.8170 (m110)
REVERT: R  121 LYS cc_start: 0.8164 (ttpp) cc_final: 0.7821 (ttpt)
  outliers start: 58
  outliers final: 36
  residues processed: 384
  average time/residue: 0.3336
  time to fit residues: 167.1097
Evaluate side-chains
  383 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 336
  time to evaluate  : 1.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  122 GLU
Chi-restraints excluded: chain F residue   92 LEU
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  122 GLU
Chi-restraints excluded: chain F residue  153 LEU
Chi-restraints excluded: chain G residue   92 LEU
Chi-restraints excluded: chain G residue  122 GLU
Chi-restraints excluded: chain H residue   92 LEU
Chi-restraints excluded: chain H residue  102 ILE
Chi-restraints excluded: chain H residue  105 LEU
Chi-restraints excluded: chain H residue  122 GLU
Chi-restraints excluded: chain I residue  100 GLU
Chi-restraints excluded: chain J residue   92 LEU
Chi-restraints excluded: chain J residue  102 ILE
Chi-restraints excluded: chain J residue  105 LEU
Chi-restraints excluded: chain J residue  106 ASN
Chi-restraints excluded: chain J residue  110 THR
Chi-restraints excluded: chain J residue  122 GLU
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain K residue   92 LEU
Chi-restraints excluded: chain K residue  102 ILE
Chi-restraints excluded: chain L residue  102 ILE
Chi-restraints excluded: chain L residue  122 GLU
Chi-restraints excluded: chain M residue   92 LEU
Chi-restraints excluded: chain M residue  119 ASN
Chi-restraints excluded: chain N residue  102 ILE
Chi-restraints excluded: chain N residue  153 LEU
Chi-restraints excluded: chain O residue  102 ILE
Chi-restraints excluded: chain P residue  102 ILE
Chi-restraints excluded: chain P residue  153 LEU
Chi-restraints excluded: chain Q residue  100 GLU
Chi-restraints excluded: chain Q residue  102 ILE
Chi-restraints excluded: chain Q residue  105 LEU
Chi-restraints excluded: chain Q residue  122 GLU
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  102 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0470
   chunk 76 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 11 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 115 optimal weight:    0.9980
   chunk 107 optimal weight:    0.3980
   chunk 101 optimal weight:    4.9990
   chunk 117 optimal weight:    0.8980
   overall best weight:    1.2680

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 119 ASN
D 124 ASN
H 124 ASN
J 124 ASN
N 124 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.122727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.105161 restraints weight = 14470.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.37
r_work: 0.3102 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.3611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12006  Z= 0.140
  Angle     :  0.598   5.935  16236  Z= 0.324
  Chirality :  0.052   0.202   1836
  Planarity :  0.006   0.062   2016
  Dihedral  :  4.252  17.457   1602
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 26.68 %
    Favored  : 69.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.22), residues: 1386
  helix: -0.46 (0.39), residues: 180
  sheet: -1.85 (0.20), residues: 594
  loop : -1.60 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP N 123 
 HIS   0.003   0.001   HIS Q 139 
 PHE   0.012   0.001   PHE P 117 
 TYR   0.013   0.001   TYR P 151 
 ARG   0.015   0.002   ARG H 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05155 (  360)
  hydrogen bonds       : angle       6.35856 ( 1026)
  covalent geometry    : bond        0.00325 (12006)
  covalent geometry    : angle       0.59807 (16236)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6536.25 seconds
wall clock time: 116 minutes 28.01 seconds (6988.01 seconds total)