Starting phenix.real_space_refine
on Wed Mar  4 09:44:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wo0_32637/03_2026/7wo0_32637.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wo0_32637/03_2026/7wo0_32637.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wo0_32637/03_2026/7wo0_32637.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wo0_32637/03_2026/7wo0_32637.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wo0_32637/03_2026/7wo0_32637.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wo0_32637/03_2026/7wo0_32637.map"
  }
  resolution = 2.7
  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=   0.002
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
     C    3948      2.51       5
     N    1092      2.21       5
     O    1302      1.98       5
     H    6622      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12964
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "C"
      Number of atoms: 926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 926
          Classifications: {'peptide': 65}
          Modifications used: {'NH3': 1}
          Link IDs: {'TRANS': 64}
  Restraints were copied for chains:
    A, B, D, E, F, G, O, P, Q, R, S, T, U
  Time building chain proxies: 0.95, per 1000 atoms: 0.07
  Number of scatterers: 12964
  At special positions: 0
  Unit cell: (100.43, 110.39, 54.78, 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)
     O    1302      8.00
     N    1092      7.00
     C    3948      6.00
     H    6622      1.00
    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: 1.10
  Conformation dependent library (CDL) restraints added in 416.9 milliseconds
  

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1540

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 49.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 44
      removed outlier: 6.382A  pdb=" N   LEU A  38 " --> pdb=" O   TYR B  39 " (cutoff:3.500A)
      removed outlier: 8.044A  pdb=" N   GLY B  41 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   VAL A  40 " --> pdb=" O   GLY B  41 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   LYS B  43 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   SER A  42 " --> pdb=" O   LYS B  43 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   LEU D  38 " --> pdb=" O   TYR E  39 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   GLY E  41 " --> pdb=" O   LEU D  38 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   VAL D  40 " --> pdb=" O   GLY E  41 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   LYS E  43 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   SER D  42 " --> pdb=" O   LYS E  43 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   LEU E  38 " --> pdb=" O   TYR F  39 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   GLY F  41 " --> pdb=" O   LEU E  38 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   VAL E  40 " --> pdb=" O   GLY F  41 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   LYS F  43 " --> pdb=" O   VAL E  40 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   SER E  42 " --> pdb=" O   LYS F  43 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   LEU F  38 " --> pdb=" O   TYR G  39 " (cutoff:3.500A)
      removed outlier: 8.055A  pdb=" N   GLY G  41 " --> pdb=" O   LEU F  38 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   VAL F  40 " --> pdb=" O   GLY G  41 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   LYS G  43 " --> pdb=" O   VAL F  40 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   SER F  42 " --> pdb=" O   LYS G  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 57
      removed outlier: 6.834A  pdb=" N   VAL A  48 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   VAL B  49 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   HIS A  50 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   GLY B  51 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
      removed outlier: 9.208A  pdb=" N   GLY C  47 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 10.349A  pdb=" N   HIS B  50 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 8.779A  pdb=" N   VAL C  49 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 9.940A  pdb=" N   VAL B  52 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   GLY C  51 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   THR B  54 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   THR C  53 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 8.148A  pdb=" N   ALA B  56 " --> pdb=" O   THR C  53 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   VAL C  55 " --> pdb=" O   ALA B  56 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   VAL C  48 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   VAL D  49 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   HIS C  50 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   GLY D  51 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   VAL D  48 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   VAL E  49 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   HIS D  50 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   GLY E  51 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL E  48 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   VAL F  49 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   HIS E  50 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   GLY F  51 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   VAL F  48 " --> pdb=" O   GLY G  47 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   VAL G  49 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   HIS F  50 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   GLY G  51 " --> pdb=" O   HIS F  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66
      removed outlier: 6.338A  pdb=" N   THR A  64 " --> pdb=" O   ASN B  65 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   THR C  64 " --> pdb=" O   ASN D  65 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   THR D  64 " --> pdb=" O   ASN E  65 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   THR E  64 " --> pdb=" O   ASN F  65 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   THR F  64 " --> pdb=" O   ASN G  65 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 72
      removed outlier: 6.456A  pdb=" N   VAL C  71 " --> pdb=" O   THR B  72 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 77 through 78
      removed outlier: 6.547A  pdb=" N   VAL A  77 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   VAL C  77 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   VAL D  77 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   VAL E  77 " --> pdb=" O   ALA F  78 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL F  77 " --> pdb=" O   ALA G  78 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 83
      removed outlier: 6.243A  pdb=" N   VAL C  82 " --> pdb=" O   GLU B  83 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 89
      removed outlier: 6.854A  pdb=" N   ILE A  88 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ILE C  88 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   ILE D  88 " --> pdb=" O   ALA E  89 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ILE E  88 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ILE F  88 " --> pdb=" O   ALA G  89 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 98
      removed outlier: 6.793A  pdb=" N   GLY A  93 " --> pdb=" O   THR B  92 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   THR C  92 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
      removed outlier: 8.252A  pdb=" N   VAL B  95 " --> pdb=" O   THR C  92 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   PHE C  94 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
      removed outlier: 8.431A  pdb=" N   LYS B  97 " --> pdb=" O   PHE C  94 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LYS C  96 " --> pdb=" O   LYS B  97 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   GLY C  93 " --> pdb=" O   THR D  92 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   GLY D  93 " --> pdb=" O   THR E  92 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   GLY E  93 " --> pdb=" O   THR F  92 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   GLY F  93 " --> pdb=" O   THR G  92 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'O' and resid 37 through 44
      removed outlier: 6.381A  pdb=" N   LEU O  38 " --> pdb=" O   TYR P  39 " (cutoff:3.500A)
      removed outlier: 8.044A  pdb=" N   GLY P  41 " --> pdb=" O   LEU O  38 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   VAL O  40 " --> pdb=" O   GLY P  41 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   LYS P  43 " --> pdb=" O   VAL O  40 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   SER O  42 " --> pdb=" O   LYS P  43 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   LEU P  38 " --> pdb=" O   TYR Q  39 " (cutoff:3.500A)
      removed outlier: 8.055A  pdb=" N   GLY Q  41 " --> pdb=" O   LEU P  38 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   VAL P  40 " --> pdb=" O   GLY Q  41 " (cutoff:3.500A)
      removed outlier: 8.104A  pdb=" N   LYS Q  43 " --> pdb=" O   VAL P  40 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   SER P  42 " --> pdb=" O   LYS Q  43 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   LEU Q  38 " --> pdb=" O   TYR R  39 " (cutoff:3.500A)
      removed outlier: 8.062A  pdb=" N   GLY R  41 " --> pdb=" O   LEU Q  38 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   VAL Q  40 " --> pdb=" O   GLY R  41 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   LYS R  43 " --> pdb=" O   VAL Q  40 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   SER Q  42 " --> pdb=" O   LYS R  43 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   LEU R  38 " --> pdb=" O   TYR S  39 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   GLY S  41 " --> pdb=" O   LEU R  38 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   VAL R  40 " --> pdb=" O   GLY S  41 " (cutoff:3.500A)
      removed outlier: 8.103A  pdb=" N   LYS S  43 " --> pdb=" O   VAL R  40 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   SER R  42 " --> pdb=" O   LYS S  43 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   LEU S  38 " --> pdb=" O   TYR T  39 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   GLY T  41 " --> pdb=" O   LEU S  38 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   VAL S  40 " --> pdb=" O   GLY T  41 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   LYS T  43 " --> pdb=" O   VAL S  40 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   SER S  42 " --> pdb=" O   LYS T  43 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   LEU T  38 " --> pdb=" O   TYR U  39 " (cutoff:3.500A)
      removed outlier: 8.055A  pdb=" N   GLY U  41 " --> pdb=" O   LEU T  38 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   VAL T  40 " --> pdb=" O   GLY U  41 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   LYS U  43 " --> pdb=" O   VAL T  40 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   SER T  42 " --> pdb=" O   LYS U  43 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'O' and resid 47 through 57
      removed outlier: 6.835A  pdb=" N   VAL O  48 " --> pdb=" O   GLY P  47 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   VAL P  49 " --> pdb=" O   VAL O  48 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   HIS O  50 " --> pdb=" O   VAL P  49 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   GLY P  51 " --> pdb=" O   HIS O  50 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   VAL P  48 " --> pdb=" O   GLY Q  47 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   VAL Q  49 " --> pdb=" O   VAL P  48 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   HIS P  50 " --> pdb=" O   VAL Q  49 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   GLY Q  51 " --> pdb=" O   HIS P  50 " (cutoff:3.500A)
      removed outlier: 8.759A  pdb=" N   VAL Q  48 " --> pdb=" O   VAL R  49 " (cutoff:3.500A)
      removed outlier: 10.308A  pdb=" N   GLY R  51 " --> pdb=" O   VAL Q  48 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   HIS Q  50 " --> pdb=" O   GLY R  51 " (cutoff:3.500A)
      removed outlier: 8.575A  pdb=" N   THR R  53 " --> pdb=" O   HIS Q  50 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   VAL Q  52 " --> pdb=" O   THR R  53 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   VAL R  55 " --> pdb=" O   VAL Q  52 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   THR Q  54 " --> pdb=" O   VAL R  55 " (cutoff:3.500A)
      removed outlier: 7.867A  pdb=" N   GLU R  57 " --> pdb=" O   THR Q  54 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ALA Q  56 " --> pdb=" O   GLU R  57 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   VAL R  48 " --> pdb=" O   GLY S  47 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   VAL S  49 " --> pdb=" O   VAL R  48 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   HIS R  50 " --> pdb=" O   VAL S  49 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   GLY S  51 " --> pdb=" O   HIS R  50 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL S  48 " --> pdb=" O   GLY T  47 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   VAL T  49 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   HIS S  50 " --> pdb=" O   VAL T  49 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   GLY T  51 " --> pdb=" O   HIS S  50 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   VAL T  48 " --> pdb=" O   GLY U  47 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   VAL U  49 " --> pdb=" O   VAL T  48 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   HIS T  50 " --> pdb=" O   VAL U  49 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   GLY U  51 " --> pdb=" O   HIS T  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'O' and resid 63 through 66
      removed outlier: 6.337A  pdb=" N   THR O  64 " --> pdb=" O   ASN P  65 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   THR P  64 " --> pdb=" O   ASN Q  65 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   THR Q  64 " --> pdb=" O   ASN R  65 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   THR R  64 " --> pdb=" O   ASN S  65 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   THR S  64 " --> pdb=" O   ASN T  65 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   THR T  64 " --> pdb=" O   ASN U  65 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'O' and resid 70 through 72
    Processing sheet with id=AB4, first strand: chain 'O' and resid 77 through 78
      removed outlier: 6.547A  pdb=" N   VAL O  77 " --> pdb=" O   ALA P  78 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   VAL P  77 " --> pdb=" O   ALA Q  78 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   VAL Q  77 " --> pdb=" O   ALA R  78 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL R  77 " --> pdb=" O   ALA S  78 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   VAL S  77 " --> pdb=" O   ALA T  78 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   VAL T  77 " --> pdb=" O   ALA U  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'O' and resid 81 through 83
    Processing sheet with id=AB6, first strand: chain 'O' and resid 88 through 89
      removed outlier: 6.854A  pdb=" N   ILE O  88 " --> pdb=" O   ALA P  89 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ILE P  88 " --> pdb=" O   ALA Q  89 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   ILE Q  88 " --> pdb=" O   ALA R  89 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ILE R  88 " --> pdb=" O   ALA S  89 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ILE S  88 " --> pdb=" O   ALA T  89 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ILE T  88 " --> pdb=" O   ALA U  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'O' and resid 92 through 98
      removed outlier: 6.793A  pdb=" N   GLY O  93 " --> pdb=" O   THR P  92 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   GLY P  93 " --> pdb=" O   THR Q  92 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   GLY Q  93 " --> pdb=" O   THR R  92 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   GLY R  93 " --> pdb=" O   THR S  92 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   GLY S  93 " --> pdb=" O   THR T  92 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   GLY T  93 " --> pdb=" O   THR U  92 " (cutoff:3.500A)

    177 hydrogen bonds defined for protein.
    531 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.89

  Time building geometry restraints manager: 1.55 seconds

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

  Histogram of bond lengths:
        0.87 -     1.00: 392
        1.00 -     1.14: 6230
        1.14 -     1.28: 1134
        1.28 -     1.41: 1204
        1.41 -     1.55: 4032
  Bond restraints: 12992
  Sorted by residual:
  bond pdb=" N   GLU D  61 "
       pdb=" H   GLU D  61 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" ND2 ASN F  65 "
       pdb="HD22 ASN F  65 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" N   GLU P  61 "
       pdb=" H   GLU P  61 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" N   THR P  81 "
       pdb=" H   THR P  81 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" N   THR Q  54 "
       pdb=" H   THR Q  54 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  ... (remaining 12987 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 21446
        2.07 -     4.14: 356
        4.14 -     6.21: 1788
        6.21 -     8.28: 14
        8.28 -    10.35: 28
  Bond angle restraints: 23632
  Sorted by residual:
  angle pdb=" C   ASP Q  98 "
        pdb=" CA  ASP Q  98 "
        pdb=" CB  ASP Q  98 "
      ideal   model   delta    sigma   weight residual
     110.42  118.66   -8.24 1.99e+00 2.53e-01 1.71e+01
  angle pdb=" C   ASP U  98 "
        pdb=" CA  ASP U  98 "
        pdb=" CB  ASP U  98 "
      ideal   model   delta    sigma   weight residual
     110.42  118.63   -8.21 1.99e+00 2.53e-01 1.70e+01
  angle pdb=" C   ASP O  98 "
        pdb=" CA  ASP O  98 "
        pdb=" CB  ASP O  98 "
      ideal   model   delta    sigma   weight residual
     110.42  118.62   -8.20 1.99e+00 2.53e-01 1.70e+01
  angle pdb=" C   ASP S  98 "
        pdb=" CA  ASP S  98 "
        pdb=" CB  ASP S  98 "
      ideal   model   delta    sigma   weight residual
     110.42  118.62   -8.20 1.99e+00 2.53e-01 1.70e+01
  angle pdb=" C   ASP C  98 "
        pdb=" CA  ASP C  98 "
        pdb=" CB  ASP C  98 "
      ideal   model   delta    sigma   weight residual
     110.42  118.61   -8.19 1.99e+00 2.53e-01 1.69e+01
  ... (remaining 23627 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 4956
       17.77 -    35.53: 322
       35.53 -    53.30: 252
       53.30 -    71.06: 392
       71.06 -    88.83: 14
  Dihedral angle restraints: 5936
    sinusoidal: 3318
      harmonic: 2618
  Sorted by residual:
  dihedral pdb=" CA  LYS A  45 "
           pdb=" CB  LYS A  45 "
           pdb=" CG  LYS A  45 "
           pdb=" CD  LYS A  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.75   57.75     3      1.50e+01 4.44e-03 9.45e+00
  dihedral pdb=" CA  LYS D  45 "
           pdb=" CB  LYS D  45 "
           pdb=" CG  LYS D  45 "
           pdb=" CD  LYS D  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.75   57.75     3      1.50e+01 4.44e-03 9.45e+00
  dihedral pdb=" CA  LYS P  45 "
           pdb=" CB  LYS P  45 "
           pdb=" CG  LYS P  45 "
           pdb=" CD  LYS P  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.74   57.74     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 5933 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 444
       0.027 -    0.053: 320
       0.053 -    0.080: 100
       0.080 -    0.107: 179
       0.107 -    0.133: 77
  Chirality restraints: 1120
  Sorted by residual:
  chirality pdb=" CA  VAL P  95 "
            pdb=" N   VAL P  95 "
            pdb=" C   VAL P  95 "
            pdb=" CB  VAL P  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.43e-01
  chirality pdb=" CA  VAL S  95 "
            pdb=" N   VAL S  95 "
            pdb=" C   VAL S  95 "
            pdb=" CB  VAL S  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.42e-01
  chirality pdb=" CA  VAL F  95 "
            pdb=" N   VAL F  95 "
            pdb=" C   VAL F  95 "
            pdb=" CB  VAL F  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.34e-01
  ... (remaining 1117 not shown)

  Planarity restraints: 1974
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A  99 "    0.030 2.00e-02 2.50e+03   4.42e-01 2.93e+03
        pdb=" CD  GLN A  99 "   -0.017 2.00e-02 2.50e+03
        pdb=" OE1 GLN A  99 "   -0.023 2.00e-02 2.50e+03
        pdb=" NE2 GLN A  99 "   -0.001 2.00e-02 2.50e+03
        pdb="HE21 GLN A  99 "   -0.760 2.00e-02 2.50e+03
        pdb="HE22 GLN A  99 "    0.771 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN S  99 "   -0.029 2.00e-02 2.50e+03   4.42e-01 2.93e+03
        pdb=" CD  GLN S  99 "    0.016 2.00e-02 2.50e+03
        pdb=" OE1 GLN S  99 "    0.023 2.00e-02 2.50e+03
        pdb=" NE2 GLN S  99 "    0.001 2.00e-02 2.50e+03
        pdb="HE21 GLN S  99 "    0.760 2.00e-02 2.50e+03
        pdb="HE22 GLN S  99 "   -0.771 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B  99 "    0.030 2.00e-02 2.50e+03   4.42e-01 2.93e+03
        pdb=" CD  GLN B  99 "   -0.017 2.00e-02 2.50e+03
        pdb=" OE1 GLN B  99 "   -0.024 2.00e-02 2.50e+03
        pdb=" NE2 GLN B  99 "   -0.000 2.00e-02 2.50e+03
        pdb="HE21 GLN B  99 "   -0.759 2.00e-02 2.50e+03
        pdb="HE22 GLN B  99 "    0.770 2.00e-02 2.50e+03
  ... (remaining 1971 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.20: 1616
        2.20 -     2.77: 24667
        2.77 -     3.35: 32275
        3.35 -     3.92: 48036
        3.92 -     4.50: 65038
  Nonbonded interactions: 171632
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU D  35 "
            pdb=" H3  GLU D  35 "
     model   vdw
     1.619 2.450
  nonbonded pdb=" OE1 GLU R  35 "
            pdb=" H3  GLU R  35 "
     model   vdw
     1.619 2.450
  nonbonded pdb=" OE1 GLU E  35 "
            pdb=" H3  GLU E  35 "
     model   vdw
     1.619 2.450
  nonbonded pdb=" OE1 GLU G  35 "
            pdb=" H3  GLU G  35 "
     model   vdw
     1.620 2.450
  nonbonded pdb=" OE1 GLU Q  35 "
            pdb=" H3  GLU Q  35 "
     model   vdw
     1.620 2.450
  ... (remaining 171627 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  selection = chain 'R'
  selection = chain 'S'
  selection = chain 'T'
  selection = chain 'U'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.090
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.180
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
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      :  0.007   0.050   6370  Z= 0.398
  Angle     :  0.905   8.238   8610  Z= 0.530
  Chirality :  0.056   0.133   1120
  Planarity :  0.005   0.026   1078
  Dihedral  : 15.451  69.877   2184
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.64 %
    Favored  : 89.36 %
  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: -3.84 (0.18), residues: 882
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.14), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.033   0.009   TYR D  39 
 PHE   0.022   0.006   PHE A  94 
 HIS   0.002   0.001   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00727 ( 6370)
  covalent geometry    : angle       0.90538 ( 8610)
  hydrogen bonds       : bond        0.16223 (  177)
  hydrogen bonds       : angle       8.53851 (  531)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   45 LYS cc_start: 0.8271 (tmtt) cc_final: 0.7955 (tttp)
REVERT: T   60 LYS cc_start: 0.8171 (mttt) cc_final: 0.7864 (mtpt)
REVERT: T   61 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8060 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 1.7560
  time to fit residues: 143.7531
Evaluate side-chains
  65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.167173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.122424 restraints weight = 19419.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3990 rms_B_bonded: 2.50
r_work: 0.3806 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3666 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   6370  Z= 0.137
  Angle     :  0.482   4.462   8610  Z= 0.277
  Chirality :  0.056   0.128   1120
  Planarity :  0.002   0.011   1078
  Dihedral  :  4.595  15.541    910
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 1.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.03 %
    Favored  : 89.97 %
  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: -2.82 (0.21), residues: 882
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.16), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR D  39 
 PHE   0.016   0.004   PHE P  94 
 HIS   0.001   0.000   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6370)
  covalent geometry    : angle       0.48204 ( 8610)
  hydrogen bonds       : bond        0.03455 (  177)
  hydrogen bonds       : angle       6.06479 (  531)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   45 LYS cc_start: 0.8045 (tmtt) cc_final: 0.7590 (tmtm)
REVERT: D   60 LYS cc_start: 0.8354 (mttt) cc_final: 0.7897 (mtpp)
REVERT: G   60 LYS cc_start: 0.8482 (mttt) cc_final: 0.7950 (mtpt)
REVERT: R   60 LYS cc_start: 0.8308 (mttt) cc_final: 0.7880 (mtpt)
REVERT: T   60 LYS cc_start: 0.8374 (mttt) cc_final: 0.7876 (mtpt)
REVERT: U   60 LYS cc_start: 0.8341 (mttt) cc_final: 0.7779 (mtpt)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 2.1351
  time to fit residues: 142.9363
Evaluate side-chains
  61 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 78 optimal weight:    9.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN
B  79 GLN
D  79 GLN
E  79 GLN
F  79 GLN
G  79 GLN
O  79 GLN
P  79 GLN
Q  79 GLN
T  79 GLN
U  79 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.162768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.117384 restraints weight = 19867.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3918 rms_B_bonded: 2.59
r_work: 0.3734 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3594 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.034   6370  Z= 0.347
  Angle     :  0.600   5.948   8610  Z= 0.343
  Chirality :  0.057   0.133   1120
  Planarity :  0.003   0.011   1078
  Dihedral  :  5.429  15.963    910
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 11.85 %
    Favored  : 87.69 %
  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: -2.72 (0.21), residues: 882
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.16), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR D  39 
 PHE   0.024   0.006   PHE R  94 
 HIS   0.003   0.001   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00673 ( 6370)
  covalent geometry    : angle       0.60020 ( 8610)
  hydrogen bonds       : bond        0.04394 (  177)
  hydrogen bonds       : angle       6.21737 (  531)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.387 
Fit side-chains
REVERT: C   45 LYS cc_start: 0.8030 (tmtt) cc_final: 0.7621 (tmtm)
REVERT: C   60 LYS cc_start: 0.8242 (mttt) cc_final: 0.7755 (mtpp)
REVERT: D   60 LYS cc_start: 0.8430 (mttt) cc_final: 0.7921 (mtpp)
REVERT: F   60 LYS cc_start: 0.8515 (mttt) cc_final: 0.8087 (mtpt)
REVERT: G   60 LYS cc_start: 0.8596 (mttt) cc_final: 0.8072 (mtpt)
REVERT: Q   60 LYS cc_start: 0.8351 (mttt) cc_final: 0.7902 (mtpp)
REVERT: R   60 LYS cc_start: 0.8497 (mttt) cc_final: 0.8030 (mtpt)
REVERT: S   45 LYS cc_start: 0.8162 (tmtt) cc_final: 0.7819 (tttp)
REVERT: T   60 LYS cc_start: 0.8540 (mttt) cc_final: 0.8029 (mtpt)
REVERT: U   60 LYS cc_start: 0.8416 (mttt) cc_final: 0.7802 (mtpt)
  outliers start: 3
  outliers final: 0
  residues processed: 68
  average time/residue: 2.0575
  time to fit residues: 144.4624
Evaluate side-chains
  65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 24 optimal weight:    8.9990
   chunk 70 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 60 optimal weight:    8.9990
   chunk 53 optimal weight:    0.6980
   chunk 78 optimal weight:    8.9990
   chunk 83 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    2.1388

-------------------------------------------------------------------------------
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 = 0.4559 r_free = 0.4559 target = 0.164381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.119217 restraints weight = 19781.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 2.57
r_work: 0.3774 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3636 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025   6370  Z= 0.270
  Angle     :  0.529   4.786   8610  Z= 0.305
  Chirality :  0.055   0.125   1120
  Planarity :  0.002   0.009   1078
  Dihedral  :  5.249  15.978    910
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 12.16 %
    Favored  : 87.39 %
  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: -2.73 (0.21), residues: 882
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.16), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR D  39 
 PHE   0.019   0.005   PHE P  94 
 HIS   0.002   0.001   HIS T  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 ( 6370)
  covalent geometry    : angle       0.52893 ( 8610)
  hydrogen bonds       : bond        0.03773 (  177)
  hydrogen bonds       : angle       5.94611 (  531)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.367 
Fit side-chains
REVERT: C   45 LYS cc_start: 0.7963 (tmtt) cc_final: 0.7575 (tmtm)
REVERT: C   60 LYS cc_start: 0.8263 (mttt) cc_final: 0.7791 (mtpp)
REVERT: A   46 GLU cc_start: 0.7676 (tt0) cc_final: 0.7254 (tm-30)
REVERT: G   60 LYS cc_start: 0.8647 (mttt) cc_final: 0.8120 (mtpt)
REVERT: Q   60 LYS cc_start: 0.8295 (mttt) cc_final: 0.7878 (mtpp)
REVERT: R   60 LYS cc_start: 0.8480 (mttt) cc_final: 0.8063 (mtpt)
REVERT: S   45 LYS cc_start: 0.8140 (tmtt) cc_final: 0.7797 (tttp)
REVERT: T   60 LYS cc_start: 0.8551 (mttt) cc_final: 0.8067 (mtpt)
REVERT: U   60 LYS cc_start: 0.8452 (mttt) cc_final: 0.7857 (mtpt)
  outliers start: 3
  outliers final: 2
  residues processed: 61
  average time/residue: 2.2257
  time to fit residues: 139.8908
Evaluate side-chains
  63 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain R residue   83 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 54 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 66 optimal weight:   10.0000
   chunk 62 optimal weight:    2.9990
   chunk 78 optimal weight:    7.9990
   chunk 4 optimal weight:    0.4980
   overall best weight:    1.6586

-------------------------------------------------------------------------------
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 = 0.4571 r_free = 0.4571 target = 0.164794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.119376 restraints weight = 19959.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3960 rms_B_bonded: 2.60
r_work: 0.3788 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3650 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   6370  Z= 0.221
  Angle     :  0.492   4.291   8610  Z= 0.285
  Chirality :  0.055   0.125   1120
  Planarity :  0.002   0.009   1078
  Dihedral  :  5.075  16.101    910
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 12.61 %
    Favored  : 86.93 %
  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: -2.69 (0.21), residues: 882
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.16), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR D  39 
 PHE   0.020   0.005   PHE D  94 
 HIS   0.002   0.001   HIS T  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 6370)
  covalent geometry    : angle       0.49235 ( 8610)
  hydrogen bonds       : bond        0.03476 (  177)
  hydrogen bonds       : angle       5.70659 (  531)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.324 
Fit side-chains
REVERT: C   45 LYS cc_start: 0.8005 (tmtt) cc_final: 0.7580 (tmtm)
REVERT: C   60 LYS cc_start: 0.8264 (mttt) cc_final: 0.7815 (mtpp)
REVERT: A   46 GLU cc_start: 0.7645 (tt0) cc_final: 0.7232 (tm-30)
REVERT: D   60 LYS cc_start: 0.8407 (mttt) cc_final: 0.7955 (mtpp)
REVERT: G   60 LYS cc_start: 0.8639 (mttt) cc_final: 0.8112 (mtpt)
REVERT: Q   60 LYS cc_start: 0.8290 (mttt) cc_final: 0.7812 (mtpp)
REVERT: R   60 LYS cc_start: 0.8467 (mttt) cc_final: 0.8034 (mtpt)
REVERT: S   45 LYS cc_start: 0.8084 (tmtt) cc_final: 0.7821 (tttp)
REVERT: T   60 LYS cc_start: 0.8545 (mttt) cc_final: 0.8060 (mtpt)
REVERT: U   60 LYS cc_start: 0.8441 (mttt) cc_final: 0.7839 (mtpt)
  outliers start: 3
  outliers final: 2
  residues processed: 66
  average time/residue: 2.1384
  time to fit residues: 145.4623
Evaluate side-chains
  65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain R residue   83 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 72 optimal weight:    9.9990
   chunk 80 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 30 optimal weight:    8.9990
   chunk 79 optimal weight:    0.0370
   chunk 75 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 14 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.8460

-------------------------------------------------------------------------------
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 = 0.4608 r_free = 0.4608 target = 0.166931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.122169 restraints weight = 19819.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.4006 rms_B_bonded: 2.56
r_work: 0.3827 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3690 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.2968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.013   6370  Z= 0.127
  Angle     :  0.428   4.113   8610  Z= 0.251
  Chirality :  0.054   0.126   1120
  Planarity :  0.002   0.008   1078
  Dihedral  :  4.624  15.988    910
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 12.92 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.72 (0.21), residues: 882
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.16), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.000   TYR D  39 
 PHE   0.017   0.004   PHE D  94 
 HIS   0.001   0.000   HIS T  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 6370)
  covalent geometry    : angle       0.42795 ( 8610)
  hydrogen bonds       : bond        0.02941 (  177)
  hydrogen bonds       : angle       5.44253 (  531)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.307 
Fit side-chains
REVERT: C   45 LYS cc_start: 0.7997 (tmtt) cc_final: 0.7586 (tmtm)
REVERT: C   60 LYS cc_start: 0.8220 (mttt) cc_final: 0.7809 (mtpp)
REVERT: D   60 LYS cc_start: 0.8321 (mttt) cc_final: 0.7911 (mtpt)
REVERT: G   60 LYS cc_start: 0.8670 (mttt) cc_final: 0.8157 (mtpt)
REVERT: Q   60 LYS cc_start: 0.8282 (mttt) cc_final: 0.7803 (mtpp)
REVERT: R   60 LYS cc_start: 0.8399 (mttt) cc_final: 0.7989 (mtpt)
REVERT: T   60 LYS cc_start: 0.8514 (mttt) cc_final: 0.8065 (mtpt)
REVERT: U   60 LYS cc_start: 0.8449 (mttt) cc_final: 0.7916 (mtpt)
  outliers start: 2
  outliers final: 2
  residues processed: 66
  average time/residue: 2.1949
  time to fit residues: 149.2184
Evaluate side-chains
  63 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain R residue   83 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 54 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 42 optimal weight:    7.9990
   chunk 76 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 = 0.4555 r_free = 0.4555 target = 0.163890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.119676 restraints weight = 19822.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3948 rms_B_bonded: 2.51
r_work: 0.3767 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3625 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   6370  Z= 0.282
  Angle     :  0.527   4.909   8610  Z= 0.304
  Chirality :  0.055   0.127   1120
  Planarity :  0.002   0.010   1078
  Dihedral  :  5.163  16.472    910
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 13.68 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.61 (0.22), residues: 882
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.17), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.000   TYR D  39 
 PHE   0.023   0.006   PHE D  94 
 HIS   0.002   0.001   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 ( 6370)
  covalent geometry    : angle       0.52664 ( 8610)
  hydrogen bonds       : bond        0.03633 (  177)
  hydrogen bonds       : angle       5.68503 (  531)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.350 
Fit side-chains
REVERT: C   45 LYS cc_start: 0.7955 (tmtt) cc_final: 0.7531 (tmtm)
REVERT: C   60 LYS cc_start: 0.8196 (mttt) cc_final: 0.7734 (mtpp)
REVERT: A   46 GLU cc_start: 0.7649 (tt0) cc_final: 0.7203 (tm-30)
REVERT: D   60 LYS cc_start: 0.8329 (mttt) cc_final: 0.7861 (mtpp)
REVERT: F   60 LYS cc_start: 0.8443 (mttt) cc_final: 0.8025 (mtpt)
REVERT: G   60 LYS cc_start: 0.8630 (mttt) cc_final: 0.8082 (mtpt)
REVERT: Q   60 LYS cc_start: 0.8241 (mttt) cc_final: 0.7719 (mtpp)
REVERT: R   60 LYS cc_start: 0.8410 (mttt) cc_final: 0.7911 (mtpt)
REVERT: S   45 LYS cc_start: 0.8077 (tmtt) cc_final: 0.7812 (tttp)
REVERT: T   60 LYS cc_start: 0.8523 (mttt) cc_final: 0.7989 (mtpt)
REVERT: U   60 LYS cc_start: 0.8423 (mttt) cc_final: 0.7842 (mtpt)
  outliers start: 3
  outliers final: 3
  residues processed: 66
  average time/residue: 2.1339
  time to fit residues: 145.2329
Evaluate side-chains
  67 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain P residue   83 GLU
Chi-restraints excluded: chain R residue   83 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 62 optimal weight:    1.9990
   chunk 78 optimal weight:   10.0000
   chunk 81 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 82 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.4589 r_free = 0.4589 target = 0.165229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.121182 restraints weight = 19526.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3983 rms_B_bonded: 2.49
r_work: 0.3811 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3670 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.3084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   6370  Z= 0.165
  Angle     :  0.451   4.181   8610  Z= 0.262
  Chirality :  0.054   0.127   1120
  Planarity :  0.002   0.008   1078
  Dihedral  :  4.810  16.414    910
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 13.98 %
    Favored  : 85.71 %
  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: -2.67 (0.21), residues: 882
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.16), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.000   TYR E  39 
 PHE   0.018   0.004   PHE D  94 
 HIS   0.001   0.001   HIS U  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6370)
  covalent geometry    : angle       0.45144 ( 8610)
  hydrogen bonds       : bond        0.03079 (  177)
  hydrogen bonds       : angle       5.46710 (  531)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.332 
Fit side-chains
REVERT: C   45 LYS cc_start: 0.7946 (tmtt) cc_final: 0.7516 (tmtm)
REVERT: C   60 LYS cc_start: 0.8170 (mttt) cc_final: 0.7733 (mtpp)
REVERT: A   46 GLU cc_start: 0.7638 (tt0) cc_final: 0.7206 (tm-30)
REVERT: D   60 LYS cc_start: 0.8277 (mttt) cc_final: 0.7833 (mtpt)
REVERT: G   60 LYS cc_start: 0.8683 (mttt) cc_final: 0.8132 (mtpt)
REVERT: Q   60 LYS cc_start: 0.8201 (mttt) cc_final: 0.7716 (mtpp)
REVERT: R   60 LYS cc_start: 0.8354 (mttt) cc_final: 0.7910 (mtpt)
REVERT: T   60 LYS cc_start: 0.8531 (mttt) cc_final: 0.8030 (mtpt)
REVERT: U   60 LYS cc_start: 0.8437 (mttt) cc_final: 0.7873 (mtpt)
  outliers start: 2
  outliers final: 2
  residues processed: 63
  average time/residue: 2.2043
  time to fit residues: 143.1866
Evaluate side-chains
  65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   83 GLU
Chi-restraints excluded: chain R residue   83 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0870
   chunk 23 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 12 optimal weight:    7.9990
   chunk 35 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    1.1760

-------------------------------------------------------------------------------
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 = 0.4594 r_free = 0.4594 target = 0.165503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.121269 restraints weight = 19683.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3986 rms_B_bonded: 2.50
r_work: 0.3817 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3678 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   6370  Z= 0.166
  Angle     :  0.452   4.122   8610  Z= 0.263
  Chirality :  0.054   0.126   1120
  Planarity :  0.002   0.008   1078
  Dihedral  :  4.731  16.216    910
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 14.44 %
    Favored  : 85.26 %
  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: -2.59 (0.22), residues: 882
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.16), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.000   TYR Q  39 
 PHE   0.018   0.004   PHE D  94 
 HIS   0.001   0.000   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6370)
  covalent geometry    : angle       0.45173 ( 8610)
  hydrogen bonds       : bond        0.03128 (  177)
  hydrogen bonds       : angle       5.40220 (  531)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.432 
Fit side-chains
REVERT: C   60 LYS cc_start: 0.8176 (mttt) cc_final: 0.7739 (mtpp)
REVERT: A   46 GLU cc_start: 0.7617 (tt0) cc_final: 0.7189 (tm-30)
REVERT: D   60 LYS cc_start: 0.8303 (mttt) cc_final: 0.7853 (mtpt)
REVERT: F   60 LYS cc_start: 0.8389 (mttt) cc_final: 0.7985 (mtpt)
REVERT: G   60 LYS cc_start: 0.8643 (mttt) cc_final: 0.8092 (mtpt)
REVERT: Q   60 LYS cc_start: 0.8222 (mttt) cc_final: 0.7728 (mtpp)
REVERT: R   60 LYS cc_start: 0.8375 (mttt) cc_final: 0.7926 (mtpt)
REVERT: T   60 LYS cc_start: 0.8523 (mttt) cc_final: 0.8024 (mtpt)
REVERT: U   60 LYS cc_start: 0.8437 (mttt) cc_final: 0.7871 (mtpt)
  outliers start: 2
  outliers final: 2
  residues processed: 63
  average time/residue: 2.1794
  time to fit residues: 141.5183
Evaluate side-chains
  65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   83 GLU
Chi-restraints excluded: chain R residue   83 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 81 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.4573 r_free = 0.4573 target = 0.164251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.119907 restraints weight = 19783.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3959 rms_B_bonded: 2.52
r_work: 0.3783 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3643 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   6370  Z= 0.250
  Angle     :  0.506   4.587   8610  Z= 0.293
  Chirality :  0.055   0.127   1120
  Planarity :  0.002   0.009   1078
  Dihedral  :  5.073  16.486    910
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 14.29 %
    Favored  : 85.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.57 (0.22), residues: 882
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.95 (0.17), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR E  39 
 PHE   0.021   0.005   PHE D  94 
 HIS   0.002   0.001   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 6370)
  covalent geometry    : angle       0.50626 ( 8610)
  hydrogen bonds       : bond        0.03458 (  177)
  hydrogen bonds       : angle       5.55845 (  531)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.359 
Fit side-chains
REVERT: C   60 LYS cc_start: 0.8174 (mttt) cc_final: 0.7735 (mtpp)
REVERT: A   46 GLU cc_start: 0.7603 (tt0) cc_final: 0.7147 (tm-30)
REVERT: D   60 LYS cc_start: 0.8348 (mttt) cc_final: 0.7894 (mtpp)
REVERT: F   60 LYS cc_start: 0.8429 (mttt) cc_final: 0.8013 (mtpt)
REVERT: G   60 LYS cc_start: 0.8648 (mttt) cc_final: 0.8092 (mtpt)
REVERT: Q   60 LYS cc_start: 0.8222 (mttt) cc_final: 0.7730 (mtpp)
REVERT: R   60 LYS cc_start: 0.8388 (mttt) cc_final: 0.7929 (mtpt)
REVERT: S   45 LYS cc_start: 0.8069 (tmtt) cc_final: 0.7802 (tttp)
REVERT: T   60 LYS cc_start: 0.8539 (mttt) cc_final: 0.8027 (mtpt)
REVERT: U   60 LYS cc_start: 0.8445 (mttt) cc_final: 0.7818 (mtpt)
  outliers start: 2
  outliers final: 2
  residues processed: 64
  average time/residue: 2.2019
  time to fit residues: 145.2790
Evaluate side-chains
  65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   83 GLU
Chi-restraints excluded: chain R residue   83 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 82 optimal weight:    0.4980
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 11 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.4595 r_free = 0.4595 target = 0.165493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.121399 restraints weight = 19501.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3988 rms_B_bonded: 2.49
r_work: 0.3818 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3679 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   6370  Z= 0.152
  Angle     :  0.443   4.119   8610  Z= 0.258
  Chirality :  0.054   0.126   1120
  Planarity :  0.002   0.008   1078
  Dihedral  :  4.709  16.226    910
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 13.98 %
    Favored  : 85.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.59 (0.22), residues: 882
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.16), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.000   TYR E  39 
 PHE   0.019   0.004   PHE D  94 
 HIS   0.001   0.001   HIS T  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6370)
  covalent geometry    : angle       0.44306 ( 8610)
  hydrogen bonds       : bond        0.03020 (  177)
  hydrogen bonds       : angle       5.38751 (  531)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5171.19 seconds
wall clock time: 88 minutes 30.17 seconds (5310.17 seconds total)