Starting phenix.real_space_refine
on Thu Jul 31 07:22:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6e0f_8946/07_2025/6e0f_8946.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6e0f_8946/07_2025/6e0f_8946.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6e0f_8946/07_2025/6e0f_8946.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6e0f_8946/07_2025/6e0f_8946.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6e0f_8946/07_2025/6e0f_8946.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6e0f_8946/07_2025/6e0f_8946.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      80      5.16       5
     C    8700      2.51       5
     N    2320      2.21       5
     O    2550      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13650
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1365
          Classifications: {'peptide': 174}
          Link IDs: {'PTRANS': 7, 'TRANS': 166}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 4.16, per 1000 atoms: 0.30
  Number of scatterers: 13650
  At special positions: 0
  Unit cell: (133, 135, 61, 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      80     16.00
     O    2550      8.00
     N    2320      7.00
     C    8700      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: 3.02
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3240

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 15 sheets defined
      27.6% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.45
  Creating SS restraints...
    Processing helix  chain 'J' and resid 61 through 64
      removed outlier: 3.623A  pdb=" N   LYS J  64 " --> pdb=" O   ASN J  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 61 through 64'
    Processing helix  chain 'J' and resid 82 through 90
      removed outlier: 4.199A  pdb=" N   PHE J  88 " --> pdb=" O   GLU J  84 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER J  89 " --> pdb=" O   ILE J  85 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 92 through 97
      removed outlier: 3.634A  pdb=" N   GLU J  96 " --> pdb=" O   HIS J  92 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS J  97 " --> pdb=" O   ALA J  93 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 92 through 97'
    Processing helix  chain 'J' and resid 109 through 119
    Processing helix  chain 'J' and resid 181 through 198
      removed outlier: 3.961A  pdb=" N   LEU J 189 " --> pdb=" O   ALA J 185 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLN J 193 " --> pdb=" O   LEU J 189 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ASN J 198 " --> pdb=" O   TYR J 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 64
      removed outlier: 3.622A  pdb=" N   LYS A  64 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 61 through 64'
    Processing helix  chain 'A' and resid 82 through 90
      removed outlier: 4.200A  pdb=" N   PHE A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 97
      removed outlier: 3.633A  pdb=" N   GLU A  96 " --> pdb=" O   HIS A  92 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LYS A  97 " --> pdb=" O   ALA A  93 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 92 through 97'
    Processing helix  chain 'A' and resid 109 through 119
    Processing helix  chain 'A' and resid 181 through 198
      removed outlier: 3.961A  pdb=" N   LEU A 189 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   GLN A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ASN A 198 " --> pdb=" O   TYR A 194 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 61 through 64
      removed outlier: 3.623A  pdb=" N   LYS I  64 " --> pdb=" O   ASN I  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 61 through 64'
    Processing helix  chain 'I' and resid 82 through 90
      removed outlier: 4.198A  pdb=" N   PHE I  88 " --> pdb=" O   GLU I  84 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER I  89 " --> pdb=" O   ILE I  85 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 92 through 97
      removed outlier: 3.633A  pdb=" N   GLU I  96 " --> pdb=" O   HIS I  92 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS I  97 " --> pdb=" O   ALA I  93 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 92 through 97'
    Processing helix  chain 'I' and resid 109 through 119
    Processing helix  chain 'I' and resid 181 through 198
      removed outlier: 3.960A  pdb=" N   LEU I 189 " --> pdb=" O   ALA I 185 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLN I 193 " --> pdb=" O   LEU I 189 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ASN I 198 " --> pdb=" O   TYR I 194 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 61 through 64
      removed outlier: 3.623A  pdb=" N   LYS E  64 " --> pdb=" O   ASN E  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 61 through 64'
    Processing helix  chain 'E' and resid 82 through 90
      removed outlier: 4.199A  pdb=" N   PHE E  88 " --> pdb=" O   GLU E  84 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER E  89 " --> pdb=" O   ILE E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 92 through 97
      removed outlier: 3.634A  pdb=" N   GLU E  96 " --> pdb=" O   HIS E  92 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS E  97 " --> pdb=" O   ALA E  93 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 92 through 97'
    Processing helix  chain 'E' and resid 109 through 119
    Processing helix  chain 'E' and resid 181 through 198
      removed outlier: 3.961A  pdb=" N   LEU E 189 " --> pdb=" O   ALA E 185 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLN E 193 " --> pdb=" O   LEU E 189 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ASN E 198 " --> pdb=" O   TYR E 194 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 61 through 64
      removed outlier: 3.623A  pdb=" N   LYS G  64 " --> pdb=" O   ASN G  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 61 through 64'
    Processing helix  chain 'G' and resid 82 through 90
      removed outlier: 4.199A  pdb=" N   PHE G  88 " --> pdb=" O   GLU G  84 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER G  89 " --> pdb=" O   ILE G  85 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 97
      removed outlier: 3.634A  pdb=" N   GLU G  96 " --> pdb=" O   HIS G  92 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LYS G  97 " --> pdb=" O   ALA G  93 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 92 through 97'
    Processing helix  chain 'G' and resid 109 through 119
    Processing helix  chain 'G' and resid 181 through 198
      removed outlier: 3.960A  pdb=" N   LEU G 189 " --> pdb=" O   ALA G 185 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   GLN G 193 " --> pdb=" O   LEU G 189 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASN G 198 " --> pdb=" O   TYR G 194 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 61 through 64
      removed outlier: 3.622A  pdb=" N   LYS F  64 " --> pdb=" O   ASN F  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 61 through 64'
    Processing helix  chain 'F' and resid 82 through 90
      removed outlier: 4.199A  pdb=" N   PHE F  88 " --> pdb=" O   GLU F  84 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER F  89 " --> pdb=" O   ILE F  85 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 92 through 97
      removed outlier: 3.634A  pdb=" N   GLU F  96 " --> pdb=" O   HIS F  92 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS F  97 " --> pdb=" O   ALA F  93 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 92 through 97'
    Processing helix  chain 'F' and resid 109 through 119
    Processing helix  chain 'F' and resid 181 through 198
      removed outlier: 3.960A  pdb=" N   LEU F 189 " --> pdb=" O   ALA F 185 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLN F 193 " --> pdb=" O   LEU F 189 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASN F 198 " --> pdb=" O   TYR F 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 64
      removed outlier: 3.623A  pdb=" N   LYS B  64 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 61 through 64'
    Processing helix  chain 'B' and resid 82 through 90
      removed outlier: 4.198A  pdb=" N   PHE B  88 " --> pdb=" O   GLU B  84 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER B  89 " --> pdb=" O   ILE B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 97
      removed outlier: 3.634A  pdb=" N   GLU B  96 " --> pdb=" O   HIS B  92 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS B  97 " --> pdb=" O   ALA B  93 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 92 through 97'
    Processing helix  chain 'B' and resid 109 through 119
    Processing helix  chain 'B' and resid 181 through 198
      removed outlier: 3.960A  pdb=" N   LEU B 189 " --> pdb=" O   ALA B 185 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLN B 193 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASN B 198 " --> pdb=" O   TYR B 194 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 64
      removed outlier: 3.622A  pdb=" N   LYS C  64 " --> pdb=" O   ASN C  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 61 through 64'
    Processing helix  chain 'C' and resid 82 through 90
      removed outlier: 4.199A  pdb=" N   PHE C  88 " --> pdb=" O   GLU C  84 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER C  89 " --> pdb=" O   ILE C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 97
      removed outlier: 3.633A  pdb=" N   GLU C  96 " --> pdb=" O   HIS C  92 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS C  97 " --> pdb=" O   ALA C  93 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 92 through 97'
    Processing helix  chain 'C' and resid 109 through 119
    Processing helix  chain 'C' and resid 181 through 198
      removed outlier: 3.960A  pdb=" N   LEU C 189 " --> pdb=" O   ALA C 185 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLN C 193 " --> pdb=" O   LEU C 189 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASN C 198 " --> pdb=" O   TYR C 194 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 64
      removed outlier: 3.623A  pdb=" N   LYS D  64 " --> pdb=" O   ASN D  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 61 through 64'
    Processing helix  chain 'D' and resid 82 through 90
      removed outlier: 4.199A  pdb=" N   PHE D  88 " --> pdb=" O   GLU D  84 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER D  89 " --> pdb=" O   ILE D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 97
      removed outlier: 3.634A  pdb=" N   GLU D  96 " --> pdb=" O   HIS D  92 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS D  97 " --> pdb=" O   ALA D  93 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 92 through 97'
    Processing helix  chain 'D' and resid 109 through 119
    Processing helix  chain 'D' and resid 181 through 198
      removed outlier: 3.961A  pdb=" N   LEU D 189 " --> pdb=" O   ALA D 185 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   GLN D 193 " --> pdb=" O   LEU D 189 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ASN D 198 " --> pdb=" O   TYR D 194 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 61 through 64
      removed outlier: 3.622A  pdb=" N   LYS H  64 " --> pdb=" O   ASN H  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 61 through 64'
    Processing helix  chain 'H' and resid 82 through 90
      removed outlier: 4.198A  pdb=" N   PHE H  88 " --> pdb=" O   GLU H  84 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER H  89 " --> pdb=" O   ILE H  85 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 92 through 97
      removed outlier: 3.633A  pdb=" N   GLU H  96 " --> pdb=" O   HIS H  92 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LYS H  97 " --> pdb=" O   ALA H  93 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 92 through 97'
    Processing helix  chain 'H' and resid 109 through 119
    Processing helix  chain 'H' and resid 181 through 198
      removed outlier: 3.960A  pdb=" N   LEU H 189 " --> pdb=" O   ALA H 185 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLN H 193 " --> pdb=" O   LEU H 189 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ASN H 198 " --> pdb=" O   TYR H 194 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'J' and resid 54 through 59
    Processing sheet with id=AA2, first strand: chain 'J' and resid 100 through 105
      removed outlier: 6.251A  pdb=" N   TYR J  67 " --> pdb=" O   GLN J 101 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   VAL J 103 " --> pdb=" O   TYR J  67 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   VAL J  69 " --> pdb=" O   VAL J 103 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   VAL J 105 " --> pdb=" O   VAL J  69 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   PHE J  71 " --> pdb=" O   VAL J 105 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   TYR A  67 " --> pdb=" O   GLN A 101 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   VAL A 103 " --> pdb=" O   TYR A  67 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   VAL A  69 " --> pdb=" O   VAL A 103 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   VAL A 105 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   PHE A  71 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 59
    Processing sheet with id=AA4, first strand: chain 'I' and resid 54 through 59
    Processing sheet with id=AA5, first strand: chain 'I' and resid 100 through 105
      removed outlier: 6.251A  pdb=" N   TYR I  67 " --> pdb=" O   GLN I 101 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   VAL I 103 " --> pdb=" O   TYR I  67 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   VAL I  69 " --> pdb=" O   VAL I 103 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   VAL I 105 " --> pdb=" O   VAL I  69 " (cutoff:3.500A)
      removed outlier: 5.526A  pdb=" N   PHE I  71 " --> pdb=" O   VAL I 105 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   TYR E  67 " --> pdb=" O   GLN E 101 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   VAL E 103 " --> pdb=" O   TYR E  67 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   VAL E  69 " --> pdb=" O   VAL E 103 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   VAL E 105 " --> pdb=" O   VAL E  69 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   PHE E  71 " --> pdb=" O   VAL E 105 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 54 through 59
    Processing sheet with id=AA7, first strand: chain 'G' and resid 54 through 59
    Processing sheet with id=AA8, first strand: chain 'G' and resid 100 through 105
      removed outlier: 6.251A  pdb=" N   TYR G  67 " --> pdb=" O   GLN G 101 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   VAL G 103 " --> pdb=" O   TYR G  67 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   VAL G  69 " --> pdb=" O   VAL G 103 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   VAL G 105 " --> pdb=" O   VAL G  69 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   PHE G  71 " --> pdb=" O   VAL G 105 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   TYR C  67 " --> pdb=" O   GLN C 101 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   VAL C 103 " --> pdb=" O   TYR C  67 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   VAL C  69 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   VAL C 105 " --> pdb=" O   VAL C  69 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   PHE C  71 " --> pdb=" O   VAL C 105 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 54 through 59
    Processing sheet with id=AB1, first strand: chain 'F' and resid 100 through 105
      removed outlier: 6.251A  pdb=" N   TYR F  67 " --> pdb=" O   GLN F 101 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   VAL F 103 " --> pdb=" O   TYR F  67 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   VAL F  69 " --> pdb=" O   VAL F 103 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   VAL F 105 " --> pdb=" O   VAL F  69 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   PHE F  71 " --> pdb=" O   VAL F 105 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   TYR B  67 " --> pdb=" O   GLN B 101 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   VAL B 103 " --> pdb=" O   TYR B  67 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   VAL B  69 " --> pdb=" O   VAL B 103 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   VAL B 105 " --> pdb=" O   VAL B  69 " (cutoff:3.500A)
      removed outlier: 5.528A  pdb=" N   PHE B  71 " --> pdb=" O   VAL B 105 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 54 through 59
    Processing sheet with id=AB3, first strand: chain 'C' and resid 54 through 59
    Processing sheet with id=AB4, first strand: chain 'D' and resid 54 through 59
    Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 105
      removed outlier: 6.251A  pdb=" N   TYR D  67 " --> pdb=" O   GLN D 101 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   VAL D 103 " --> pdb=" O   TYR D  67 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   VAL D  69 " --> pdb=" O   VAL D 103 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   VAL D 105 " --> pdb=" O   VAL D  69 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   PHE D  71 " --> pdb=" O   VAL D 105 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   TYR H  67 " --> pdb=" O   GLN H 101 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   VAL H 103 " --> pdb=" O   TYR H  67 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   VAL H  69 " --> pdb=" O   VAL H 103 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   VAL H 105 " --> pdb=" O   VAL H  69 " (cutoff:3.500A)
      removed outlier: 5.528A  pdb=" N   PHE H  71 " --> pdb=" O   VAL H 105 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 54 through 59

    410 hydrogen bonds defined for protein.
    1140 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: 3.54

  Time building geometry restraints manager: 3.62 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4480
        1.34 -     1.46: 2581
        1.46 -     1.57: 6739
        1.57 -     1.69: 0
        1.69 -     1.81: 130
  Bond restraints: 13930
  Sorted by residual:
  bond pdb=" CB  PHE D  71 "
       pdb=" CG  PHE D  71 "
    ideal  model  delta    sigma   weight residual
    1.502  1.435  0.067 2.30e-02 1.89e+03 8.55e+00
  bond pdb=" CB  PHE H  71 "
       pdb=" CG  PHE H  71 "
    ideal  model  delta    sigma   weight residual
    1.502  1.435  0.067 2.30e-02 1.89e+03 8.52e+00
  bond pdb=" CB  PHE E  71 "
       pdb=" CG  PHE E  71 "
    ideal  model  delta    sigma   weight residual
    1.502  1.435  0.067 2.30e-02 1.89e+03 8.49e+00
  bond pdb=" CB  PHE J  71 "
       pdb=" CG  PHE J  71 "
    ideal  model  delta    sigma   weight residual
    1.502  1.435  0.067 2.30e-02 1.89e+03 8.45e+00
  bond pdb=" CB  PHE F  71 "
       pdb=" CG  PHE F  71 "
    ideal  model  delta    sigma   weight residual
    1.502  1.435  0.067 2.30e-02 1.89e+03 8.41e+00
  ... (remaining 13925 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 17087
        1.59 -     3.19: 1508
        3.19 -     4.78: 185
        4.78 -     6.38: 60
        6.38 -     7.97: 20
  Bond angle restraints: 18860
  Sorted by residual:
  angle pdb=" N   VAL F  38 "
        pdb=" CA  VAL F  38 "
        pdb=" CB  VAL F  38 "
      ideal   model   delta    sigma   weight residual
     112.08  105.85    6.23 1.68e+00 3.54e-01 1.37e+01
  angle pdb=" N   VAL A  38 "
        pdb=" CA  VAL A  38 "
        pdb=" CB  VAL A  38 "
      ideal   model   delta    sigma   weight residual
     112.08  105.88    6.20 1.68e+00 3.54e-01 1.36e+01
  angle pdb=" N   VAL I  38 "
        pdb=" CA  VAL I  38 "
        pdb=" CB  VAL I  38 "
      ideal   model   delta    sigma   weight residual
     112.08  105.89    6.19 1.68e+00 3.54e-01 1.36e+01
  angle pdb=" N   VAL C  38 "
        pdb=" CA  VAL C  38 "
        pdb=" CB  VAL C  38 "
      ideal   model   delta    sigma   weight residual
     112.08  105.89    6.19 1.68e+00 3.54e-01 1.36e+01
  angle pdb=" N   VAL J  38 "
        pdb=" CA  VAL J  38 "
        pdb=" CB  VAL J  38 "
      ideal   model   delta    sigma   weight residual
     112.08  105.90    6.18 1.68e+00 3.54e-01 1.35e+01
  ... (remaining 18855 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.34: 7092
        9.34 -    18.69: 958
       18.69 -    28.03: 210
       28.03 -    37.38: 50
       37.38 -    46.72: 40
  Dihedral angle restraints: 8350
    sinusoidal: 3310
      harmonic: 5040
  Sorted by residual:
  dihedral pdb=" CA  ARG G 121 "
           pdb=" C   ARG G 121 "
           pdb=" N   LYS G 122 "
           pdb=" CA  LYS G 122 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.56  -20.44     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  ARG F 121 "
           pdb=" C   ARG F 121 "
           pdb=" N   LYS F 122 "
           pdb=" CA  LYS F 122 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.56  -20.44     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  ARG C 121 "
           pdb=" C   ARG C 121 "
           pdb=" N   LYS C 122 "
           pdb=" CA  LYS C 122 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.57  -20.43     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 8347 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1294
       0.054 -    0.108: 598
       0.108 -    0.162: 168
       0.162 -    0.215: 20
       0.215 -    0.269: 20
  Chirality restraints: 2100
  Sorted by residual:
  chirality pdb=" CA  TYR G  33 "
            pdb=" N   TYR G  33 "
            pdb=" C   TYR G  33 "
            pdb=" CB  TYR G  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  TYR H  33 "
            pdb=" N   TYR H  33 "
            pdb=" C   TYR H  33 "
            pdb=" CB  TYR H  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  TYR E  33 "
            pdb=" N   TYR E  33 "
            pdb=" C   TYR E  33 "
            pdb=" CB  TYR E  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.80e+00
  ... (remaining 2097 not shown)

  Planarity restraints: 2460
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP F 116 "    0.023 2.00e-02 2.50e+03   1.61e-02 6.45e+00
        pdb=" CG  TRP F 116 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP F 116 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP F 116 "   -0.011 2.00e-02 2.50e+03
        pdb=" NE1 TRP F 116 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP F 116 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP F 116 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP F 116 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP F 116 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP F 116 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP G 116 "   -0.024 2.00e-02 2.50e+03   1.60e-02 6.43e+00
        pdb=" CG  TRP G 116 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP G 116 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP G 116 "    0.012 2.00e-02 2.50e+03
        pdb=" NE1 TRP G 116 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP G 116 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP G 116 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP G 116 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP G 116 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP G 116 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 116 "    0.023 2.00e-02 2.50e+03   1.60e-02 6.41e+00
        pdb=" CG  TRP B 116 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 116 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 116 "   -0.011 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 116 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 116 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 116 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 116 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 116 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 116 "    0.000 2.00e-02 2.50e+03
  ... (remaining 2457 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 137
        2.58 -     3.16: 11462
        3.16 -     3.74: 20443
        3.74 -     4.32: 31323
        4.32 -     4.90: 48905
  Nonbonded interactions: 112270
  Sorted by model distance:
  nonbonded pdb=" O   ARG E  34 "
            pdb=" OG1 THR E  35 "
     model   vdw
     1.999 3.040
  nonbonded pdb=" O   ARG J  34 "
            pdb=" OG1 THR J  35 "
     model   vdw
     1.999 3.040
  nonbonded pdb=" O   ARG I  34 "
            pdb=" OG1 THR I  35 "
     model   vdw
     1.999 3.040
  nonbonded pdb=" O   ARG D  34 "
            pdb=" OG1 THR D  35 "
     model   vdw
     1.999 3.040
  nonbonded pdb=" O   ARG A  34 "
            pdb=" OG1 THR A  35 "
     model   vdw
     1.999 3.040
  ... (remaining 112265 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: 0.12
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 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.250
  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:          0.500
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     27.190
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
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      :  0.010   0.067  13930  Z= 0.479
  Angle     :  1.010   7.971  18860  Z= 0.571
  Chirality :  0.068   0.269   2100
  Planarity :  0.006   0.048   2460
  Dihedral  :  9.643  46.720   5110
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  8.14 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  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: -4.79 (0.16), residues: 1720
  helix: -4.51 (0.09), residues: 500
  sheet: -2.48 (0.23), residues: 390
  loop : -2.53 (0.20), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.010   TRP F 116 
 HIS   0.009   0.003   HIS H 113 
 PHE   0.023   0.006   PHE I 160 
 TYR   0.029   0.003   TYR B  67 
 ARG   0.002   0.000   ARG I  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.29771 (  410)
  hydrogen bonds       : angle      10.94973 ( 1140)
  covalent geometry    : bond        0.01041 (13930)
  covalent geometry    : angle       1.01012 (18860)

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

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

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  616 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 616
  time to evaluate  : 1.618 
Fit side-chains
REVERT: A  169 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.8073 (mtt-85)
REVERT: I  100 THR cc_start: 0.9030 (t) cc_final: 0.8811 (m)
REVERT: I  109 SER cc_start: 0.8250 (t) cc_final: 0.8004 (m)
REVERT: I  169 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8219 (mtp85)
REVERT: E  169 ARG cc_start: 0.8421 (mmm-85) cc_final: 0.8131 (mtp85)
REVERT: E  190 GLU cc_start: 0.7754 (tt0) cc_final: 0.7482 (tm-30)
REVERT: G   62 ASP cc_start: 0.8340 (m-30) cc_final: 0.7944 (t0)
REVERT: G  163 ASP cc_start: 0.7090 (p0) cc_final: 0.6789 (p0)
REVERT: G  167 ILE cc_start: 0.8781 (mm) cc_final: 0.8579 (mt)
REVERT: G  169 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.7783 (mtt-85)
REVERT: F   60 MET cc_start: 0.8230 (ttt) cc_final: 0.7535 (ttt)
REVERT: F   62 ASP cc_start: 0.8086 (m-30) cc_final: 0.7823 (t0)
REVERT: F  143 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8210 (ttm-80)
REVERT: F  169 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.8141 (mtp85)
REVERT: B   73 TYR cc_start: 0.8959 (p90) cc_final: 0.8740 (p90)
REVERT: B  164 LYS cc_start: 0.8135 (pttt) cc_final: 0.7933 (ptmt)
REVERT: B  169 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.8025 (mmt90)
REVERT: C   99 ASN cc_start: 0.8348 (t0) cc_final: 0.8127 (t0)
REVERT: D   60 MET cc_start: 0.8263 (ttt) cc_final: 0.6935 (ttt)
REVERT: D   62 ASP cc_start: 0.8229 (m-30) cc_final: 0.7705 (t0)
REVERT: D  108 ASP cc_start: 0.7915 (m-30) cc_final: 0.6922 (m-30)
REVERT: D  169 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.7994 (mtp85)
  outliers start: 0
  outliers final: 0
  residues processed: 616
  average time/residue: 0.2815
  time to fit residues: 242.8632
Evaluate side-chains
  420 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 420
  time to evaluate  : 1.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 143 optimal weight:    2.9990
   chunk 128 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 133 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 81 optimal weight:    0.8980
   chunk 99 optimal weight:    5.9990
   chunk 154 optimal weight:    5.9990
   overall best weight:    1.3784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.156400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.131397 restraints weight = 18640.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.135559 restraints weight = 11268.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.138535 restraints weight = 8029.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  13930  Z= 0.158
  Angle     :  0.653   7.938  18860  Z= 0.354
  Chirality :  0.050   0.153   2100
  Planarity :  0.005   0.042   2460
  Dihedral  :  5.441  17.616   1890
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 16.71 %
    Favored  : 80.62 %
  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: -3.47 (0.20), residues: 1720
  helix: -3.08 (0.16), residues: 490
  sheet: -2.60 (0.24), residues: 440
  loop : -1.35 (0.24), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP C 116 
 HIS   0.004   0.001   HIS I 170 
 PHE   0.017   0.002   PHE D  77 
 TYR   0.017   0.002   TYR J 194 
 ARG   0.008   0.001   ARG H 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03784 (  410)
  hydrogen bonds       : angle       5.87138 ( 1140)
  covalent geometry    : bond        0.00336 (13930)
  covalent geometry    : angle       0.65281 (18860)

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

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

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  565 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 526
  time to evaluate  : 1.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   58 ILE cc_start: 0.8751 (mm) cc_final: 0.8429 (mt)
REVERT: J   59 ASN cc_start: 0.7650 (t0) cc_final: 0.7370 (t0)
REVERT: J   62 ASP cc_start: 0.8315 (m-30) cc_final: 0.8019 (t0)
REVERT: J  108 ASP cc_start: 0.8139 (m-30) cc_final: 0.7843 (m-30)
REVERT: A   57 ASP cc_start: 0.7802 (m-30) cc_final: 0.7591 (m-30)
REVERT: A   63 TYR cc_start: 0.8636 (m-80) cc_final: 0.8177 (m-80)
REVERT: A   73 TYR cc_start: 0.8594 (p90) cc_final: 0.8265 (p90)
REVERT: A   76 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7180 (m-30)
REVERT: I   48 GLN cc_start: 0.8771 (mt0) cc_final: 0.8404 (mt0)
REVERT: I   62 ASP cc_start: 0.8153 (m-30) cc_final: 0.7668 (t0)
REVERT: I   63 TYR cc_start: 0.8555 (m-80) cc_final: 0.8284 (m-80)
REVERT: I   76 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7258 (m-30)
REVERT: I  108 ASP cc_start: 0.7722 (m-30) cc_final: 0.7481 (m-30)
REVERT: I  169 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.7999 (mmt90)
REVERT: G   62 ASP cc_start: 0.8337 (m-30) cc_final: 0.7887 (t0)
REVERT: G   66 LYS cc_start: 0.6656 (mtmm) cc_final: 0.6416 (mtmm)
REVERT: F   44 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7201 (mm-40)
REVERT: F   60 MET cc_start: 0.8401 (ttt) cc_final: 0.8013 (ttt)
REVERT: F   62 ASP cc_start: 0.8242 (m-30) cc_final: 0.7877 (t0)
REVERT: F  100 THR cc_start: 0.8861 (m) cc_final: 0.8598 (p)
REVERT: F  169 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.8052 (mmt90)
REVERT: B   60 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.6680 (ttp)
REVERT: B  145 TYR cc_start: 0.9065 (m-10) cc_final: 0.8763 (m-80)
REVERT: C   67 TYR cc_start: 0.8122 (m-10) cc_final: 0.7422 (m-10)
REVERT: C   84 GLU cc_start: 0.7976 (tp30) cc_final: 0.7666 (tp30)
REVERT: D   62 ASP cc_start: 0.8246 (m-30) cc_final: 0.7789 (t0)
REVERT: D   63 TYR cc_start: 0.8561 (m-80) cc_final: 0.8117 (m-80)
REVERT: D   67 TYR cc_start: 0.7899 (m-10) cc_final: 0.7311 (m-10)
REVERT: D   76 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6898 (m-30)
REVERT: D   99 ASN cc_start: 0.8022 (t0) cc_final: 0.7813 (t0)
REVERT: D  100 THR cc_start: 0.8873 (m) cc_final: 0.8658 (p)
REVERT: D  131 ILE cc_start: 0.9043 (mt) cc_final: 0.8755 (tt)
REVERT: D  143 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7834 (ttm-80)
REVERT: H  100 THR cc_start: 0.9040 (t) cc_final: 0.8783 (p)
REVERT: H  145 TYR cc_start: 0.9017 (m-10) cc_final: 0.8813 (m-80)
REVERT: H  169 ARG cc_start: 0.8486 (mmm-85) cc_final: 0.8221 (mtt-85)
REVERT: H  197 GLU cc_start: 0.7520 (tt0) cc_final: 0.7298 (tt0)
  outliers start: 39
  outliers final: 17
  residues processed: 538
  average time/residue: 0.2528
  time to fit residues: 196.8347
Evaluate side-chains
  470 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 449
  time to evaluate  : 1.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  109 SER
Chi-restraints excluded: chain A residue   76 ASP
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  108 ASP
Chi-restraints excluded: chain I residue   76 ASP
Chi-restraints excluded: chain E residue   66 LYS
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain E residue  109 SER
Chi-restraints excluded: chain G residue   68 ILE
Chi-restraints excluded: chain G residue  109 SER
Chi-restraints excluded: chain G residue  186 LEU
Chi-restraints excluded: chain F residue   68 ILE
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain C residue   68 ILE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  109 SER
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue   76 ASP
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain H residue  109 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 119 optimal weight:   10.0000
   chunk 134 optimal weight:   10.0000
   chunk 107 optimal weight:    8.9990
   chunk 160 optimal weight:   10.0000
   chunk 130 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 123 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 165 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 92 optimal weight:    0.4980
   overall best weight:    3.2988

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

Flipped N/Q/H residues before XYZ refinement:
J  52 ASN
A  59 ASN
E  52 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.150585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.123102 restraints weight = 19102.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.127150 restraints weight = 12024.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.130002 restraints weight = 8842.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.3350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.031  13930  Z= 0.246
  Angle     :  0.665   7.094  18860  Z= 0.357
  Chirality :  0.051   0.145   2100
  Planarity :  0.004   0.036   2460
  Dihedral  :  5.156  19.076   1890
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 17.74 %
    Favored  : 79.18 %
  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 (0.21), residues: 1720
  helix: -2.05 (0.19), residues: 470
  sheet: -2.16 (0.26), residues: 410
  loop : -1.45 (0.25), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP I 116 
 HIS   0.006   0.002   HIS B 113 
 PHE   0.027   0.002   PHE I  77 
 TYR   0.023   0.002   TYR G  67 
 ARG   0.008   0.001   ARG D 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03932 (  410)
  hydrogen bonds       : angle       5.60582 ( 1140)
  covalent geometry    : bond        0.00551 (13930)
  covalent geometry    : angle       0.66543 (18860)

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

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

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  537 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 492
  time to evaluate  : 1.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   58 ILE cc_start: 0.8873 (mm) cc_final: 0.8549 (mt)
REVERT: J   84 GLU cc_start: 0.7900 (tp30) cc_final: 0.7619 (tp30)
REVERT: J  108 ASP cc_start: 0.8261 (m-30) cc_final: 0.7976 (m-30)
REVERT: J  190 GLU cc_start: 0.7854 (tt0) cc_final: 0.7452 (tm-30)
REVERT: A   48 GLN cc_start: 0.8755 (mt0) cc_final: 0.8439 (mt0)
REVERT: A   57 ASP cc_start: 0.7918 (m-30) cc_final: 0.7714 (m-30)
REVERT: A   62 ASP cc_start: 0.8175 (m-30) cc_final: 0.7879 (t0)
REVERT: A   67 TYR cc_start: 0.7945 (m-10) cc_final: 0.7537 (m-10)
REVERT: A   76 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7261 (m-30)
REVERT: A  147 VAL cc_start: 0.9256 (m) cc_final: 0.8895 (p)
REVERT: A  186 LEU cc_start: 0.9168 (mt) cc_final: 0.8743 (mt)
REVERT: A  190 GLU cc_start: 0.7977 (tt0) cc_final: 0.7708 (tm-30)
REVERT: A  193 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7773 (mp10)
REVERT: A  196 ASP cc_start: 0.7280 (m-30) cc_final: 0.7043 (m-30)
REVERT: I   62 ASP cc_start: 0.8289 (m-30) cc_final: 0.7926 (t0)
REVERT: I  190 GLU cc_start: 0.7947 (tt0) cc_final: 0.7455 (tm-30)
REVERT: E   76 ASP cc_start: 0.8150 (m-30) cc_final: 0.7834 (m-30)
REVERT: E   77 PHE cc_start: 0.8895 (m-80) cc_final: 0.8663 (m-10)
REVERT: E  190 GLU cc_start: 0.7747 (tt0) cc_final: 0.7439 (tm-30)
REVERT: G   58 ILE cc_start: 0.8698 (mm) cc_final: 0.8492 (mt)
REVERT: G   62 ASP cc_start: 0.8281 (m-30) cc_final: 0.7930 (t0)
REVERT: G   99 ASN cc_start: 0.8503 (t0) cc_final: 0.8212 (t0)
REVERT: F   44 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7244 (mm-40)
REVERT: F   60 MET cc_start: 0.8521 (ttt) cc_final: 0.8106 (ttt)
REVERT: F   62 ASP cc_start: 0.8216 (m-30) cc_final: 0.7907 (t0)
REVERT: F   64 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.7048 (ttmm)
REVERT: F   67 TYR cc_start: 0.7787 (m-10) cc_final: 0.7158 (m-10)
REVERT: F  100 THR cc_start: 0.8880 (m) cc_final: 0.8596 (p)
REVERT: B   58 ILE cc_start: 0.8771 (mm) cc_final: 0.8484 (mt)
REVERT: B   63 TYR cc_start: 0.8634 (m-80) cc_final: 0.8245 (m-80)
REVERT: B   98 LEU cc_start: 0.8394 (mt) cc_final: 0.8113 (tp)
REVERT: B   99 ASN cc_start: 0.8300 (t0) cc_final: 0.8059 (t0)
REVERT: B  108 ASP cc_start: 0.7754 (m-30) cc_final: 0.7447 (m-30)
REVERT: B  145 TYR cc_start: 0.9093 (m-10) cc_final: 0.8809 (m-80)
REVERT: C   67 TYR cc_start: 0.8098 (m-10) cc_final: 0.7703 (m-10)
REVERT: C   99 ASN cc_start: 0.8300 (t0) cc_final: 0.7914 (t0)
REVERT: D   63 TYR cc_start: 0.8588 (m-80) cc_final: 0.8213 (m-80)
REVERT: D   64 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.7008 (ttmm)
REVERT: D   99 ASN cc_start: 0.8331 (t0) cc_final: 0.8047 (t0)
REVERT: D  100 THR cc_start: 0.8948 (m) cc_final: 0.8609 (p)
REVERT: D  108 ASP cc_start: 0.7857 (t0) cc_final: 0.7362 (t70)
REVERT: D  190 GLU cc_start: 0.7787 (tt0) cc_final: 0.7379 (tm-30)
REVERT: D  194 TYR cc_start: 0.8068 (t80) cc_final: 0.7758 (t80)
REVERT: H   58 ILE cc_start: 0.8726 (mm) cc_final: 0.8481 (mt)
REVERT: H  145 TYR cc_start: 0.9113 (m-10) cc_final: 0.8902 (m-80)
REVERT: H  190 GLU cc_start: 0.7927 (tt0) cc_final: 0.7464 (tm-30)
  outliers start: 45
  outliers final: 24
  residues processed: 504
  average time/residue: 0.2350
  time to fit residues: 173.1310
Evaluate side-chains
  477 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 449
  time to evaluate  : 1.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   46 SER
Chi-restraints excluded: chain J residue  100 THR
Chi-restraints excluded: chain J residue  109 SER
Chi-restraints excluded: chain A residue   76 ASP
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain E residue   46 SER
Chi-restraints excluded: chain E residue   66 LYS
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain E residue  109 SER
Chi-restraints excluded: chain G residue   57 ASP
Chi-restraints excluded: chain G residue   68 ILE
Chi-restraints excluded: chain G residue  109 SER
Chi-restraints excluded: chain G residue  178 VAL
Chi-restraints excluded: chain F residue   64 LYS
Chi-restraints excluded: chain F residue   68 ILE
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain C residue   68 ILE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  109 SER
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  178 VAL
Chi-restraints excluded: chain D residue   64 LYS
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain H residue   68 ILE
Chi-restraints excluded: chain H residue  109 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 132 optimal weight:    0.7980
   chunk 135 optimal weight:   10.0000
   chunk 154 optimal weight:    7.9990
   chunk 23 optimal weight:   10.0000
   chunk 133 optimal weight:    0.6980
   chunk 120 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 157 optimal weight:    1.9990
   chunk 103 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 99 optimal weight:    6.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
G  48 GLN
G 193 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.152438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.126212 restraints weight = 18713.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.130296 restraints weight = 11625.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.133069 restraints weight = 8464.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.3779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024  13930  Z= 0.165
  Angle     :  0.616   8.396  18860  Z= 0.327
  Chirality :  0.049   0.147   2100
  Planarity :  0.004   0.034   2460
  Dihedral  :  4.809  18.484   1890
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 20.96 %
    Favored  : 76.78 %
  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: -2.35 (0.21), residues: 1720
  helix: -1.31 (0.22), residues: 470
  sheet: -2.57 (0.24), residues: 440
  loop : -0.88 (0.25), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D 116 
 HIS   0.004   0.001   HIS B 113 
 PHE   0.018   0.002   PHE I  77 
 TYR   0.021   0.002   TYR G  67 
 ARG   0.006   0.001   ARG C 157 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03318 (  410)
  hydrogen bonds       : angle       5.39168 ( 1140)
  covalent geometry    : bond        0.00367 (13930)
  covalent geometry    : angle       0.61611 (18860)

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

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

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  505 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 472
  time to evaluate  : 1.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   58 ILE cc_start: 0.8833 (mm) cc_final: 0.8522 (mt)
REVERT: J  190 GLU cc_start: 0.7750 (tt0) cc_final: 0.7385 (tm-30)
REVERT: A   48 GLN cc_start: 0.8714 (mt0) cc_final: 0.8460 (mt0)
REVERT: A   64 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7298 (ttmm)
REVERT: A   67 TYR cc_start: 0.8089 (m-10) cc_final: 0.7850 (m-10)
REVERT: A   76 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7278 (m-30)
REVERT: A  108 ASP cc_start: 0.7870 (m-30) cc_final: 0.7293 (m-30)
REVERT: A  147 VAL cc_start: 0.9202 (m) cc_final: 0.8889 (p)
REVERT: A  190 GLU cc_start: 0.7922 (tt0) cc_final: 0.7646 (tm-30)
REVERT: A  193 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7655 (mp10)
REVERT: I   58 ILE cc_start: 0.8636 (mm) cc_final: 0.8430 (mt)
REVERT: I   76 ASP cc_start: 0.7691 (m-30) cc_final: 0.7390 (m-30)
REVERT: I  169 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.8111 (mmt90)
REVERT: I  190 GLU cc_start: 0.7877 (tt0) cc_final: 0.7415 (tm-30)
REVERT: E   58 ILE cc_start: 0.8755 (mm) cc_final: 0.8502 (mt)
REVERT: E   76 ASP cc_start: 0.8074 (m-30) cc_final: 0.7709 (m-30)
REVERT: E   84 GLU cc_start: 0.8082 (tp30) cc_final: 0.7447 (tp30)
REVERT: G   58 ILE cc_start: 0.8670 (mm) cc_final: 0.8438 (mt)
REVERT: G   63 TYR cc_start: 0.8671 (m-80) cc_final: 0.8121 (m-80)
REVERT: G   99 ASN cc_start: 0.8432 (t0) cc_final: 0.8169 (t0)
REVERT: F   44 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7351 (mm-40)
REVERT: F   59 ASN cc_start: 0.7723 (t0) cc_final: 0.7517 (t0)
REVERT: F   60 MET cc_start: 0.8464 (ttt) cc_final: 0.7931 (ttt)
REVERT: F   62 ASP cc_start: 0.8090 (m-30) cc_final: 0.7871 (t0)
REVERT: F   67 TYR cc_start: 0.7968 (m-10) cc_final: 0.7336 (m-10)
REVERT: F  100 THR cc_start: 0.8878 (m) cc_final: 0.8645 (p)
REVERT: F  108 ASP cc_start: 0.7893 (m-30) cc_final: 0.7387 (m-30)
REVERT: F  169 ARG cc_start: 0.8099 (mmm-85) cc_final: 0.7862 (mmt90)
REVERT: F  193 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7731 (mp10)
REVERT: B   58 ILE cc_start: 0.8741 (mm) cc_final: 0.8413 (mt)
REVERT: B   63 TYR cc_start: 0.8368 (m-80) cc_final: 0.8097 (m-80)
REVERT: B   84 GLU cc_start: 0.8085 (tp30) cc_final: 0.7730 (tp30)
REVERT: B   99 ASN cc_start: 0.8301 (t0) cc_final: 0.8008 (t0)
REVERT: B  108 ASP cc_start: 0.7785 (m-30) cc_final: 0.7472 (m-30)
REVERT: B  145 TYR cc_start: 0.9017 (m-10) cc_final: 0.8734 (m-80)
REVERT: B  193 GLN cc_start: 0.7987 (mt0) cc_final: 0.7756 (mt0)
REVERT: C   58 ILE cc_start: 0.8709 (mm) cc_final: 0.8485 (mt)
REVERT: C   67 TYR cc_start: 0.7969 (m-10) cc_final: 0.7528 (m-10)
REVERT: C   99 ASN cc_start: 0.8293 (t0) cc_final: 0.8088 (t0)
REVERT: D   63 TYR cc_start: 0.8481 (m-80) cc_final: 0.8045 (m-80)
REVERT: D   67 TYR cc_start: 0.8133 (m-10) cc_final: 0.7529 (m-10)
REVERT: D  100 THR cc_start: 0.8984 (m) cc_final: 0.8744 (p)
REVERT: D  190 GLU cc_start: 0.7738 (tt0) cc_final: 0.7301 (tm-30)
REVERT: H   58 ILE cc_start: 0.8758 (mm) cc_final: 0.8478 (mt)
REVERT: H   99 ASN cc_start: 0.8474 (t0) cc_final: 0.8100 (t0)
REVERT: H  145 TYR cc_start: 0.9008 (m-10) cc_final: 0.8737 (m-80)
REVERT: H  186 LEU cc_start: 0.9368 (mt) cc_final: 0.7991 (mt)
REVERT: H  190 GLU cc_start: 0.7952 (tt0) cc_final: 0.7514 (tm-30)
REVERT: H  193 GLN cc_start: 0.7623 (mt0) cc_final: 0.7279 (mt0)
  outliers start: 33
  outliers final: 17
  residues processed: 484
  average time/residue: 0.2422
  time to fit residues: 171.4040
Evaluate side-chains
  449 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 428
  time to evaluate  : 1.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   46 SER
Chi-restraints excluded: chain J residue  109 SER
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue   76 ASP
Chi-restraints excluded: chain A residue  129 MET
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain E residue   46 SER
Chi-restraints excluded: chain E residue  109 SER
Chi-restraints excluded: chain G residue  109 SER
Chi-restraints excluded: chain G residue  154 ILE
Chi-restraints excluded: chain F residue   68 ILE
Chi-restraints excluded: chain F residue  193 GLN
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain C residue  109 SER
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain C residue  178 VAL
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain H residue  109 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 114 optimal weight:    0.9990
   chunk 97 optimal weight:    8.9990
   chunk 115 optimal weight:    3.9990
   chunk 142 optimal weight:    0.0770
   chunk 108 optimal weight:    8.9990
   chunk 157 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0370
   chunk 21 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.7420

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
I  59 ASN
C  48 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.157255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.130794 restraints weight = 18759.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.135072 restraints weight = 11546.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.138121 restraints weight = 8355.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.4266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13930  Z= 0.122
  Angle     :  0.614   8.998  18860  Z= 0.320
  Chirality :  0.048   0.141   2100
  Planarity :  0.004   0.038   2460
  Dihedral  :  4.503  18.084   1890
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 23.70 %
    Favored  : 74.11 %
  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: -2.08 (0.21), residues: 1720
  helix: -0.84 (0.23), residues: 470
  sheet: -2.24 (0.24), residues: 460
  loop : -0.96 (0.25), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E 116 
 HIS   0.003   0.001   HIS E 113 
 PHE   0.026   0.002   PHE E  77 
 TYR   0.022   0.002   TYR E  67 
 ARG   0.006   0.000   ARG H 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02994 (  410)
  hydrogen bonds       : angle       5.18789 ( 1140)
  covalent geometry    : bond        0.00264 (13930)
  covalent geometry    : angle       0.61432 (18860)

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

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

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  503 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 471
  time to evaluate  : 1.557 
Fit side-chains
   revert: symmetry clash
REVERT: J   58 ILE cc_start: 0.8801 (mm) cc_final: 0.8476 (mt)
REVERT: A   48 GLN cc_start: 0.8729 (mt0) cc_final: 0.8393 (mt0)
REVERT: A  108 ASP cc_start: 0.7923 (m-30) cc_final: 0.7340 (m-30)
REVERT: A  147 VAL cc_start: 0.9214 (m) cc_final: 0.8923 (p)
REVERT: A  190 GLU cc_start: 0.7856 (tt0) cc_final: 0.7486 (tm-30)
REVERT: A  193 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7614 (mp10)
REVERT: I   76 ASP cc_start: 0.7737 (m-30) cc_final: 0.7387 (m-30)
REVERT: I  169 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.7986 (mmt90)
REVERT: E   58 ILE cc_start: 0.8740 (mm) cc_final: 0.8459 (mt)
REVERT: E   66 LYS cc_start: 0.6652 (mtmm) cc_final: 0.6192 (ptpt)
REVERT: E   76 ASP cc_start: 0.8060 (m-30) cc_final: 0.7675 (m-30)
REVERT: E   84 GLU cc_start: 0.8015 (tp30) cc_final: 0.7517 (tp30)
REVERT: E   99 ASN cc_start: 0.8097 (t0) cc_final: 0.7669 (t0)
REVERT: E  134 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8828 (tt)
REVERT: G   58 ILE cc_start: 0.8785 (mm) cc_final: 0.8498 (mt)
REVERT: G   63 TYR cc_start: 0.8462 (m-80) cc_final: 0.8066 (m-80)
REVERT: G   64 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7196 (ttmm)
REVERT: G   73 TYR cc_start: 0.8518 (p90) cc_final: 0.8226 (p90)
REVERT: F   44 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7440 (mm-40)
REVERT: F   60 MET cc_start: 0.8375 (ttt) cc_final: 0.7807 (ttt)
REVERT: F   67 TYR cc_start: 0.7933 (m-10) cc_final: 0.7409 (m-10)
REVERT: F  100 THR cc_start: 0.8827 (m) cc_final: 0.8623 (p)
REVERT: F  108 ASP cc_start: 0.7863 (m-30) cc_final: 0.7328 (m-30)
REVERT: B   58 ILE cc_start: 0.8790 (mm) cc_final: 0.8437 (mt)
REVERT: B   63 TYR cc_start: 0.8154 (m-80) cc_final: 0.7936 (m-80)
REVERT: B   76 ASP cc_start: 0.7663 (m-30) cc_final: 0.7424 (m-30)
REVERT: B   84 GLU cc_start: 0.8090 (tp30) cc_final: 0.7786 (tp30)
REVERT: B  108 ASP cc_start: 0.7905 (m-30) cc_final: 0.7674 (m-30)
REVERT: C   58 ILE cc_start: 0.8774 (mm) cc_final: 0.8544 (mt)
REVERT: C   63 TYR cc_start: 0.8337 (m-80) cc_final: 0.8082 (m-80)
REVERT: C   67 TYR cc_start: 0.7962 (m-10) cc_final: 0.7376 (m-10)
REVERT: C  163 ASP cc_start: 0.7490 (m-30) cc_final: 0.6951 (m-30)
REVERT: C  190 GLU cc_start: 0.7912 (tt0) cc_final: 0.7565 (tm-30)
REVERT: D   58 ILE cc_start: 0.8800 (mm) cc_final: 0.8526 (mt)
REVERT: D   67 TYR cc_start: 0.8139 (m-10) cc_final: 0.7485 (m-10)
REVERT: D  100 THR cc_start: 0.8879 (m) cc_final: 0.8641 (p)
REVERT: D  108 ASP cc_start: 0.7442 (t0) cc_final: 0.7088 (m-30)
REVERT: D  147 VAL cc_start: 0.9230 (m) cc_final: 0.8972 (p)
REVERT: D  190 GLU cc_start: 0.7745 (tt0) cc_final: 0.7309 (tm-30)
REVERT: H   58 ILE cc_start: 0.8748 (mm) cc_final: 0.8477 (mt)
REVERT: H   66 LYS cc_start: 0.6453 (mtmm) cc_final: 0.6052 (ptpt)
REVERT: H  145 TYR cc_start: 0.8913 (m-10) cc_final: 0.8623 (m-80)
REVERT: H  169 ARG cc_start: 0.8435 (mmt90) cc_final: 0.8068 (mmm-85)
  outliers start: 32
  outliers final: 19
  residues processed: 486
  average time/residue: 0.2368
  time to fit residues: 169.1803
Evaluate side-chains
  448 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 426
  time to evaluate  : 1.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   46 SER
Chi-restraints excluded: chain J residue  109 SER
Chi-restraints excluded: chain A residue  129 MET
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain I residue  200 ASP
Chi-restraints excluded: chain E residue   46 SER
Chi-restraints excluded: chain E residue  109 SER
Chi-restraints excluded: chain E residue  134 LEU
Chi-restraints excluded: chain G residue   64 LYS
Chi-restraints excluded: chain G residue  109 SER
Chi-restraints excluded: chain F residue   68 ILE
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain C residue   40 GLU
Chi-restraints excluded: chain C residue   89 SER
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  109 SER
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain H residue  109 SER
Chi-restraints excluded: chain H residue  122 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 73 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 96 optimal weight:    6.9990
   chunk 116 optimal weight:    7.9990
   chunk 98 optimal weight:    1.9990
   chunk 162 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 106 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
J 198 ASN
E 198 ASN
F 130 HIS
H 101 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.147264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.120534 restraints weight = 19203.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.124376 restraints weight = 12139.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.127181 restraints weight = 8966.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.4304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057  13930  Z= 0.307
  Angle     :  0.736   9.673  18860  Z= 0.394
  Chirality :  0.053   0.182   2100
  Planarity :  0.004   0.043   2460
  Dihedral  :  4.894  17.706   1890
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 17.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 22.81 %
    Favored  : 73.56 %
  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: -2.18 (0.21), residues: 1720
  helix: -1.01 (0.22), residues: 470
  sheet: -2.34 (0.23), residues: 460
  loop : -0.92 (0.26), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.004   TRP E 116 
 HIS   0.007   0.002   HIS E 113 
 PHE   0.038   0.003   PHE E  77 
 TYR   0.027   0.003   TYR I  67 
 ARG   0.005   0.001   ARG J 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03848 (  410)
  hydrogen bonds       : angle       5.51035 ( 1140)
  covalent geometry    : bond        0.00704 (13930)
  covalent geometry    : angle       0.73584 (18860)

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

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

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  536 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 483
  time to evaluate  : 1.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   58 ILE cc_start: 0.8777 (mm) cc_final: 0.8499 (mt)
REVERT: J   84 GLU cc_start: 0.8014 (tp30) cc_final: 0.7574 (tp30)
REVERT: A   48 GLN cc_start: 0.8685 (mt0) cc_final: 0.8301 (mt0)
REVERT: A  190 GLU cc_start: 0.7957 (tt0) cc_final: 0.7624 (tm-30)
REVERT: A  193 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7834 (mp10)
REVERT: I   58 ILE cc_start: 0.8759 (mm) cc_final: 0.8558 (mt)
REVERT: I   76 ASP cc_start: 0.8082 (m-30) cc_final: 0.7595 (m-30)
REVERT: I  186 LEU cc_start: 0.9343 (mt) cc_final: 0.8089 (mt)
REVERT: E   48 GLN cc_start: 0.8881 (mt0) cc_final: 0.8551 (mt0)
REVERT: E   58 ILE cc_start: 0.8811 (mm) cc_final: 0.8574 (mt)
REVERT: E   76 ASP cc_start: 0.8395 (m-30) cc_final: 0.7936 (m-30)
REVERT: E   84 GLU cc_start: 0.8124 (tp30) cc_final: 0.7803 (tp30)
REVERT: E   99 ASN cc_start: 0.8378 (t0) cc_final: 0.8031 (t0)
REVERT: G   58 ILE cc_start: 0.8753 (mm) cc_final: 0.8523 (mt)
REVERT: G   63 TYR cc_start: 0.8610 (m-80) cc_final: 0.7941 (m-80)
REVERT: F   44 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7484 (mm-40)
REVERT: F   60 MET cc_start: 0.8532 (ttt) cc_final: 0.8030 (ttt)
REVERT: F   67 TYR cc_start: 0.8103 (m-10) cc_final: 0.7705 (m-10)
REVERT: F   99 ASN cc_start: 0.8303 (t0) cc_final: 0.8028 (t0)
REVERT: F  100 THR cc_start: 0.9048 (m) cc_final: 0.8789 (p)
REVERT: F  108 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7776 (m-30)
REVERT: F  190 GLU cc_start: 0.7812 (tt0) cc_final: 0.7396 (tm-30)
REVERT: B   58 ILE cc_start: 0.8817 (mm) cc_final: 0.8474 (mt)
REVERT: B   62 ASP cc_start: 0.7965 (m-30) cc_final: 0.7611 (t0)
REVERT: B   63 TYR cc_start: 0.8430 (m-80) cc_final: 0.8101 (m-80)
REVERT: B   76 ASP cc_start: 0.8122 (m-30) cc_final: 0.7904 (m-30)
REVERT: B   84 GLU cc_start: 0.8191 (tp30) cc_final: 0.7888 (tp30)
REVERT: B  108 ASP cc_start: 0.8236 (m-30) cc_final: 0.7639 (m-30)
REVERT: B  145 TYR cc_start: 0.9013 (m-10) cc_final: 0.8813 (m-80)
REVERT: C   58 ILE cc_start: 0.8731 (mm) cc_final: 0.8526 (mt)
REVERT: C   63 TYR cc_start: 0.8640 (m-80) cc_final: 0.8117 (m-80)
REVERT: C   64 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7265 (ttmm)
REVERT: C   67 TYR cc_start: 0.8113 (m-10) cc_final: 0.7484 (m-10)
REVERT: D   58 ILE cc_start: 0.8800 (mm) cc_final: 0.8557 (mt)
REVERT: D   64 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7139 (ttmm)
REVERT: D   67 TYR cc_start: 0.8251 (m-10) cc_final: 0.7812 (m-10)
REVERT: D  114 LEU cc_start: 0.9195 (tt) cc_final: 0.8921 (tt)
REVERT: D  190 GLU cc_start: 0.7788 (tt0) cc_final: 0.7392 (tm-30)
REVERT: H   58 ILE cc_start: 0.8785 (mm) cc_final: 0.8508 (mt)
REVERT: H   76 ASP cc_start: 0.7989 (m-30) cc_final: 0.7775 (m-30)
REVERT: H  145 TYR cc_start: 0.9051 (m-10) cc_final: 0.8829 (m-80)
REVERT: H  169 ARG cc_start: 0.8474 (mmt90) cc_final: 0.7941 (mmm-85)
REVERT: H  190 GLU cc_start: 0.7938 (tt0) cc_final: 0.7556 (tm-30)
  outliers start: 53
  outliers final: 36
  residues processed: 500
  average time/residue: 0.2409
  time to fit residues: 177.2261
Evaluate side-chains
  499 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 459
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   46 SER
Chi-restraints excluded: chain J residue  100 THR
Chi-restraints excluded: chain J residue  109 SER
Chi-restraints excluded: chain A residue  129 MET
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain I residue   38 VAL
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain I residue  167 ILE
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain E residue   46 SER
Chi-restraints excluded: chain E residue  109 SER
Chi-restraints excluded: chain G residue   64 LYS
Chi-restraints excluded: chain G residue  100 THR
Chi-restraints excluded: chain G residue  109 SER
Chi-restraints excluded: chain G residue  129 MET
Chi-restraints excluded: chain G residue  154 ILE
Chi-restraints excluded: chain F residue   46 SER
Chi-restraints excluded: chain F residue   68 ILE
Chi-restraints excluded: chain F residue  108 ASP
Chi-restraints excluded: chain F residue  129 MET
Chi-restraints excluded: chain F residue  167 ILE
Chi-restraints excluded: chain B residue   64 LYS
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  109 SER
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain D residue   64 LYS
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  129 MET
Chi-restraints excluded: chain H residue   40 GLU
Chi-restraints excluded: chain H residue   68 ILE
Chi-restraints excluded: chain H residue  102 VAL
Chi-restraints excluded: chain H residue  109 SER
Chi-restraints excluded: chain H residue  122 LYS
Chi-restraints excluded: chain H residue  167 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 167 optimal weight:    1.9990
   chunk 95 optimal weight:    4.9990
   chunk 88 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 155 optimal weight:    2.9990
   chunk 159 optimal weight:   10.0000
   chunk 123 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
D 118 ASN
H 101 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.154056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.127442 restraints weight = 18687.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.131387 restraints weight = 11708.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.134376 restraints weight = 8616.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.4681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13930  Z= 0.162
  Angle     :  0.675   9.936  18860  Z= 0.355
  Chirality :  0.049   0.146   2100
  Planarity :  0.004   0.043   2460
  Dihedral  :  4.645  21.618   1890
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 15.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 24.32 %
    Favored  : 72.47 %
  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: -2.09 (0.21), residues: 1720
  helix: -0.91 (0.22), residues: 490
  sheet: -2.40 (0.23), residues: 460
  loop : -0.81 (0.26), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP E 116 
 HIS   0.004   0.001   HIS E 113 
 PHE   0.034   0.002   PHE E  77 
 TYR   0.032   0.002   TYR A  67 
 ARG   0.007   0.000   ARG D 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03310 (  410)
  hydrogen bonds       : angle       5.37441 ( 1140)
  covalent geometry    : bond        0.00364 (13930)
  covalent geometry    : angle       0.67507 (18860)

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

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

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  494 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 447
  time to evaluate  : 1.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   58 ILE cc_start: 0.8768 (mm) cc_final: 0.8474 (mt)
REVERT: J   84 GLU cc_start: 0.7992 (tp30) cc_final: 0.7621 (tp30)
REVERT: J  147 VAL cc_start: 0.9181 (m) cc_final: 0.8979 (p)
REVERT: A   76 ASP cc_start: 0.7719 (m-30) cc_final: 0.7486 (m-30)
REVERT: A  190 GLU cc_start: 0.7900 (tt0) cc_final: 0.7498 (tm-30)
REVERT: A  193 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7946 (mp10)
REVERT: I   58 ILE cc_start: 0.8788 (mm) cc_final: 0.8544 (mt)
REVERT: I  108 ASP cc_start: 0.8354 (m-30) cc_final: 0.7690 (m-30)
REVERT: E   58 ILE cc_start: 0.8854 (mm) cc_final: 0.8530 (mt)
REVERT: E   84 GLU cc_start: 0.8195 (tp30) cc_final: 0.7683 (tp30)
REVERT: E   94 ASP cc_start: 0.7982 (t0) cc_final: 0.7608 (t0)
REVERT: E   99 ASN cc_start: 0.8305 (t0) cc_final: 0.7785 (t0)
REVERT: E  122 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.6878 (tptt)
REVERT: G   58 ILE cc_start: 0.8719 (mm) cc_final: 0.8469 (mt)
REVERT: G   59 ASN cc_start: 0.7243 (t0) cc_final: 0.6942 (t0)
REVERT: G   63 TYR cc_start: 0.8410 (m-80) cc_final: 0.7924 (m-80)
REVERT: G   64 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7061 (ttmm)
REVERT: G  147 VAL cc_start: 0.9193 (m) cc_final: 0.8873 (p)
REVERT: F   44 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7497 (mm-40)
REVERT: F   60 MET cc_start: 0.8413 (ttt) cc_final: 0.7901 (ttt)
REVERT: F   67 TYR cc_start: 0.8046 (m-10) cc_final: 0.7626 (m-10)
REVERT: F  100 THR cc_start: 0.8796 (m) cc_final: 0.8451 (p)
REVERT: F  108 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7530 (m-30)
REVERT: F  190 GLU cc_start: 0.7746 (tt0) cc_final: 0.7285 (tm-30)
REVERT: B   58 ILE cc_start: 0.8767 (mm) cc_final: 0.8431 (mt)
REVERT: B   60 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7329 (mtp)
REVERT: B   63 TYR cc_start: 0.8090 (m-80) cc_final: 0.7716 (m-80)
REVERT: B   66 LYS cc_start: 0.6788 (mtmm) cc_final: 0.6459 (ptmt)
REVERT: B   84 GLU cc_start: 0.8127 (tp30) cc_final: 0.7865 (tp30)
REVERT: B  108 ASP cc_start: 0.8148 (m-30) cc_final: 0.7585 (m-30)
REVERT: B  159 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8525 (tt)
REVERT: C   58 ILE cc_start: 0.8726 (mm) cc_final: 0.8520 (mt)
REVERT: C   62 ASP cc_start: 0.7958 (m-30) cc_final: 0.7711 (t0)
REVERT: C   63 TYR cc_start: 0.8362 (m-80) cc_final: 0.7977 (m-80)
REVERT: C   67 TYR cc_start: 0.8056 (m-10) cc_final: 0.7390 (m-10)
REVERT: D   58 ILE cc_start: 0.8823 (mm) cc_final: 0.8510 (mt)
REVERT: D   67 TYR cc_start: 0.7836 (m-10) cc_final: 0.7502 (m-10)
REVERT: D   99 ASN cc_start: 0.8171 (t0) cc_final: 0.7912 (t0)
REVERT: H   58 ILE cc_start: 0.8729 (mm) cc_final: 0.8464 (mt)
REVERT: H   76 ASP cc_start: 0.7880 (m-30) cc_final: 0.7575 (m-30)
REVERT: H  101 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.8007 (tt0)
REVERT: H  145 TYR cc_start: 0.8956 (m-10) cc_final: 0.8690 (m-80)
REVERT: H  169 ARG cc_start: 0.8445 (mmt90) cc_final: 0.7938 (mmm-85)
  outliers start: 47
  outliers final: 27
  residues processed: 463
  average time/residue: 0.2446
  time to fit residues: 165.3543
Evaluate side-chains
  465 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 431
  time to evaluate  : 1.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   46 SER
Chi-restraints excluded: chain J residue  100 THR
Chi-restraints excluded: chain J residue  109 SER
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue  129 MET
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain I residue   38 VAL
Chi-restraints excluded: chain I residue   64 LYS
Chi-restraints excluded: chain I residue   97 LYS
Chi-restraints excluded: chain E residue   40 GLU
Chi-restraints excluded: chain E residue   46 SER
Chi-restraints excluded: chain E residue  109 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain G residue   40 GLU
Chi-restraints excluded: chain G residue   64 LYS
Chi-restraints excluded: chain G residue  100 THR
Chi-restraints excluded: chain G residue  109 SER
Chi-restraints excluded: chain G residue  129 MET
Chi-restraints excluded: chain F residue   46 SER
Chi-restraints excluded: chain F residue  108 ASP
Chi-restraints excluded: chain F residue  129 MET
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain C residue   94 ASP
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  109 SER
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  129 MET
Chi-restraints excluded: chain H residue  101 GLN
Chi-restraints excluded: chain H residue  109 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 142 optimal weight:   10.0000
   chunk 73 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 87 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9980
   chunk 101 optimal weight:    7.9990
   chunk 46 optimal weight:    0.5980
   chunk 145 optimal weight:    7.9990
   chunk 41 optimal weight:    0.4980
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.163527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.136441 restraints weight = 18331.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.140765 restraints weight = 11687.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.143837 restraints weight = 8581.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.4935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13930  Z= 0.137
  Angle     :  0.669   9.922  18860  Z= 0.350
  Chirality :  0.048   0.142   2100
  Planarity :  0.004   0.043   2460
  Dihedral  :  4.609  21.760   1890
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.60 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 24.66 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.21), residues: 1720
  helix: -0.73 (0.22), residues: 490
  sheet: -2.31 (0.23), residues: 460
  loop : -0.82 (0.25), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP J 116 
 HIS   0.005   0.001   HIS E 113 
 PHE   0.050   0.002   PHE J  77 
 TYR   0.046   0.002   TYR B  67 
 ARG   0.007   0.000   ARG B 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03199 (  410)
  hydrogen bonds       : angle       5.28477 ( 1140)
  covalent geometry    : bond        0.00302 (13930)
  covalent geometry    : angle       0.66906 (18860)

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

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

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  475 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 438
  time to evaluate  : 1.582 
Fit side-chains
   revert: symmetry clash
REVERT: J   58 ILE cc_start: 0.8807 (mm) cc_final: 0.8504 (mt)
REVERT: J   84 GLU cc_start: 0.7925 (tp30) cc_final: 0.7613 (tp30)
REVERT: A   76 ASP cc_start: 0.7700 (m-30) cc_final: 0.7421 (m-30)
REVERT: I   58 ILE cc_start: 0.8830 (mm) cc_final: 0.8611 (mt)
REVERT: I   76 ASP cc_start: 0.8028 (m-30) cc_final: 0.7531 (m-30)
REVERT: I   84 GLU cc_start: 0.7979 (tp30) cc_final: 0.7719 (tp30)
REVERT: E   58 ILE cc_start: 0.8795 (mm) cc_final: 0.8506 (mt)
REVERT: E   84 GLU cc_start: 0.8137 (tp30) cc_final: 0.7684 (tp30)
REVERT: E   99 ASN cc_start: 0.8202 (t0) cc_final: 0.7996 (t0)
REVERT: E  122 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.6970 (tptt)
REVERT: E  145 TYR cc_start: 0.9057 (m-80) cc_final: 0.8527 (m-80)
REVERT: G   58 ILE cc_start: 0.8654 (mm) cc_final: 0.8435 (mt)
REVERT: G   63 TYR cc_start: 0.8305 (m-80) cc_final: 0.7951 (m-80)
REVERT: G  147 VAL cc_start: 0.9180 (m) cc_final: 0.8883 (p)
REVERT: F   44 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7207 (mm-40)
REVERT: F   60 MET cc_start: 0.8253 (ttt) cc_final: 0.7818 (ttt)
REVERT: F   67 TYR cc_start: 0.7971 (m-10) cc_final: 0.7744 (m-10)
REVERT: F  108 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7618 (m-30)
REVERT: B   58 ILE cc_start: 0.8768 (mm) cc_final: 0.8400 (mt)
REVERT: B   60 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7244 (mtp)
REVERT: B   63 TYR cc_start: 0.7825 (m-80) cc_final: 0.7534 (m-80)
REVERT: B   64 LYS cc_start: 0.7388 (ttmm) cc_final: 0.7127 (ttmm)
REVERT: B   76 ASP cc_start: 0.7955 (m-30) cc_final: 0.7638 (m-30)
REVERT: B   84 GLU cc_start: 0.8071 (tp30) cc_final: 0.7819 (tp30)
REVERT: B   94 ASP cc_start: 0.8361 (t0) cc_final: 0.8133 (t0)
REVERT: B  147 VAL cc_start: 0.9152 (m) cc_final: 0.8899 (p)
REVERT: B  159 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8481 (tt)
REVERT: C   58 ILE cc_start: 0.8719 (mm) cc_final: 0.8513 (mt)
REVERT: C   63 TYR cc_start: 0.8204 (m-80) cc_final: 0.7864 (m-80)
REVERT: C   67 TYR cc_start: 0.8024 (m-10) cc_final: 0.7374 (m-10)
REVERT: C  190 GLU cc_start: 0.7774 (tt0) cc_final: 0.7431 (tm-30)
REVERT: D   58 ILE cc_start: 0.8783 (mm) cc_final: 0.8521 (mt)
REVERT: D   67 TYR cc_start: 0.7973 (m-10) cc_final: 0.7601 (m-10)
REVERT: H   58 ILE cc_start: 0.8739 (mm) cc_final: 0.8462 (mt)
REVERT: H   66 LYS cc_start: 0.6217 (mtmm) cc_final: 0.5798 (ptpt)
REVERT: H   76 ASP cc_start: 0.7774 (m-30) cc_final: 0.7556 (m-30)
REVERT: H  145 TYR cc_start: 0.8872 (m-10) cc_final: 0.8571 (m-80)
REVERT: H  147 VAL cc_start: 0.9185 (m) cc_final: 0.8972 (p)
  outliers start: 37
  outliers final: 22
  residues processed: 452
  average time/residue: 0.2396
  time to fit residues: 158.8230
Evaluate side-chains
  442 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 416
  time to evaluate  : 1.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   46 SER
Chi-restraints excluded: chain J residue  100 THR
Chi-restraints excluded: chain J residue  109 SER
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  129 MET
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain I residue   64 LYS
Chi-restraints excluded: chain E residue   40 GLU
Chi-restraints excluded: chain E residue   46 SER
Chi-restraints excluded: chain E residue  109 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain G residue  100 THR
Chi-restraints excluded: chain G residue  109 SER
Chi-restraints excluded: chain G residue  129 MET
Chi-restraints excluded: chain F residue  108 ASP
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  109 SER
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  129 MET
Chi-restraints excluded: chain H residue  109 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 72 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 132 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 109 optimal weight:   10.0000
   chunk 104 optimal weight:    8.9990
   chunk 115 optimal weight:    0.8980
   chunk 155 optimal weight:   10.0000
   chunk 77 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
H 198 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.165636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.138803 restraints weight = 18229.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.143073 restraints weight = 11649.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.146129 restraints weight = 8571.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.5111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13930  Z= 0.150
  Angle     :  0.675  10.503  18860  Z= 0.356
  Chirality :  0.049   0.380   2100
  Planarity :  0.004   0.044   2460
  Dihedral  :  4.674  23.180   1890
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.78 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 25.55 %
    Favored  : 71.92 %
  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: -1.88 (0.21), residues: 1720
  helix: -0.55 (0.22), residues: 490
  sheet: -2.24 (0.23), residues: 460
  loop : -0.85 (0.25), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP J 116 
 HIS   0.004   0.001   HIS J 113 
 PHE   0.018   0.002   PHE J  77 
 TYR   0.020   0.002   TYR C 194 
 ARG   0.006   0.000   ARG B 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03237 (  410)
  hydrogen bonds       : angle       5.21572 ( 1140)
  covalent geometry    : bond        0.00336 (13930)
  covalent geometry    : angle       0.67494 (18860)

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

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

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  455 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 418
  time to evaluate  : 1.472 
Fit side-chains
   revert: symmetry clash
REVERT: J   58 ILE cc_start: 0.8789 (mm) cc_final: 0.8517 (mt)
REVERT: A   48 GLN cc_start: 0.8725 (mt0) cc_final: 0.8462 (mt0)
REVERT: A   76 ASP cc_start: 0.7833 (m-30) cc_final: 0.7399 (m-30)
REVERT: I   48 GLN cc_start: 0.8573 (mt0) cc_final: 0.8325 (mt0)
REVERT: I   58 ILE cc_start: 0.8881 (mm) cc_final: 0.8589 (mt)
REVERT: I   76 ASP cc_start: 0.8189 (m-30) cc_final: 0.7944 (m-30)
REVERT: I   84 GLU cc_start: 0.7963 (tp30) cc_final: 0.7730 (tp30)
REVERT: E   58 ILE cc_start: 0.8761 (mm) cc_final: 0.8479 (mt)
REVERT: E   84 GLU cc_start: 0.8139 (tp30) cc_final: 0.7736 (tp30)
REVERT: E   99 ASN cc_start: 0.8377 (t0) cc_final: 0.8090 (t0)
REVERT: E  122 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.6942 (tptt)
REVERT: E  145 TYR cc_start: 0.9039 (m-80) cc_final: 0.8521 (m-80)
REVERT: G   58 ILE cc_start: 0.8677 (mm) cc_final: 0.8421 (mt)
REVERT: G   63 TYR cc_start: 0.8192 (m-80) cc_final: 0.7961 (m-80)
REVERT: G  147 VAL cc_start: 0.9198 (m) cc_final: 0.8951 (p)
REVERT: F   44 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7151 (mm-40)
REVERT: F   60 MET cc_start: 0.8282 (ttt) cc_final: 0.7886 (ttt)
REVERT: F   67 TYR cc_start: 0.7948 (m-10) cc_final: 0.7733 (m-10)
REVERT: B   58 ILE cc_start: 0.8787 (mm) cc_final: 0.8404 (mt)
REVERT: B   60 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7405 (mtp)
REVERT: B   63 TYR cc_start: 0.7799 (m-80) cc_final: 0.7490 (m-80)
REVERT: B   66 LYS cc_start: 0.5820 (ptmt) cc_final: 0.5593 (ptmt)
REVERT: B   76 ASP cc_start: 0.7978 (m-30) cc_final: 0.7553 (m-30)
REVERT: B   84 GLU cc_start: 0.8062 (tp30) cc_final: 0.7824 (tp30)
REVERT: B  147 VAL cc_start: 0.9161 (m) cc_final: 0.8904 (p)
REVERT: B  159 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8452 (tt)
REVERT: C   62 ASP cc_start: 0.7877 (t0) cc_final: 0.7530 (t0)
REVERT: C   63 TYR cc_start: 0.8119 (m-80) cc_final: 0.7695 (m-10)
REVERT: C   67 TYR cc_start: 0.7956 (m-10) cc_final: 0.7306 (m-10)
REVERT: C   84 GLU cc_start: 0.8130 (tp30) cc_final: 0.7647 (tp30)
REVERT: C  190 GLU cc_start: 0.7814 (tt0) cc_final: 0.7447 (tm-30)
REVERT: D   58 ILE cc_start: 0.8789 (mm) cc_final: 0.8547 (mt)
REVERT: D   67 TYR cc_start: 0.8134 (m-10) cc_final: 0.7736 (m-10)
REVERT: D   76 ASP cc_start: 0.8030 (m-30) cc_final: 0.7782 (m-30)
REVERT: D  147 VAL cc_start: 0.9166 (m) cc_final: 0.8938 (p)
REVERT: H   58 ILE cc_start: 0.8841 (mm) cc_final: 0.8542 (mt)
REVERT: H   66 LYS cc_start: 0.6332 (mtmm) cc_final: 0.6070 (ptmt)
REVERT: H  147 VAL cc_start: 0.9256 (m) cc_final: 0.9041 (p)
REVERT: H  169 ARG cc_start: 0.8360 (mmt90) cc_final: 0.8097 (mmm-85)
  outliers start: 37
  outliers final: 26
  residues processed: 432
  average time/residue: 0.2414
  time to fit residues: 153.5164
Evaluate side-chains
  424 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 395
  time to evaluate  : 1.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   46 SER
Chi-restraints excluded: chain J residue  100 THR
Chi-restraints excluded: chain J residue  109 SER
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  129 MET
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain I residue   64 LYS
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain E residue   40 GLU
Chi-restraints excluded: chain E residue   46 SER
Chi-restraints excluded: chain E residue  109 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain G residue   40 GLU
Chi-restraints excluded: chain G residue  100 THR
Chi-restraints excluded: chain G residue  103 VAL
Chi-restraints excluded: chain G residue  109 SER
Chi-restraints excluded: chain G residue  129 MET
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain F residue  129 MET
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  109 SER
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  129 MET
Chi-restraints excluded: chain H residue  109 SER
Chi-restraints excluded: chain H residue  186 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 151 optimal weight:    2.9990
   chunk 106 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 122 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   chunk 167 optimal weight:    0.7980
   chunk 92 optimal weight:    0.3980
   chunk 22 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    1.2182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.166633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.139882 restraints weight = 18233.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.144131 restraints weight = 11708.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.147188 restraints weight = 8663.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.5260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13930  Z= 0.145
  Angle     :  0.684  10.305  18860  Z= 0.359
  Chirality :  0.048   0.144   2100
  Planarity :  0.004   0.063   2460
  Dihedral  :  4.638  20.811   1890
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.95 %
    Favored  : 91.05 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 26.85 %
    Favored  : 71.10 %
  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: -1.83 (0.21), residues: 1720
  helix: -0.44 (0.22), residues: 490
  sheet: -2.22 (0.23), residues: 460
  loop : -0.87 (0.25), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP J 116 
 HIS   0.004   0.001   HIS J 113 
 PHE   0.032   0.002   PHE B  77 
 TYR   0.020   0.002   TYR G  67 
 ARG   0.014   0.001   ARG B 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03274 (  410)
  hydrogen bonds       : angle       5.15957 ( 1140)
  covalent geometry    : bond        0.00324 (13930)
  covalent geometry    : angle       0.68410 (18860)

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

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

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3440 Ramachandran restraints generated.
    1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  435 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 405
  time to evaluate  : 1.366 
Fit side-chains
   revert: symmetry clash
REVERT: J   58 ILE cc_start: 0.8878 (mm) cc_final: 0.8608 (mt)
REVERT: A   48 GLN cc_start: 0.8671 (mt0) cc_final: 0.8415 (mt0)
REVERT: A   76 ASP cc_start: 0.7850 (m-30) cc_final: 0.7492 (m-30)
REVERT: I   58 ILE cc_start: 0.8916 (mm) cc_final: 0.8679 (mt)
REVERT: I   84 GLU cc_start: 0.7979 (tp30) cc_final: 0.7739 (tp30)
REVERT: E   58 ILE cc_start: 0.8831 (mm) cc_final: 0.8586 (mt)
REVERT: E   66 LYS cc_start: 0.6150 (mtmm) cc_final: 0.5899 (pttp)
REVERT: E   84 GLU cc_start: 0.8142 (tp30) cc_final: 0.7740 (tp30)
REVERT: E   99 ASN cc_start: 0.8267 (t0) cc_final: 0.7802 (t0)
REVERT: E  122 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7020 (tptt)
REVERT: E  145 TYR cc_start: 0.9032 (m-80) cc_final: 0.8524 (m-80)
REVERT: G   58 ILE cc_start: 0.8682 (mm) cc_final: 0.8443 (mt)
REVERT: G  122 LYS cc_start: 0.8252 (tptt) cc_final: 0.7846 (pttm)
REVERT: G  163 ASP cc_start: 0.7051 (m-30) cc_final: 0.6833 (m-30)
REVERT: F   44 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7184 (mm-40)
REVERT: F   60 MET cc_start: 0.8235 (ttt) cc_final: 0.7901 (ttt)
REVERT: F   67 TYR cc_start: 0.8038 (m-10) cc_final: 0.7816 (m-10)
REVERT: B   58 ILE cc_start: 0.8775 (mm) cc_final: 0.8356 (mt)
REVERT: B   63 TYR cc_start: 0.7894 (m-80) cc_final: 0.7588 (m-80)
REVERT: B   76 ASP cc_start: 0.8027 (m-30) cc_final: 0.7637 (m-30)
REVERT: B   84 GLU cc_start: 0.8045 (tp30) cc_final: 0.7807 (tp30)
REVERT: B  147 VAL cc_start: 0.9152 (m) cc_final: 0.8911 (p)
REVERT: B  159 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8378 (tt)
REVERT: C   63 TYR cc_start: 0.8120 (m-80) cc_final: 0.7780 (m-10)
REVERT: C   67 TYR cc_start: 0.7922 (m-10) cc_final: 0.7214 (m-10)
REVERT: C  190 GLU cc_start: 0.7822 (tt0) cc_final: 0.7442 (tm-30)
REVERT: D   58 ILE cc_start: 0.8864 (mm) cc_final: 0.8614 (mt)
REVERT: D   67 TYR cc_start: 0.8093 (m-10) cc_final: 0.7720 (m-10)
REVERT: D   76 ASP cc_start: 0.8104 (m-30) cc_final: 0.7834 (m-30)
REVERT: D  147 VAL cc_start: 0.9165 (m) cc_final: 0.8942 (p)
REVERT: D  190 GLU cc_start: 0.7718 (tt0) cc_final: 0.7316 (tm-30)
REVERT: H   58 ILE cc_start: 0.8836 (mm) cc_final: 0.8480 (mt)
REVERT: H   66 LYS cc_start: 0.6418 (mtmm) cc_final: 0.6122 (ptmt)
REVERT: H  147 VAL cc_start: 0.9269 (m) cc_final: 0.9017 (p)
REVERT: H  169 ARG cc_start: 0.8373 (mmt90) cc_final: 0.8099 (mmm-85)
  outliers start: 30
  outliers final: 22
  residues processed: 413
  average time/residue: 0.2447
  time to fit residues: 147.1036
Evaluate side-chains
  420 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 396
  time to evaluate  : 1.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   46 SER
Chi-restraints excluded: chain J residue  109 SER
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  129 MET
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain I residue   64 LYS
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain E residue   40 GLU
Chi-restraints excluded: chain E residue   46 SER
Chi-restraints excluded: chain E residue  109 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain E residue  129 MET
Chi-restraints excluded: chain G residue   67 TYR
Chi-restraints excluded: chain G residue  100 THR
Chi-restraints excluded: chain G residue  109 SER
Chi-restraints excluded: chain G residue  129 MET
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain F residue  129 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  109 SER
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  129 MET
Chi-restraints excluded: chain H residue  109 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 125 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9990
   chunk 13 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9990
   chunk 165 optimal weight:    0.0020
   chunk 130 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   chunk 79 optimal weight:    6.9990
   chunk 97 optimal weight:    3.9990
   chunk 89 optimal weight:    0.7980
   chunk 134 optimal weight:    9.9990
   overall best weight:    0.5790

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.172148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.145020 restraints weight = 18455.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.149446 restraints weight = 11737.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.152696 restraints weight = 8593.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.5550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  13930  Z= 0.125
  Angle     :  0.666  10.392  18860  Z= 0.349
  Chirality :  0.047   0.139   2100
  Planarity :  0.004   0.044   2460
  Dihedral  :  4.547  21.078   1890
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 26.64 %
    Favored  : 71.23 %
  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: -1.66 (0.21), residues: 1720
  helix: -0.19 (0.23), residues: 490
  sheet: -1.93 (0.24), residues: 440
  loop : -1.04 (0.24), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP J 116 
 HIS   0.004   0.001   HIS H 113 
 PHE   0.022   0.002   PHE B  77 
 TYR   0.021   0.002   TYR C 194 
 ARG   0.005   0.000   ARG C 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03134 (  410)
  hydrogen bonds       : angle       5.03668 ( 1140)
  covalent geometry    : bond        0.00273 (13930)
  covalent geometry    : angle       0.66626 (18860)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4550.14 seconds
wall clock time: 79 minutes 35.63 seconds (4775.63 seconds total)