Starting phenix.real_space_refine
on Tue Feb  3 21:33:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bdr_44466/02_2026/9bdr_44466.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bdr_44466/02_2026/9bdr_44466.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bdr_44466/02_2026/9bdr_44466.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bdr_44466/02_2026/9bdr_44466.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bdr_44466/02_2026/9bdr_44466.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bdr_44466/02_2026/9bdr_44466.map"
  }
  resolution = 3.82
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    4545      2.51       5
     N    1155      2.21       5
     O    1320      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7030
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 707
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 4, 'TRANS': 85}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 699
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 4, 'TRANS': 84}
          Chain breaks: 1
  Restraints were copied for chains:
    D, B, E, A, G, F, H, J
  Time building chain proxies: 0.89, per 1000 atoms: 0.13
  Number of scatterers: 7030
  At special positions: 0
  Unit cell: (114.466, 134.332, 61.49, 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      10     16.00
     O    1320      8.00
     N    1155      7.00
     C    4545      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.48
  Conformation dependent library (CDL) restraints added in 234.8 milliseconds
  

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1710

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 25 sheets defined
      0.0% alpha, 41.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'E' and resid 12 through 16
      removed outlier: 6.703A  pdb=" N   MET D  13 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   VAL E  16 " --> pdb=" O   MET D  13 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LYS D  15 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   MET C  13 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 8.086A  pdb=" N   VAL D  16 " --> pdb=" O   MET C  13 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   LYS C  15 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 19 through 20
      removed outlier: 6.303A  pdb=" N   ALA D  19 " --> pdb=" O   VAL E  20 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   ALA C  19 " --> pdb=" O   VAL D  20 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 25 through 27
      removed outlier: 6.573A  pdb=" N   ILE C  26 " --> pdb=" O   ASN B  27 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ILE B  26 " --> pdb=" O   ASN A  27 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 30 through 34
      removed outlier: 6.489A  pdb=" N   VAL C  30 " --> pdb=" O   HIS B  31 " (cutoff:3.500A)
      removed outlier: 8.177A  pdb=" N   PHE B  33 " --> pdb=" O   VAL C  30 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   VAL C  32 " --> pdb=" O   PHE B  33 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   VAL B  30 " --> pdb=" O   HIS A  31 " (cutoff:3.500A)
      removed outlier: 8.162A  pdb=" N   PHE A  33 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   VAL B  32 " --> pdb=" O   PHE A  33 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 59 through 62
      removed outlier: 6.475A  pdb=" N   THR C  59 " --> pdb=" O   THR B  60 " (cutoff:3.500A)
      removed outlier: 8.484A  pdb=" N   GLU B  62 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   GLU C  61 " --> pdb=" O   GLU B  62 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   THR B  59 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      removed outlier: 8.495A  pdb=" N   GLU A  62 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   GLU B  61 " --> pdb=" O   GLU A  62 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 65 through 66
      removed outlier: 6.378A  pdb=" N   VAL D  65 " --> pdb=" O   GLU E  66 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   VAL C  65 " --> pdb=" O   GLU D  66 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 69 through 73
      removed outlier: 6.645A  pdb=" N   LYS C  70 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   ILE B  73 " --> pdb=" O   LYS C  70 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   GLU C  72 " --> pdb=" O   ILE B  73 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LYS B  70 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   ILE A  73 " --> pdb=" O   LYS B  70 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   GLU B  72 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 79 through 80
      removed outlier: 6.573A  pdb=" N   TRP D  79 " --> pdb=" O   LYS E  80 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   TRP C  79 " --> pdb=" O   LYS D  80 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 92 through 94
      removed outlier: 6.592A  pdb=" N   GLU C  92 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   GLU B  92 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 97 through 99
      removed outlier: 6.091A  pdb=" N   ALA D  97 " --> pdb=" O   ASN E  98 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   ALA C  97 " --> pdb=" O   ASN D  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 103 through 110
      removed outlier: 6.911A  pdb=" N   LEU E 110 " --> pdb=" O   ALA D 109 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   LEU D 110 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ARG C 104 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   ILE B 107 " --> pdb=" O   ARG C 104 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   THR C 106 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 7.727A  pdb=" N   ALA B 109 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   ALA C 108 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ARG B 104 " --> pdb=" O   TYR A 105 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   ILE A 107 " --> pdb=" O   ARG B 104 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   THR B 106 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.725A  pdb=" N   ALA A 109 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   ALA B 108 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 114 through 115
      removed outlier: 6.962A  pdb=" N   TYR C 114 " --> pdb=" O   SER B 115 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   TYR B 114 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 118 through 121
      removed outlier: 5.817A  pdb=" N   THR D 118 " --> pdb=" O   THR E 119 " (cutoff:3.500A)
      removed outlier: 7.243A  pdb=" N   VAL E 121 " --> pdb=" O   THR D 118 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ALA D 120 " --> pdb=" O   VAL E 121 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   THR C 118 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   VAL D 121 " --> pdb=" O   THR C 118 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   ALA C 120 " --> pdb=" O   VAL D 121 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 13 through 16
      removed outlier: 6.433A  pdb=" N   VAL G  14 " --> pdb=" O   LYS H  15 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   VAL I  14 " --> pdb=" O   LYS J  15 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 19 through 20
      removed outlier: 6.546A  pdb=" N   ALA G  19 " --> pdb=" O   VAL F  20 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ALA I  19 " --> pdb=" O   VAL H  20 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 25 through 27
      removed outlier: 7.122A  pdb=" N   ILE G  26 " --> pdb=" O   ASN H  27 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   ILE I  26 " --> pdb=" O   ASN J  27 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 30 through 33
      removed outlier: 6.553A  pdb=" N   VAL G  30 " --> pdb=" O   HIS H  31 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   PHE H  33 " --> pdb=" O   VAL G  30 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   VAL G  32 " --> pdb=" O   PHE H  33 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   VAL I  30 " --> pdb=" O   HIS J  31 " (cutoff:3.500A)
      removed outlier: 8.063A  pdb=" N   PHE J  33 " --> pdb=" O   VAL I  30 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   VAL I  32 " --> pdb=" O   PHE J  33 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 59 through 62
      removed outlier: 6.339A  pdb=" N   THR G  59 " --> pdb=" O   THR H  60 " (cutoff:3.500A)
      removed outlier: 8.135A  pdb=" N   GLU H  62 " --> pdb=" O   THR G  59 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   GLU G  61 " --> pdb=" O   GLU H  62 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   THR I  59 " --> pdb=" O   THR J  60 " (cutoff:3.500A)
      removed outlier: 8.175A  pdb=" N   GLU J  62 " --> pdb=" O   THR I  59 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   GLU I  61 " --> pdb=" O   GLU J  62 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 65 through 66
      removed outlier: 6.133A  pdb=" N   VAL G  65 " --> pdb=" O   GLU F  66 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   VAL I  65 " --> pdb=" O   GLU H  66 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 70 through 75
      removed outlier: 6.871A  pdb=" N   THR G  75 " --> pdb=" O   ASP F  74 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   LYS G  70 " --> pdb=" O   VAL H  71 " (cutoff:3.500A)
      removed outlier: 7.986A  pdb=" N   ILE H  73 " --> pdb=" O   LYS G  70 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   GLU G  72 " --> pdb=" O   ILE H  73 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   THR H  75 " --> pdb=" O   GLU G  72 " (cutoff:3.500A)
      removed outlier: 7.621A  pdb=" N   ASP G  74 " --> pdb=" O   THR H  75 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   THR I  75 " --> pdb=" O   ASP H  74 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   LYS I  70 " --> pdb=" O   VAL J  71 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   ILE J  73 " --> pdb=" O   LYS I  70 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   GLU I  72 " --> pdb=" O   ILE J  73 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   THR J  75 " --> pdb=" O   GLU I  72 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   ASP I  74 " --> pdb=" O   THR J  75 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 78 through 80
      removed outlier: 8.000A  pdb=" N   TYR G  78 " --> pdb=" O   TRP F  79 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   LYS H  80 " --> pdb=" O   TRP G  79 " (cutoff:3.500A)
      removed outlier: 7.985A  pdb=" N   TYR I  78 " --> pdb=" O   TRP H  79 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   LYS J  80 " --> pdb=" O   TRP I  79 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'F' and resid 92 through 99
      removed outlier: 6.769A  pdb=" N   VAL G  93 " --> pdb=" O   VAL F  94 " (cutoff:3.500A)
      removed outlier: 7.931A  pdb=" N   THR F  96 " --> pdb=" O   VAL G  93 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   PHE G  95 " --> pdb=" O   THR F  96 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   ASN F  98 " --> pdb=" O   PHE G  95 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   ALA G  97 " --> pdb=" O   ASN F  98 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   VAL I  93 " --> pdb=" O   VAL H  94 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   THR H  96 " --> pdb=" O   VAL I  93 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   PHE I  95 " --> pdb=" O   THR H  96 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   ASN H  98 " --> pdb=" O   PHE I  95 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   ALA I  97 " --> pdb=" O   ASN H  98 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 103 through 110
      removed outlier: 6.964A  pdb=" N   LEU F 110 " --> pdb=" O   ALA G 109 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   ARG G 104 " --> pdb=" O   TYR H 105 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   ILE H 107 " --> pdb=" O   ARG G 104 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   THR G 106 " --> pdb=" O   ILE H 107 " (cutoff:3.500A)
      removed outlier: 7.732A  pdb=" N   ALA H 109 " --> pdb=" O   THR G 106 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   ALA G 108 " --> pdb=" O   ALA H 109 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   LEU H 110 " --> pdb=" O   ALA I 109 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   ARG I 104 " --> pdb=" O   TYR J 105 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   ILE J 107 " --> pdb=" O   ARG I 104 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   THR I 106 " --> pdb=" O   ILE J 107 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   ALA J 109 " --> pdb=" O   THR I 106 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   ALA I 108 " --> pdb=" O   ALA J 109 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'F' and resid 114 through 115
      removed outlier: 6.907A  pdb=" N   TYR G 114 " --> pdb=" O   SER H 115 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   TYR I 114 " --> pdb=" O   SER J 115 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'F' and resid 118 through 122
      removed outlier: 5.874A  pdb=" N   THR G 118 " --> pdb=" O   THR F 119 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   VAL F 121 " --> pdb=" O   THR G 118 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ALA G 120 " --> pdb=" O   VAL F 121 " (cutoff:3.500A)
      removed outlier: 5.871A  pdb=" N   THR I 118 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   VAL H 121 " --> pdb=" O   THR I 118 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ALA I 120 " --> pdb=" O   VAL H 121 " (cutoff:3.500A)

    140 hydrogen bonds defined for protein.
    420 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.00

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2199
        1.34 -     1.46: 1338
        1.46 -     1.57: 3638
        1.57 -     1.69: 0
        1.69 -     1.80: 20
  Bond restraints: 7195
  Sorted by residual:
  bond pdb=" C   SER D  85 "
       pdb=" O   SER D  85 "
    ideal  model  delta    sigma   weight residual
    1.235  1.240 -0.005 4.70e-03 4.53e+04 1.06e+00
  bond pdb=" C   SER C  85 "
       pdb=" O   SER C  85 "
    ideal  model  delta    sigma   weight residual
    1.235  1.240 -0.005 4.70e-03 4.53e+04 1.06e+00
  bond pdb=" C   SER E  85 "
       pdb=" O   SER E  85 "
    ideal  model  delta    sigma   weight residual
    1.235  1.239 -0.004 4.70e-03 4.53e+04 8.78e-01
  bond pdb=" C   SER B  85 "
       pdb=" O   SER B  85 "
    ideal  model  delta    sigma   weight residual
    1.235  1.239 -0.004 4.70e-03 4.53e+04 8.47e-01
  bond pdb=" N   GLU E  63 "
       pdb=" CA  GLU E  63 "
    ideal  model  delta    sigma   weight residual
    1.460  1.474 -0.014 1.51e-02 4.39e+03 8.09e-01
  ... (remaining 7190 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 9087
        1.06 -     2.11: 494
        2.11 -     3.17: 154
        3.17 -     4.22: 39
        4.22 -     5.28: 21
  Bond angle restraints: 9795
  Sorted by residual:
  angle pdb=" N   GLU E  62 "
        pdb=" CA  GLU E  62 "
        pdb=" C   GLU E  62 "
      ideal   model   delta    sigma   weight residual
     108.32  113.60   -5.28 1.64e+00 3.72e-01 1.04e+01
  angle pdb=" N   GLU D  62 "
        pdb=" CA  GLU D  62 "
        pdb=" C   GLU D  62 "
      ideal   model   delta    sigma   weight residual
     108.32  113.60   -5.28 1.64e+00 3.72e-01 1.03e+01
  angle pdb=" N   GLU B  62 "
        pdb=" CA  GLU B  62 "
        pdb=" C   GLU B  62 "
      ideal   model   delta    sigma   weight residual
     108.32  113.57   -5.25 1.64e+00 3.72e-01 1.02e+01
  angle pdb=" N   GLU A  62 "
        pdb=" CA  GLU A  62 "
        pdb=" C   GLU A  62 "
      ideal   model   delta    sigma   weight residual
     108.32  113.56   -5.24 1.64e+00 3.72e-01 1.02e+01
  angle pdb=" N   GLU C  62 "
        pdb=" CA  GLU C  62 "
        pdb=" C   GLU C  62 "
      ideal   model   delta    sigma   weight residual
     108.32  113.56   -5.24 1.64e+00 3.72e-01 1.02e+01
  ... (remaining 9790 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.98: 3418
        8.98 -    17.96: 472
       17.96 -    26.94: 200
       26.94 -    35.92: 115
       35.92 -    44.90: 35
  Dihedral angle restraints: 4240
    sinusoidal: 1605
      harmonic: 2635
  Sorted by residual:
  dihedral pdb=" N   GLU B  63 "
           pdb=" C   GLU B  63 "
           pdb=" CA  GLU B  63 "
           pdb=" CB  GLU B  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.29   -8.49     0      2.50e+00 1.60e-01 1.15e+01
  dihedral pdb=" N   GLU A  63 "
           pdb=" C   GLU A  63 "
           pdb=" CA  GLU A  63 "
           pdb=" CB  GLU A  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.27   -8.47     0      2.50e+00 1.60e-01 1.15e+01
  dihedral pdb=" N   GLU C  63 "
           pdb=" C   GLU C  63 "
           pdb=" CA  GLU C  63 "
           pdb=" CB  GLU C  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.24   -8.44     0      2.50e+00 1.60e-01 1.14e+01
  ... (remaining 4237 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 944
       0.060 -    0.119: 186
       0.119 -    0.179: 20
       0.179 -    0.238: 0
       0.238 -    0.298: 5
  Chirality restraints: 1155
  Sorted by residual:
  chirality pdb=" CA  GLU A  63 "
            pdb=" N   GLU A  63 "
            pdb=" C   GLU A  63 "
            pdb=" CB  GLU A  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.22e+00
  chirality pdb=" CA  GLU B  63 "
            pdb=" N   GLU B  63 "
            pdb=" C   GLU B  63 "
            pdb=" CB  GLU B  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.21e+00
  chirality pdb=" CA  GLU D  63 "
            pdb=" N   GLU D  63 "
            pdb=" C   GLU D  63 "
            pdb=" CB  GLU D  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.30 2.00e-01 2.50e+01 2.18e+00
  ... (remaining 1152 not shown)

  Planarity restraints: 1210
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  85 "   -0.036 5.00e-02 4.00e+02   5.54e-02 4.92e+00
        pdb=" N   PRO B  86 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO B  86 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B  86 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D  85 "   -0.036 5.00e-02 4.00e+02   5.54e-02 4.91e+00
        pdb=" N   PRO D  86 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO D  86 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO D  86 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  85 "   -0.036 5.00e-02 4.00e+02   5.53e-02 4.89e+00
        pdb=" N   PRO A  86 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A  86 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  86 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1207 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1361
        2.79 -     3.32: 5963
        3.32 -     3.85: 11288
        3.85 -     4.37: 12302
        4.37 -     4.90: 21582
  Nonbonded interactions: 52496
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B  74 "
            pdb=" NZ  LYS B  76 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" OD1 ASP D  74 "
            pdb=" NZ  LYS D  76 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" OD1 ASP E  74 "
            pdb=" NZ  LYS E  76 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" OD1 ASP C  74 "
            pdb=" NZ  LYS C  76 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" OD1 ASP A  74 "
            pdb=" NZ  LYS A  76 "
     model   vdw
     2.268 3.120
  ... (remaining 52491 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'A'
}
ncs_group {
  reference = chain 'I'
  selection = chain 'G'
  selection = chain 'F'
  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:             1.990
  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:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.840
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:0.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
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      :  0.003   0.044   7195  Z= 0.151
  Angle     :  0.644   5.281   9795  Z= 0.369
  Chirality :  0.054   0.298   1155
  Planarity :  0.005   0.055   1210
  Dihedral  : 12.213  44.896   2530
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.42 %
    Favored  : 87.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.91 (0.25), residues: 855
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.21 (0.19), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  21 
 TYR   0.013   0.002   TYR H  78 
 PHE   0.009   0.002   PHE H  64 
 TRP   0.004   0.001   TRP B  79 
 HIS   0.006   0.001   HIS H  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 7195)
  covalent geometry    : angle       0.64384 ( 9795)
  hydrogen bonds       : bond        0.23192 (  140)
  hydrogen bonds       : angle       7.60221 (  420)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  395 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 395
  time to evaluate  : 0.268 
Fit side-chains
REVERT: C   59 THR cc_start: 0.8698 (m) cc_final: 0.8204 (p)
REVERT: C   70 LYS cc_start: 0.9213 (ttpt) cc_final: 0.8859 (ttpt)
REVERT: C   76 LYS cc_start: 0.8508 (mppt) cc_final: 0.8179 (mptt)
REVERT: D   59 THR cc_start: 0.8648 (m) cc_final: 0.8304 (p)
REVERT: D   63 GLU cc_start: 0.8374 (pm20) cc_final: 0.7562 (pm20)
REVERT: D   70 LYS cc_start: 0.9047 (ttpt) cc_final: 0.8724 (tttp)
REVERT: D   71 VAL cc_start: 0.9418 (t) cc_final: 0.9033 (p)
REVERT: D  104 ARG cc_start: 0.8507 (ttm110) cc_final: 0.8045 (mtm-85)
REVERT: D  106 THR cc_start: 0.9499 (m) cc_final: 0.9206 (p)
REVERT: B   59 THR cc_start: 0.8796 (m) cc_final: 0.8534 (p)
REVERT: B   70 LYS cc_start: 0.9305 (ttpt) cc_final: 0.8626 (ttpt)
REVERT: B   89 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8177 (pt0)
REVERT: B  106 THR cc_start: 0.9564 (m) cc_final: 0.9205 (p)
REVERT: E   33 PHE cc_start: 0.8085 (t80) cc_final: 0.7270 (p90)
REVERT: E   70 LYS cc_start: 0.8808 (ttpt) cc_final: 0.8253 (tppt)
REVERT: E   76 LYS cc_start: 0.8028 (mppt) cc_final: 0.6977 (pttm)
REVERT: E  104 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7728 (mmp-170)
REVERT: E  119 THR cc_start: 0.9372 (m) cc_final: 0.9157 (p)
REVERT: A   62 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7770 (tt0)
REVERT: A   63 GLU cc_start: 0.8086 (pm20) cc_final: 0.7786 (pm20)
REVERT: A   70 LYS cc_start: 0.9000 (ttpt) cc_final: 0.8260 (pttm)
REVERT: I   99 ASP cc_start: 0.8536 (t0) cc_final: 0.8313 (t0)
REVERT: I  119 THR cc_start: 0.9418 (m) cc_final: 0.9075 (p)
REVERT: G   64 PHE cc_start: 0.8640 (p90) cc_final: 0.8393 (p90)
REVERT: F   70 LYS cc_start: 0.7893 (tttt) cc_final: 0.7535 (tppt)
REVERT: F   76 LYS cc_start: 0.8869 (mttp) cc_final: 0.7883 (pttm)
REVERT: F   80 LYS cc_start: 0.9054 (tttm) cc_final: 0.8421 (tppt)
REVERT: H   93 VAL cc_start: 0.9631 (t) cc_final: 0.9425 (m)
REVERT: H   99 ASP cc_start: 0.8228 (t0) cc_final: 0.7969 (t0)
REVERT: H  114 TYR cc_start: 0.9299 (p90) cc_final: 0.9082 (p90)
REVERT: J   99 ASP cc_start: 0.8522 (t0) cc_final: 0.8306 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 395
  average time/residue: 0.0801
  time to fit residues: 41.2007
Evaluate side-chains
  249 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.2980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.5982

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

Flipped N/Q/H residues before XYZ refinement:
** D  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 123 ASN
F 123 ASN
H  31 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.120468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.101399 restraints weight = 14044.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.103879 restraints weight = 5907.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.105447 restraints weight = 3589.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.106394 restraints weight = 2705.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.106730 restraints weight = 2299.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   7195  Z= 0.178
  Angle     :  0.707   7.116   9795  Z= 0.378
  Chirality :  0.051   0.153   1155
  Planarity :  0.005   0.037   1210
  Dihedral  :  5.189  16.345    965
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 19.08 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.88 (0.26), residues: 855
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.19), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG G 104 
 TYR   0.024   0.002   TYR G 114 
 PHE   0.034   0.002   PHE D  87 
 TRP   0.012   0.001   TRP E  79 
 HIS   0.005   0.001   HIS F  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 7195)
  covalent geometry    : angle       0.70653 ( 9795)
  hydrogen bonds       : bond        0.03478 (  140)
  hydrogen bonds       : angle       5.65815 (  420)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 275
  time to evaluate  : 0.182 
Fit side-chains
REVERT: C   13 MET cc_start: 0.7685 (ptm) cc_final: 0.7402 (ptm)
REVERT: C   61 GLU cc_start: 0.8241 (mp0) cc_final: 0.7974 (mp0)
REVERT: C   63 GLU cc_start: 0.8085 (pt0) cc_final: 0.7089 (pt0)
REVERT: C   70 LYS cc_start: 0.8979 (ttpt) cc_final: 0.8464 (ttpt)
REVERT: C   72 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7161 (mt-10)
REVERT: C   76 LYS cc_start: 0.8528 (mppt) cc_final: 0.7963 (mptt)
REVERT: C  119 THR cc_start: 0.9439 (m) cc_final: 0.8860 (p)
REVERT: D   15 LYS cc_start: 0.8311 (ttmt) cc_final: 0.8056 (mttm)
REVERT: D   23 SER cc_start: 0.8855 (p) cc_final: 0.8637 (p)
REVERT: D   63 GLU cc_start: 0.8019 (pm20) cc_final: 0.7798 (pm20)
REVERT: D   70 LYS cc_start: 0.8843 (ttpt) cc_final: 0.8461 (tttp)
REVERT: D   76 LYS cc_start: 0.8484 (mppt) cc_final: 0.8214 (mmtm)
REVERT: D  104 ARG cc_start: 0.8474 (ttm110) cc_final: 0.7842 (mtm-85)
REVERT: D  106 THR cc_start: 0.9576 (m) cc_final: 0.9211 (p)
REVERT: B   61 GLU cc_start: 0.8141 (mp0) cc_final: 0.7881 (mp0)
REVERT: B   63 GLU cc_start: 0.8280 (pm20) cc_final: 0.7832 (pt0)
REVERT: B   70 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8762 (ttpt)
REVERT: B   72 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8008 (mm-30)
REVERT: B   82 LEU cc_start: 0.9136 (mt) cc_final: 0.8924 (mt)
REVERT: B  106 THR cc_start: 0.9537 (m) cc_final: 0.9106 (p)
REVERT: B  119 THR cc_start: 0.9392 (m) cc_final: 0.9021 (p)
REVERT: E   15 LYS cc_start: 0.6664 (pptt) cc_final: 0.6420 (pptt)
REVERT: E   76 LYS cc_start: 0.8091 (mppt) cc_final: 0.7103 (pttm)
REVERT: E   82 LEU cc_start: 0.9242 (mt) cc_final: 0.8920 (mt)
REVERT: E  104 ARG cc_start: 0.8054 (ttm110) cc_final: 0.7340 (mmp-170)
REVERT: E  119 THR cc_start: 0.9521 (m) cc_final: 0.9074 (p)
REVERT: A   63 GLU cc_start: 0.8126 (pm20) cc_final: 0.7866 (pm20)
REVERT: A   70 LYS cc_start: 0.8849 (ttpt) cc_final: 0.7950 (pttm)
REVERT: A  119 THR cc_start: 0.8998 (m) cc_final: 0.8773 (p)
REVERT: I   63 GLU cc_start: 0.5886 (tm-30) cc_final: 0.5576 (tm-30)
REVERT: I   99 ASP cc_start: 0.8403 (t0) cc_final: 0.8189 (t0)
REVERT: I  119 THR cc_start: 0.9554 (m) cc_final: 0.8880 (p)
REVERT: G   63 GLU cc_start: 0.8605 (tt0) cc_final: 0.8080 (tm-30)
REVERT: G  112 SER cc_start: 0.9286 (m) cc_final: 0.8754 (p)
REVERT: F   70 LYS cc_start: 0.7974 (tttt) cc_final: 0.7224 (tppt)
REVERT: F   76 LYS cc_start: 0.8874 (mttp) cc_final: 0.7988 (pttm)
REVERT: F   80 LYS cc_start: 0.9151 (tttm) cc_final: 0.8443 (tppt)
REVERT: H   13 MET cc_start: 0.8398 (ttm) cc_final: 0.7781 (tpp)
REVERT: H  114 TYR cc_start: 0.9232 (p90) cc_final: 0.9000 (p90)
REVERT: H  119 THR cc_start: 0.9719 (m) cc_final: 0.9217 (p)
REVERT: J  119 THR cc_start: 0.9191 (m) cc_final: 0.8924 (p)
  outliers start: 23
  outliers final: 10
  residues processed: 285
  average time/residue: 0.0657
  time to fit residues: 25.2838
Evaluate side-chains
  269 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 259
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain E residue   26 ILE
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain I residue   26 ILE
Chi-restraints excluded: chain F residue   18 ASP
Chi-restraints excluded: chain J residue  117 SER
Chi-restraints excluded: chain J residue  122 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 64 optimal weight:    7.9990
   chunk 13 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9990
   chunk 25 optimal weight:    0.2980
   chunk 44 optimal weight:   10.0000
   chunk 77 optimal weight:    0.0870
   chunk 40 optimal weight:    6.9990
   chunk 43 optimal weight:    0.7980
   chunk 79 optimal weight:   10.0000
   chunk 3 optimal weight:    0.0670
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
D  31 HIS
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 123 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.125039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.105401 restraints weight = 13793.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.107957 restraints weight = 5916.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.109565 restraints weight = 3602.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.110583 restraints weight = 2709.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.110868 restraints weight = 2290.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.4180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7195  Z= 0.123
  Angle     :  0.637   6.255   9795  Z= 0.341
  Chirality :  0.049   0.158   1155
  Planarity :  0.004   0.028   1210
  Dihedral  :  4.966  15.585    965
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 20.39 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.96 (0.26), residues: 855
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.20), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I 103 
 TYR   0.018   0.001   TYR G 114 
 PHE   0.025   0.002   PHE D  87 
 TRP   0.005   0.001   TRP E  79 
 HIS   0.006   0.001   HIS F  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7195)
  covalent geometry    : angle       0.63708 ( 9795)
  hydrogen bonds       : bond        0.03159 (  140)
  hydrogen bonds       : angle       5.35225 (  420)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 283
  time to evaluate  : 0.275 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8269 (mp0) cc_final: 0.7833 (mp0)
REVERT: C   70 LYS cc_start: 0.8926 (ttpt) cc_final: 0.8381 (ttpt)
REVERT: C   72 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7416 (mt-10)
REVERT: C   76 LYS cc_start: 0.8546 (mppt) cc_final: 0.8064 (mptt)
REVERT: C  112 SER cc_start: 0.9061 (m) cc_final: 0.8495 (p)
REVERT: C  119 THR cc_start: 0.9541 (m) cc_final: 0.8949 (p)
REVERT: D   15 LYS cc_start: 0.8306 (ttmt) cc_final: 0.7968 (ttmm)
REVERT: D   62 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7382 (mm-30)
REVERT: D   63 GLU cc_start: 0.8191 (pm20) cc_final: 0.7991 (pm20)
REVERT: D   70 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8488 (tttp)
REVERT: D   76 LYS cc_start: 0.8574 (mppt) cc_final: 0.8297 (mppt)
REVERT: D  104 ARG cc_start: 0.8416 (ttm110) cc_final: 0.7814 (mtm-85)
REVERT: D  106 THR cc_start: 0.9555 (m) cc_final: 0.9178 (p)
REVERT: B   61 GLU cc_start: 0.8274 (mp0) cc_final: 0.7359 (mp0)
REVERT: B   70 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8688 (ttpt)
REVERT: B   71 VAL cc_start: 0.9682 (t) cc_final: 0.9407 (p)
REVERT: B   72 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7890 (mm-30)
REVERT: B  106 THR cc_start: 0.9507 (m) cc_final: 0.9223 (p)
REVERT: B  119 THR cc_start: 0.9387 (m) cc_final: 0.9063 (p)
REVERT: E   15 LYS cc_start: 0.6606 (pptt) cc_final: 0.6401 (pptt)
REVERT: E   33 PHE cc_start: 0.8378 (t80) cc_final: 0.7563 (p90)
REVERT: E   66 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8389 (tm-30)
REVERT: E   76 LYS cc_start: 0.8198 (mppt) cc_final: 0.7703 (pttm)
REVERT: E   78 TYR cc_start: 0.7048 (m-10) cc_final: 0.4746 (p90)
REVERT: E  104 ARG cc_start: 0.7981 (ttm110) cc_final: 0.7314 (mmp-170)
REVERT: E  119 THR cc_start: 0.9401 (m) cc_final: 0.9094 (p)
REVERT: A   70 LYS cc_start: 0.8785 (ttpt) cc_final: 0.7818 (pttm)
REVERT: I   99 ASP cc_start: 0.8333 (t0) cc_final: 0.8132 (t0)
REVERT: I  119 THR cc_start: 0.9558 (m) cc_final: 0.8903 (p)
REVERT: G   63 GLU cc_start: 0.8538 (tt0) cc_final: 0.8116 (tm-30)
REVERT: G  112 SER cc_start: 0.9185 (m) cc_final: 0.8649 (p)
REVERT: G  119 THR cc_start: 0.9601 (m) cc_final: 0.9108 (p)
REVERT: F   13 MET cc_start: 0.6728 (ttt) cc_final: 0.6169 (ttp)
REVERT: F   70 LYS cc_start: 0.7982 (tttt) cc_final: 0.7172 (tppt)
REVERT: F   76 LYS cc_start: 0.8928 (mttp) cc_final: 0.8027 (pttm)
REVERT: F   80 LYS cc_start: 0.9162 (tttm) cc_final: 0.8439 (tppt)
REVERT: F  119 THR cc_start: 0.9280 (m) cc_final: 0.8895 (p)
REVERT: H   13 MET cc_start: 0.8311 (ttm) cc_final: 0.8056 (tpp)
REVERT: H   70 LYS cc_start: 0.8766 (ttpp) cc_final: 0.8484 (ttpp)
REVERT: H   93 VAL cc_start: 0.9579 (t) cc_final: 0.9104 (m)
REVERT: H   99 ASP cc_start: 0.8446 (t0) cc_final: 0.8092 (t0)
REVERT: H  114 TYR cc_start: 0.9272 (p90) cc_final: 0.9013 (p90)
REVERT: H  119 THR cc_start: 0.9709 (m) cc_final: 0.9189 (p)
REVERT: J  119 THR cc_start: 0.9189 (m) cc_final: 0.8934 (p)
  outliers start: 19
  outliers final: 9
  residues processed: 291
  average time/residue: 0.0638
  time to fit residues: 25.2064
Evaluate side-chains
  265 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 256
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   26 ILE
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain I residue   26 ILE
Chi-restraints excluded: chain I residue  115 SER
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain F residue   16 VAL
Chi-restraints excluded: chain F residue   18 ASP
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain J residue  122 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 41 optimal weight:    0.0970
   chunk 26 optimal weight:    5.9990
   chunk 68 optimal weight:    0.8980
   chunk 48 optimal weight:    8.9990
   chunk 42 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 54 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 64 optimal weight:    6.9990
   overall best weight:    2.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  31 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.118025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.099399 restraints weight = 14977.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.101763 restraints weight = 6341.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.103323 restraints weight = 3861.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.103948 restraints weight = 2898.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.104629 restraints weight = 2546.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.4628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.074   7195  Z= 0.239
  Angle     :  0.694   6.726   9795  Z= 0.372
  Chirality :  0.050   0.173   1155
  Planarity :  0.004   0.034   1210
  Dihedral  :  5.142  17.786    965
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.36 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 20.92 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.11 (0.25), residues: 855
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.36 (0.19), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG G 104 
 TYR   0.017   0.002   TYR F 105 
 PHE   0.029   0.002   PHE D  87 
 TRP   0.006   0.001   TRP G  79 
 HIS   0.004   0.001   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00575 ( 7195)
  covalent geometry    : angle       0.69421 ( 9795)
  hydrogen bonds       : bond        0.03617 (  140)
  hydrogen bonds       : angle       5.38590 (  420)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 253
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: C   61 GLU cc_start: 0.8108 (mp0) cc_final: 0.7596 (mp0)
REVERT: C   62 GLU cc_start: 0.7562 (tp30) cc_final: 0.5961 (tp30)
REVERT: C   70 LYS cc_start: 0.8956 (ttpt) cc_final: 0.8408 (ttpt)
REVERT: C   72 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7303 (mt-10)
REVERT: C  112 SER cc_start: 0.9126 (m) cc_final: 0.8538 (p)
REVERT: C  119 THR cc_start: 0.9624 (m) cc_final: 0.9038 (p)
REVERT: D   15 LYS cc_start: 0.8410 (ttmt) cc_final: 0.8134 (ttmm)
REVERT: D   61 GLU cc_start: 0.7962 (mp0) cc_final: 0.7602 (mp0)
REVERT: D   63 GLU cc_start: 0.8181 (pm20) cc_final: 0.7561 (pm20)
REVERT: D   70 LYS cc_start: 0.8742 (ttpt) cc_final: 0.8425 (tttp)
REVERT: D  106 THR cc_start: 0.9537 (m) cc_final: 0.9150 (p)
REVERT: B   61 GLU cc_start: 0.8328 (mp0) cc_final: 0.7319 (mp0)
REVERT: B   62 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7230 (tm-30)
REVERT: B   70 LYS cc_start: 0.9004 (ttpt) cc_final: 0.8776 (ttpt)
REVERT: B   72 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7956 (mm-30)
REVERT: B  106 THR cc_start: 0.9566 (m) cc_final: 0.9189 (p)
REVERT: B  119 THR cc_start: 0.9495 (m) cc_final: 0.9187 (p)
REVERT: E   33 PHE cc_start: 0.8465 (t80) cc_final: 0.7500 (p90)
REVERT: E   76 LYS cc_start: 0.8350 (mppt) cc_final: 0.7008 (pttm)
REVERT: E   78 TYR cc_start: 0.6933 (m-10) cc_final: 0.4522 (p90)
REVERT: E  104 ARG cc_start: 0.8050 (ttm110) cc_final: 0.7310 (mmp-170)
REVERT: E  119 THR cc_start: 0.9493 (m) cc_final: 0.9031 (p)
REVERT: A   70 LYS cc_start: 0.8773 (ttpt) cc_final: 0.7786 (pttm)
REVERT: A  106 THR cc_start: 0.9520 (m) cc_final: 0.9125 (p)
REVERT: I   99 ASP cc_start: 0.8296 (t0) cc_final: 0.8091 (t0)
REVERT: I  119 THR cc_start: 0.9569 (m) cc_final: 0.8861 (p)
REVERT: G   27 ASN cc_start: 0.8806 (t0) cc_final: 0.7891 (t0)
REVERT: G   63 GLU cc_start: 0.8611 (tt0) cc_final: 0.8061 (tm-30)
REVERT: G  119 THR cc_start: 0.9629 (m) cc_final: 0.9094 (p)
REVERT: F   70 LYS cc_start: 0.8251 (tttt) cc_final: 0.7416 (tppt)
REVERT: F   74 ASP cc_start: 0.8615 (t0) cc_final: 0.8361 (t0)
REVERT: F   76 LYS cc_start: 0.8994 (mttp) cc_final: 0.8026 (pttm)
REVERT: F   80 LYS cc_start: 0.9277 (tttm) cc_final: 0.8480 (tppt)
REVERT: F  119 THR cc_start: 0.9312 (m) cc_final: 0.8584 (p)
REVERT: H   13 MET cc_start: 0.8448 (ttm) cc_final: 0.8178 (tpp)
REVERT: H   58 LEU cc_start: 0.5665 (mt) cc_final: 0.5394 (mt)
REVERT: H   70 LYS cc_start: 0.8955 (ttpp) cc_final: 0.8604 (ttpp)
REVERT: H   99 ASP cc_start: 0.8573 (t0) cc_final: 0.8199 (t0)
REVERT: J   89 GLU cc_start: 0.4234 (pm20) cc_final: 0.3989 (pm20)
REVERT: J  119 THR cc_start: 0.9252 (m) cc_final: 0.9026 (p)
  outliers start: 30
  outliers final: 16
  residues processed: 268
  average time/residue: 0.0663
  time to fit residues: 24.2668
Evaluate side-chains
  253 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 237
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain D residue  115 SER
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain E residue   18 ASP
Chi-restraints excluded: chain E residue   26 ILE
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain I residue  115 SER
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain F residue   18 ASP
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue   82 LEU
Chi-restraints excluded: chain F residue  117 SER
Chi-restraints excluded: chain J residue  117 SER
Chi-restraints excluded: chain J residue  122 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 63 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 47 optimal weight:    9.9990
   chunk 56 optimal weight:    0.9980
   chunk 15 optimal weight:    8.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  31 HIS
F 123 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.126718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.104768 restraints weight = 15088.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.107187 restraints weight = 6183.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.108886 restraints weight = 3778.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.109742 restraints weight = 2823.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.110414 restraints weight = 2431.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.4932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7195  Z= 0.149
  Angle     :  0.645   6.376   9795  Z= 0.341
  Chirality :  0.049   0.140   1155
  Planarity :  0.004   0.024   1210
  Dihedral  :  4.959  18.593    965
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 22.88 %
    Favored  : 73.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.12 (0.25), residues: 855
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.19), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 104 
 TYR   0.012   0.001   TYR G  78 
 PHE   0.023   0.002   PHE D  87 
 TRP   0.004   0.001   TRP I  79 
 HIS   0.007   0.001   HIS F  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 7195)
  covalent geometry    : angle       0.64546 ( 9795)
  hydrogen bonds       : bond        0.03150 (  140)
  hydrogen bonds       : angle       5.14141 (  420)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 247
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
REVERT: C   61 GLU cc_start: 0.8110 (mp0) cc_final: 0.7633 (mp0)
REVERT: C   62 GLU cc_start: 0.7626 (tp30) cc_final: 0.6089 (tp30)
REVERT: C   70 LYS cc_start: 0.8930 (ttpt) cc_final: 0.8144 (ttpt)
REVERT: C   72 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7481 (mt-10)
REVERT: C   89 GLU cc_start: 0.8582 (mp0) cc_final: 0.8361 (mp0)
REVERT: C  112 SER cc_start: 0.9104 (m) cc_final: 0.8490 (p)
REVERT: C  119 THR cc_start: 0.9625 (m) cc_final: 0.9105 (p)
REVERT: D   15 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8282 (ttmm)
REVERT: D   63 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7595 (pm20)
REVERT: D   70 LYS cc_start: 0.8724 (ttpt) cc_final: 0.8411 (tttp)
REVERT: D  106 THR cc_start: 0.9506 (m) cc_final: 0.9176 (p)
REVERT: B   13 MET cc_start: 0.8222 (ppp) cc_final: 0.7888 (ppp)
REVERT: B   61 GLU cc_start: 0.8336 (mp0) cc_final: 0.7383 (mp0)
REVERT: B   62 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7342 (tm-30)
REVERT: B   70 LYS cc_start: 0.8873 (ttpt) cc_final: 0.8522 (ttpt)
REVERT: B   72 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7940 (mm-30)
REVERT: B  106 THR cc_start: 0.9543 (m) cc_final: 0.9192 (p)
REVERT: B  119 THR cc_start: 0.9433 (m) cc_final: 0.9134 (p)
REVERT: E   33 PHE cc_start: 0.8454 (t80) cc_final: 0.7509 (p90)
REVERT: E   66 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8421 (tm-30)
REVERT: E   76 LYS cc_start: 0.8317 (mppt) cc_final: 0.7020 (pttm)
REVERT: E   78 TYR cc_start: 0.6916 (m-10) cc_final: 0.4463 (p90)
REVERT: E  104 ARG cc_start: 0.8019 (ttm110) cc_final: 0.7251 (mmp-170)
REVERT: E  119 THR cc_start: 0.9396 (m) cc_final: 0.9099 (p)
REVERT: A   62 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7842 (tt0)
REVERT: A   63 GLU cc_start: 0.7893 (pm20) cc_final: 0.7624 (pm20)
REVERT: A   70 LYS cc_start: 0.8758 (ttpt) cc_final: 0.7739 (pttm)
REVERT: A  106 THR cc_start: 0.9519 (m) cc_final: 0.9126 (p)
REVERT: I  103 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.7813 (mtm180)
REVERT: I  119 THR cc_start: 0.9553 (m) cc_final: 0.8863 (p)
REVERT: G   63 GLU cc_start: 0.8624 (tt0) cc_final: 0.8228 (tm-30)
REVERT: G   89 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8320 (tt0)
REVERT: G  119 THR cc_start: 0.9601 (m) cc_final: 0.9089 (p)
REVERT: F   12 LEU cc_start: 0.6445 (mp) cc_final: 0.6221 (mp)
REVERT: F   61 GLU cc_start: 0.7109 (mp0) cc_final: 0.6525 (mp0)
REVERT: F   70 LYS cc_start: 0.8071 (tttt) cc_final: 0.7244 (tppt)
REVERT: F   74 ASP cc_start: 0.8591 (t0) cc_final: 0.8341 (t0)
REVERT: F   76 LYS cc_start: 0.9006 (mttp) cc_final: 0.8062 (pttm)
REVERT: F   80 LYS cc_start: 0.9246 (tttm) cc_final: 0.8435 (tppt)
REVERT: F  119 THR cc_start: 0.9306 (m) cc_final: 0.8617 (p)
REVERT: H   70 LYS cc_start: 0.8920 (ttpp) cc_final: 0.8587 (ttpp)
REVERT: H   99 ASP cc_start: 0.8578 (t0) cc_final: 0.7997 (t0)
REVERT: H  105 TYR cc_start: 0.8721 (m-80) cc_final: 0.8501 (m-80)
REVERT: J   89 GLU cc_start: 0.4367 (pm20) cc_final: 0.4134 (pm20)
REVERT: J  119 THR cc_start: 0.9229 (m) cc_final: 0.9000 (p)
  outliers start: 25
  outliers final: 17
  residues processed: 258
  average time/residue: 0.0701
  time to fit residues: 24.5554
Evaluate side-chains
  259 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 240
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue  115 SER
Chi-restraints excluded: chain B residue   72 GLU
Chi-restraints excluded: chain E residue   26 ILE
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain I residue  115 SER
Chi-restraints excluded: chain I residue  122 THR
Chi-restraints excluded: chain F residue   18 ASP
Chi-restraints excluded: chain F residue   31 HIS
Chi-restraints excluded: chain F residue   82 LEU
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  117 SER
Chi-restraints excluded: chain J residue   82 LEU
Chi-restraints excluded: chain J residue  122 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 0 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0670
   chunk 65 optimal weight:    0.0020
   chunk 81 optimal weight:    6.9990
   chunk 82 optimal weight:    0.0870
   chunk 27 optimal weight:    7.9990
   chunk 67 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.4304

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

Flipped N/Q/H residues before XYZ refinement:
E  88 HIS
A  27 ASN
F 123 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.129385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.106832 restraints weight = 14833.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.109543 restraints weight = 5901.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.111340 restraints weight = 3461.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.112422 restraints weight = 2543.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.113043 restraints weight = 2134.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.5080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7195  Z= 0.118
  Angle     :  0.633   6.495   9795  Z= 0.334
  Chirality :  0.049   0.137   1155
  Planarity :  0.003   0.023   1210
  Dihedral  :  4.791  18.226    965
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 24.05 %
    Favored  : 73.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.15 (0.25), residues: 855
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.40 (0.19), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  34 
 TYR   0.017   0.001   TYR I 114 
 PHE   0.022   0.001   PHE D  87 
 TRP   0.002   0.000   TRP E  79 
 HIS   0.011   0.001   HIS F  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7195)
  covalent geometry    : angle       0.63345 ( 9795)
  hydrogen bonds       : bond        0.02846 (  140)
  hydrogen bonds       : angle       5.06822 (  420)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 257
  time to evaluate  : 0.208 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8114 (mp0) cc_final: 0.7653 (mp0)
REVERT: C   62 GLU cc_start: 0.7712 (tp30) cc_final: 0.6942 (tp30)
REVERT: C   70 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8129 (ttpt)
REVERT: C   72 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8027 (mt-10)
REVERT: C   89 GLU cc_start: 0.8559 (mp0) cc_final: 0.8282 (mp0)
REVERT: C  112 SER cc_start: 0.9123 (m) cc_final: 0.8506 (p)
REVERT: C  119 THR cc_start: 0.9629 (m) cc_final: 0.9130 (p)
REVERT: D   15 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8204 (ttmm)
REVERT: D   61 GLU cc_start: 0.7828 (mp0) cc_final: 0.7463 (mp0)
REVERT: D   63 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7615 (pm20)
REVERT: D   70 LYS cc_start: 0.8678 (ttpt) cc_final: 0.8371 (tttp)
REVERT: D  104 ARG cc_start: 0.8435 (ttm110) cc_final: 0.7620 (mtm-85)
REVERT: D  106 THR cc_start: 0.9481 (m) cc_final: 0.9162 (p)
REVERT: B   61 GLU cc_start: 0.8353 (mp0) cc_final: 0.7498 (mp0)
REVERT: B   62 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7507 (tm-30)
REVERT: B   63 GLU cc_start: 0.8480 (pt0) cc_final: 0.7220 (pt0)
REVERT: B   70 LYS cc_start: 0.8839 (ttpt) cc_final: 0.8346 (ttpt)
REVERT: B   72 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7901 (mt-10)
REVERT: B  106 THR cc_start: 0.9514 (m) cc_final: 0.9208 (p)
REVERT: B  119 THR cc_start: 0.9429 (m) cc_final: 0.9154 (p)
REVERT: E   33 PHE cc_start: 0.8448 (t80) cc_final: 0.7462 (p90)
REVERT: E   76 LYS cc_start: 0.8289 (mppt) cc_final: 0.6991 (pttm)
REVERT: E   78 TYR cc_start: 0.6703 (m-10) cc_final: 0.4428 (p90)
REVERT: E  104 ARG cc_start: 0.8031 (ttm110) cc_final: 0.7200 (mmp-170)
REVERT: E  119 THR cc_start: 0.9397 (m) cc_final: 0.9130 (p)
REVERT: A   62 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7781 (tt0)
REVERT: A   63 GLU cc_start: 0.7955 (pm20) cc_final: 0.7638 (pm20)
REVERT: A   70 LYS cc_start: 0.8731 (ttpt) cc_final: 0.7714 (pttm)
REVERT: A  106 THR cc_start: 0.9444 (m) cc_final: 0.9094 (p)
REVERT: I   13 MET cc_start: 0.7157 (tpp) cc_final: 0.6666 (tpp)
REVERT: I  119 THR cc_start: 0.9521 (m) cc_final: 0.8842 (p)
REVERT: G   63 GLU cc_start: 0.8574 (tt0) cc_final: 0.8062 (tm-30)
REVERT: G  119 THR cc_start: 0.9589 (m) cc_final: 0.9091 (p)
REVERT: F   12 LEU cc_start: 0.6431 (mp) cc_final: 0.6202 (mp)
REVERT: F   61 GLU cc_start: 0.7037 (mp0) cc_final: 0.6435 (mp0)
REVERT: F   70 LYS cc_start: 0.8101 (tttt) cc_final: 0.7334 (tppt)
REVERT: F   74 ASP cc_start: 0.8564 (t0) cc_final: 0.8342 (t0)
REVERT: F   76 LYS cc_start: 0.9033 (mttp) cc_final: 0.8068 (pttm)
REVERT: F  119 THR cc_start: 0.9314 (m) cc_final: 0.8654 (p)
REVERT: H   70 LYS cc_start: 0.8905 (ttpp) cc_final: 0.8583 (ttpp)
REVERT: H   99 ASP cc_start: 0.8571 (t0) cc_final: 0.8220 (t0)
REVERT: H  105 TYR cc_start: 0.8686 (m-80) cc_final: 0.8467 (m-80)
REVERT: J   89 GLU cc_start: 0.4266 (pm20) cc_final: 0.4044 (pm20)
REVERT: J   92 GLU cc_start: 0.5200 (pm20) cc_final: 0.4950 (pm20)
REVERT: J  119 THR cc_start: 0.9221 (m) cc_final: 0.8987 (p)
  outliers start: 18
  outliers final: 11
  residues processed: 267
  average time/residue: 0.0768
  time to fit residues: 27.4910
Evaluate side-chains
  249 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 236
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue  115 SER
Chi-restraints excluded: chain B residue   72 GLU
Chi-restraints excluded: chain E residue   26 ILE
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain A residue   13 MET
Chi-restraints excluded: chain I residue  115 SER
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain F residue   82 LEU
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  117 SER
Chi-restraints excluded: chain J residue  122 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 28 optimal weight:    0.7980
   chunk 50 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 47 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 59 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
G  88 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.118058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.099022 restraints weight = 14944.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.101435 restraints weight = 6268.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.102798 restraints weight = 3785.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.103829 restraints weight = 2910.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.104350 restraints weight = 2454.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.5261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   7195  Z= 0.261
  Angle     :  0.716   6.171   9795  Z= 0.377
  Chirality :  0.049   0.134   1155
  Planarity :  0.004   0.028   1210
  Dihedral  :  5.042  16.318    965
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 22.75 %
    Favored  : 73.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.23 (0.25), residues: 855
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.19), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG I 103 
 TYR   0.018   0.002   TYR C 116 
 PHE   0.025   0.002   PHE D  87 
 TRP   0.011   0.001   TRP G  79 
 HIS   0.004   0.001   HIS E  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00623 ( 7195)
  covalent geometry    : angle       0.71621 ( 9795)
  hydrogen bonds       : bond        0.03487 (  140)
  hydrogen bonds       : angle       5.24295 (  420)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 225
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: C   15 LYS cc_start: 0.8705 (mttt) cc_final: 0.8480 (mttp)
REVERT: C   61 GLU cc_start: 0.8111 (mp0) cc_final: 0.7599 (mp0)
REVERT: C   62 GLU cc_start: 0.7779 (tp30) cc_final: 0.6631 (tp30)
REVERT: C   70 LYS cc_start: 0.8962 (ttpt) cc_final: 0.7989 (ttpt)
REVERT: C   72 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8066 (mt-10)
REVERT: C   89 GLU cc_start: 0.8477 (mp0) cc_final: 0.8235 (mp0)
REVERT: C  119 THR cc_start: 0.9651 (m) cc_final: 0.9149 (p)
REVERT: D   15 LYS cc_start: 0.8730 (ttmt) cc_final: 0.8288 (ttmm)
REVERT: D   61 GLU cc_start: 0.7965 (mp0) cc_final: 0.7608 (mp0)
REVERT: D   63 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7648 (pm20)
REVERT: D   70 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8480 (tttp)
REVERT: D  106 THR cc_start: 0.9497 (m) cc_final: 0.9113 (p)
REVERT: B   61 GLU cc_start: 0.8425 (mp0) cc_final: 0.7708 (mp0)
REVERT: B   62 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7460 (tm-30)
REVERT: B   70 LYS cc_start: 0.8955 (ttpt) cc_final: 0.8514 (ttpt)
REVERT: B   72 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7885 (mt-10)
REVERT: B  106 THR cc_start: 0.9546 (m) cc_final: 0.9178 (p)
REVERT: B  119 THR cc_start: 0.9503 (m) cc_final: 0.9206 (p)
REVERT: E   33 PHE cc_start: 0.8439 (t80) cc_final: 0.7373 (p90)
REVERT: E   66 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8370 (tm-30)
REVERT: E   76 LYS cc_start: 0.8429 (mppt) cc_final: 0.7045 (pttm)
REVERT: E  119 THR cc_start: 0.9481 (m) cc_final: 0.9096 (p)
REVERT: A   34 ARG cc_start: 0.7283 (ttt90) cc_final: 0.6561 (ppt170)
REVERT: A   62 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7710 (tt0)
REVERT: A   70 LYS cc_start: 0.8804 (ttpt) cc_final: 0.7785 (pttm)
REVERT: A  106 THR cc_start: 0.9525 (m) cc_final: 0.9134 (p)
REVERT: I   13 MET cc_start: 0.7240 (tpp) cc_final: 0.6663 (tpp)
REVERT: I   92 GLU cc_start: 0.7594 (mp0) cc_final: 0.7270 (mp0)
REVERT: I  119 THR cc_start: 0.9564 (m) cc_final: 0.8920 (p)
REVERT: G   27 ASN cc_start: 0.8823 (t0) cc_final: 0.8117 (t0)
REVERT: G   63 GLU cc_start: 0.8578 (tt0) cc_final: 0.8016 (tm-30)
REVERT: G  119 THR cc_start: 0.9616 (m) cc_final: 0.9065 (p)
REVERT: F   12 LEU cc_start: 0.6437 (mp) cc_final: 0.6214 (mp)
REVERT: F   27 ASN cc_start: 0.8453 (t0) cc_final: 0.8167 (t0)
REVERT: F   61 GLU cc_start: 0.6972 (mp0) cc_final: 0.6408 (mp0)
REVERT: F   70 LYS cc_start: 0.8283 (tttt) cc_final: 0.7462 (tppt)
REVERT: F   76 LYS cc_start: 0.9053 (mttp) cc_final: 0.8157 (pttm)
REVERT: F  119 THR cc_start: 0.9330 (m) cc_final: 0.8628 (p)
REVERT: H   70 LYS cc_start: 0.9049 (ttpp) cc_final: 0.8720 (ttpp)
REVERT: H   99 ASP cc_start: 0.8620 (t0) cc_final: 0.8221 (t0)
REVERT: J   26 ILE cc_start: 0.9137 (mm) cc_final: 0.8650 (pt)
REVERT: J   73 ILE cc_start: 0.8405 (mt) cc_final: 0.8088 (tt)
REVERT: J  119 THR cc_start: 0.9260 (m) cc_final: 0.9012 (p)
  outliers start: 26
  outliers final: 17
  residues processed: 237
  average time/residue: 0.0704
  time to fit residues: 22.7316
Evaluate side-chains
  237 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 218
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue  115 SER
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue   72 GLU
Chi-restraints excluded: chain E residue   18 ASP
Chi-restraints excluded: chain E residue   26 ILE
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain A residue   13 MET
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain I residue  115 SER
Chi-restraints excluded: chain I residue  117 SER
Chi-restraints excluded: chain I residue  122 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain F residue   82 LEU
Chi-restraints excluded: chain F residue  117 SER
Chi-restraints excluded: chain J residue  122 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0070
   chunk 50 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.6006

-------------------------------------------------------------------------------
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 = 0.4086 r_free = 0.4086 target = 0.127227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.104685 restraints weight = 14954.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.107252 restraints weight = 5896.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.108986 restraints weight = 3481.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.109990 restraints weight = 2567.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.110474 restraints weight = 2170.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.5404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7195  Z= 0.160
  Angle     :  0.681   9.107   9795  Z= 0.357
  Chirality :  0.049   0.172   1155
  Planarity :  0.004   0.036   1210
  Dihedral  :  4.919  16.867    965
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 24.58 %
    Favored  : 73.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.21 (0.25), residues: 855
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.44 (0.19), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I 103 
 TYR   0.016   0.002   TYR I 114 
 PHE   0.023   0.002   PHE D  87 
 TRP   0.004   0.001   TRP B  79 
 HIS   0.005   0.001   HIS F  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 7195)
  covalent geometry    : angle       0.68082 ( 9795)
  hydrogen bonds       : bond        0.02918 (  140)
  hydrogen bonds       : angle       5.11027 (  420)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 232
  time to evaluate  : 0.287 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8009 (mp0) cc_final: 0.7521 (mp0)
REVERT: C   62 GLU cc_start: 0.7794 (tp30) cc_final: 0.7046 (tp30)
REVERT: C   63 GLU cc_start: 0.8152 (pt0) cc_final: 0.7496 (pt0)
REVERT: C   70 LYS cc_start: 0.8935 (ttpt) cc_final: 0.7930 (ttpt)
REVERT: C   72 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8132 (mt-10)
REVERT: C   89 GLU cc_start: 0.8485 (mp0) cc_final: 0.8240 (mp0)
REVERT: C  119 THR cc_start: 0.9636 (m) cc_final: 0.9120 (p)
REVERT: D   15 LYS cc_start: 0.8775 (ttmt) cc_final: 0.8371 (ttmm)
REVERT: D   61 GLU cc_start: 0.7920 (mp0) cc_final: 0.7578 (mp0)
REVERT: D   63 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7604 (pm20)
REVERT: D   70 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8371 (tttp)
REVERT: D   89 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7802 (mp0)
REVERT: D  106 THR cc_start: 0.9483 (m) cc_final: 0.9132 (p)
REVERT: B   61 GLU cc_start: 0.8407 (mp0) cc_final: 0.7683 (mp0)
REVERT: B   62 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7533 (tm-30)
REVERT: B   63 GLU cc_start: 0.8537 (pt0) cc_final: 0.7305 (pt0)
REVERT: B   70 LYS cc_start: 0.8935 (ttpt) cc_final: 0.8553 (ttpt)
REVERT: B   72 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7950 (mt-10)
REVERT: B  106 THR cc_start: 0.9527 (m) cc_final: 0.9186 (p)
REVERT: B  119 THR cc_start: 0.9489 (m) cc_final: 0.9214 (p)
REVERT: E   33 PHE cc_start: 0.8478 (t80) cc_final: 0.7501 (p90)
REVERT: E   66 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8408 (tm-30)
REVERT: E   76 LYS cc_start: 0.8401 (mppt) cc_final: 0.7060 (pttm)
REVERT: E   80 LYS cc_start: 0.8956 (tttt) cc_final: 0.8702 (tttm)
REVERT: E  119 THR cc_start: 0.9400 (m) cc_final: 0.9103 (p)
REVERT: A   34 ARG cc_start: 0.7309 (ttt90) cc_final: 0.6532 (ppt170)
REVERT: A   70 LYS cc_start: 0.8861 (ttpt) cc_final: 0.7768 (pttm)
REVERT: A  106 THR cc_start: 0.9527 (m) cc_final: 0.9153 (p)
REVERT: I   92 GLU cc_start: 0.7588 (mp0) cc_final: 0.7355 (mp0)
REVERT: I  119 THR cc_start: 0.9532 (m) cc_final: 0.8894 (p)
REVERT: G   63 GLU cc_start: 0.8577 (tt0) cc_final: 0.8038 (tm-30)
REVERT: G  119 THR cc_start: 0.9580 (m) cc_final: 0.9027 (p)
REVERT: F   61 GLU cc_start: 0.6877 (mp0) cc_final: 0.6390 (mp0)
REVERT: F   70 LYS cc_start: 0.8253 (tttt) cc_final: 0.7450 (tppt)
REVERT: F   74 ASP cc_start: 0.8694 (t0) cc_final: 0.8438 (t0)
REVERT: F   76 LYS cc_start: 0.9061 (mttp) cc_final: 0.8151 (pttm)
REVERT: F  119 THR cc_start: 0.9289 (m) cc_final: 0.8599 (p)
REVERT: H   70 LYS cc_start: 0.8991 (ttpp) cc_final: 0.8648 (ttpp)
REVERT: H   99 ASP cc_start: 0.8611 (t0) cc_final: 0.8219 (t0)
REVERT: J   26 ILE cc_start: 0.9139 (mm) cc_final: 0.8628 (pt)
REVERT: J   73 ILE cc_start: 0.8404 (mt) cc_final: 0.8090 (tt)
REVERT: J  119 THR cc_start: 0.9244 (m) cc_final: 0.9013 (p)
  outliers start: 18
  outliers final: 14
  residues processed: 241
  average time/residue: 0.0634
  time to fit residues: 21.0257
Evaluate side-chains
  244 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 228
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue  115 SER
Chi-restraints excluded: chain B residue   72 GLU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain A residue   13 MET
Chi-restraints excluded: chain I residue  115 SER
Chi-restraints excluded: chain I residue  122 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain F residue   82 LEU
Chi-restraints excluded: chain F residue  117 SER
Chi-restraints excluded: chain J residue   82 LEU
Chi-restraints excluded: chain J residue  107 ILE
Chi-restraints excluded: chain J residue  122 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 82 optimal weight:    6.9990
   chunk 29 optimal weight:    8.9990
   chunk 48 optimal weight:    6.9990
   chunk 5 optimal weight:    0.1980
   chunk 11 optimal weight:    7.9990
   chunk 52 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    1.8388

-------------------------------------------------------------------------------
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 = 0.4081 r_free = 0.4081 target = 0.128132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.105068 restraints weight = 15161.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.107590 restraints weight = 5945.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.109293 restraints weight = 3502.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.110265 restraints weight = 2592.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.110450 restraints weight = 2190.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.5561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7195  Z= 0.175
  Angle     :  0.684   6.774   9795  Z= 0.358
  Chirality :  0.049   0.133   1155
  Planarity :  0.004   0.025   1210
  Dihedral  :  4.917  16.336    965
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 25.88 %
    Favored  : 71.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.23 (0.25), residues: 855
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.19), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I 103 
 TYR   0.016   0.002   TYR I 114 
 PHE   0.022   0.002   PHE D  87 
 TRP   0.011   0.001   TRP D  79 
 HIS   0.005   0.001   HIS F  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 7195)
  covalent geometry    : angle       0.68415 ( 9795)
  hydrogen bonds       : bond        0.02988 (  140)
  hydrogen bonds       : angle       5.11524 (  420)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 229
  time to evaluate  : 0.271 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.7977 (mp0) cc_final: 0.7511 (mp0)
REVERT: C   62 GLU cc_start: 0.7787 (tp30) cc_final: 0.7061 (tp30)
REVERT: C   63 GLU cc_start: 0.8157 (pt0) cc_final: 0.7500 (pt0)
REVERT: C   70 LYS cc_start: 0.8922 (ttpt) cc_final: 0.7932 (ttpt)
REVERT: C   72 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8122 (mt-10)
REVERT: C   89 GLU cc_start: 0.8532 (mp0) cc_final: 0.8209 (mp0)
REVERT: C  119 THR cc_start: 0.9620 (m) cc_final: 0.9115 (p)
REVERT: D   15 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8400 (ttmm)
REVERT: D   61 GLU cc_start: 0.7925 (mp0) cc_final: 0.7565 (mp0)
REVERT: D   63 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7635 (pm20)
REVERT: D   70 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8392 (tttp)
REVERT: D  106 THR cc_start: 0.9480 (m) cc_final: 0.9132 (p)
REVERT: B   61 GLU cc_start: 0.8399 (mp0) cc_final: 0.7700 (mp0)
REVERT: B   62 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7535 (tm-30)
REVERT: B   63 GLU cc_start: 0.8587 (pt0) cc_final: 0.7136 (pt0)
REVERT: B   70 LYS cc_start: 0.8950 (ttpt) cc_final: 0.8579 (ttpt)
REVERT: B   72 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7896 (mt-10)
REVERT: B  106 THR cc_start: 0.9520 (m) cc_final: 0.9190 (p)
REVERT: B  119 THR cc_start: 0.9495 (m) cc_final: 0.9223 (p)
REVERT: E   33 PHE cc_start: 0.8449 (t80) cc_final: 0.7501 (p90)
REVERT: E   66 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8411 (tm-30)
REVERT: E   76 LYS cc_start: 0.8417 (mppt) cc_final: 0.7016 (pttm)
REVERT: E   80 LYS cc_start: 0.8939 (tttt) cc_final: 0.8700 (tttm)
REVERT: E  119 THR cc_start: 0.9418 (m) cc_final: 0.9109 (p)
REVERT: A   34 ARG cc_start: 0.7299 (ttt90) cc_final: 0.6612 (ppt170)
REVERT: A   70 LYS cc_start: 0.8867 (ttpt) cc_final: 0.7765 (pttm)
REVERT: A  106 THR cc_start: 0.9534 (m) cc_final: 0.9161 (p)
REVERT: I   13 MET cc_start: 0.7148 (tpp) cc_final: 0.6650 (tpt)
REVERT: I  119 THR cc_start: 0.9542 (m) cc_final: 0.8930 (p)
REVERT: G   63 GLU cc_start: 0.8527 (tt0) cc_final: 0.7542 (tm-30)
REVERT: F   61 GLU cc_start: 0.6919 (mp0) cc_final: 0.6472 (mp0)
REVERT: F   70 LYS cc_start: 0.8272 (tttt) cc_final: 0.7484 (tppt)
REVERT: F   76 LYS cc_start: 0.9059 (mttp) cc_final: 0.8138 (pttm)
REVERT: F  119 THR cc_start: 0.9306 (m) cc_final: 0.8665 (p)
REVERT: H   70 LYS cc_start: 0.9003 (ttpp) cc_final: 0.8660 (ttpp)
REVERT: H   99 ASP cc_start: 0.8638 (t0) cc_final: 0.8243 (t0)
REVERT: J   26 ILE cc_start: 0.9114 (mm) cc_final: 0.8608 (pt)
REVERT: J   73 ILE cc_start: 0.8468 (mt) cc_final: 0.8171 (tt)
REVERT: J  119 THR cc_start: 0.9250 (m) cc_final: 0.9003 (p)
  outliers start: 18
  outliers final: 15
  residues processed: 239
  average time/residue: 0.0627
  time to fit residues: 20.5592
Evaluate side-chains
  240 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 223
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue  115 SER
Chi-restraints excluded: chain B residue   72 GLU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain E residue   18 ASP
Chi-restraints excluded: chain E residue   26 ILE
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain A residue   13 MET
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain I residue  115 SER
Chi-restraints excluded: chain I residue  122 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain F residue   82 LEU
Chi-restraints excluded: chain F residue  117 SER
Chi-restraints excluded: chain J residue   82 LEU
Chi-restraints excluded: chain J residue  122 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 49 optimal weight:    9.9990
   chunk 43 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    1.3588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.128705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.105734 restraints weight = 14909.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.108409 restraints weight = 5935.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.110145 restraints weight = 3479.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.111026 restraints weight = 2567.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.111693 restraints weight = 2194.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.5620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7195  Z= 0.155
  Angle     :  0.702   9.785   9795  Z= 0.367
  Chirality :  0.049   0.165   1155
  Planarity :  0.004   0.024   1210
  Dihedral  :  4.897  16.711    965
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 24.84 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.21 (0.25), residues: 855
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.44 (0.19), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I 103 
 TYR   0.016   0.001   TYR I 114 
 PHE   0.022   0.002   PHE D  87 
 TRP   0.007   0.001   TRP D  79 
 HIS   0.005   0.001   HIS F  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 7195)
  covalent geometry    : angle       0.70195 ( 9795)
  hydrogen bonds       : bond        0.02862 (  140)
  hydrogen bonds       : angle       5.10162 (  420)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 232
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
REVERT: C   61 GLU cc_start: 0.8012 (mp0) cc_final: 0.7585 (mp0)
REVERT: C   62 GLU cc_start: 0.7780 (tp30) cc_final: 0.6656 (tp30)
REVERT: C   63 GLU cc_start: 0.8204 (pt0) cc_final: 0.7438 (pt0)
REVERT: C   70 LYS cc_start: 0.8911 (ttpt) cc_final: 0.7947 (ttpt)
REVERT: C   72 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8140 (mt-10)
REVERT: C   89 GLU cc_start: 0.8493 (mp0) cc_final: 0.8225 (mp0)
REVERT: C  119 THR cc_start: 0.9622 (m) cc_final: 0.9103 (p)
REVERT: D   15 LYS cc_start: 0.8758 (ttmt) cc_final: 0.8298 (ttmm)
REVERT: D   23 SER cc_start: 0.9044 (p) cc_final: 0.8825 (p)
REVERT: D   61 GLU cc_start: 0.7979 (mp0) cc_final: 0.7602 (mp0)
REVERT: D   63 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7634 (pm20)
REVERT: D   70 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8365 (tttp)
REVERT: D  106 THR cc_start: 0.9460 (m) cc_final: 0.9122 (p)
REVERT: B   15 LYS cc_start: 0.8877 (mptt) cc_final: 0.8434 (mmtm)
REVERT: B   61 GLU cc_start: 0.8414 (mp0) cc_final: 0.7694 (mp0)
REVERT: B   62 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7376 (tm-30)
REVERT: B   70 LYS cc_start: 0.8881 (ttpt) cc_final: 0.8534 (ttpt)
REVERT: B   72 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7931 (mt-10)
REVERT: B  106 THR cc_start: 0.9511 (m) cc_final: 0.9199 (p)
REVERT: B  119 THR cc_start: 0.9484 (m) cc_final: 0.9226 (p)
REVERT: E   33 PHE cc_start: 0.8463 (t80) cc_final: 0.7508 (p90)
REVERT: E   66 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8418 (tm-30)
REVERT: E   76 LYS cc_start: 0.8435 (mppt) cc_final: 0.6963 (pttm)
REVERT: E   80 LYS cc_start: 0.8904 (tttt) cc_final: 0.8671 (tttm)
REVERT: E   82 LEU cc_start: 0.8365 (mt) cc_final: 0.7996 (mt)
REVERT: E  119 THR cc_start: 0.9420 (m) cc_final: 0.9113 (p)
REVERT: A   34 ARG cc_start: 0.7291 (ttt90) cc_final: 0.6360 (pmt-80)
REVERT: A   60 THR cc_start: 0.8488 (m) cc_final: 0.7836 (t)
REVERT: A   70 LYS cc_start: 0.8857 (ttpt) cc_final: 0.7764 (pttm)
REVERT: A  106 THR cc_start: 0.9520 (m) cc_final: 0.9138 (p)
REVERT: I   13 MET cc_start: 0.7152 (tpp) cc_final: 0.6665 (tpt)
REVERT: I  119 THR cc_start: 0.9534 (m) cc_final: 0.8922 (p)
REVERT: G   63 GLU cc_start: 0.8513 (tt0) cc_final: 0.7504 (tm-30)
REVERT: F   12 LEU cc_start: 0.6393 (mp) cc_final: 0.6142 (mp)
REVERT: F   61 GLU cc_start: 0.6906 (mp0) cc_final: 0.6494 (mp0)
REVERT: F   70 LYS cc_start: 0.8294 (tttt) cc_final: 0.7520 (tppt)
REVERT: F   74 ASP cc_start: 0.8692 (t0) cc_final: 0.8436 (t0)
REVERT: F   76 LYS cc_start: 0.9059 (mttp) cc_final: 0.8112 (pttm)
REVERT: F  119 THR cc_start: 0.9317 (m) cc_final: 0.8700 (p)
REVERT: H   70 LYS cc_start: 0.8979 (ttpp) cc_final: 0.8640 (ttpp)
REVERT: H   99 ASP cc_start: 0.8637 (t0) cc_final: 0.8232 (t0)
REVERT: J   26 ILE cc_start: 0.9012 (mm) cc_final: 0.8539 (pt)
REVERT: J   73 ILE cc_start: 0.8457 (mt) cc_final: 0.8140 (tt)
REVERT: J  119 THR cc_start: 0.9255 (m) cc_final: 0.9000 (p)
  outliers start: 21
  outliers final: 15
  residues processed: 244
  average time/residue: 0.0615
  time to fit residues: 20.3993
Evaluate side-chains
  242 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 225
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue  115 SER
Chi-restraints excluded: chain B residue   72 GLU
Chi-restraints excluded: chain E residue   26 ILE
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain A residue   13 MET
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain I residue  115 SER
Chi-restraints excluded: chain I residue  122 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain F residue   82 LEU
Chi-restraints excluded: chain F residue  117 SER
Chi-restraints excluded: chain J residue   82 LEU
Chi-restraints excluded: chain J residue  107 ILE
Chi-restraints excluded: chain J residue  122 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 40 optimal weight:    0.0570
   chunk 70 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:   10.0000
   chunk 64 optimal weight:    7.9990
   chunk 81 optimal weight:    0.8980
   chunk 2 optimal weight:   10.0000
   chunk 47 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   overall best weight:    2.7904

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

Flipped N/Q/H residues before XYZ refinement:
I  31 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.126303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.103432 restraints weight = 15112.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.105948 restraints weight = 6068.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.107647 restraints weight = 3647.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.108274 restraints weight = 2718.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.109085 restraints weight = 2393.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.5737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   7195  Z= 0.234
  Angle     :  0.740  10.687   9795  Z= 0.389
  Chirality :  0.050   0.187   1155
  Planarity :  0.004   0.028   1210
  Dihedral  :  5.053  16.838    965
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.46 %
    Favored  : 88.54 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 25.62 %
    Favored  : 71.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.27 (0.25), residues: 855
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.48 (0.19), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I 103 
 TYR   0.016   0.002   TYR I 114 
 PHE   0.023   0.002   PHE A  87 
 TRP   0.010   0.001   TRP D  79 
 HIS   0.004   0.001   HIS F  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 ( 7195)
  covalent geometry    : angle       0.73959 ( 9795)
  hydrogen bonds       : bond        0.03448 (  140)
  hydrogen bonds       : angle       5.32556 (  420)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1167.81 seconds
wall clock time: 20 minutes 49.22 seconds (1249.22 seconds total)