Starting phenix.real_space_refine
on Mon Jul 28 22:15:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6off_20044/07_2025/6off_20044_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6off_20044/07_2025/6off_20044.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6off_20044/07_2025/6off_20044.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6off_20044/07_2025/6off_20044.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6off_20044/07_2025/6off_20044_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6off_20044/07_2025/6off_20044_neut.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 3
    Type Number    sf(0)   Gaussians
     C    6966      2.51       5
     N    1818      2.21       5
     O    2232      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11016
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 612
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 74}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, R
  Time building chain proxies: 3.08, per 1000 atoms: 0.28
  Number of scatterers: 11016
  At special positions: 0
  Unit cell: (90.915, 90.915, 145.255, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O    2232      8.00
     N    1818      7.00
     C    6966      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.96
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2736

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 0 sheets defined
      91.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE A  16 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA A  36 " --> pdb=" O   ASP A  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS A  37 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU A  56 " --> pdb=" O   SER A  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL A  65 " --> pdb=" O   GLN A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 80
      No H-bonds generated for 'chain 'A' and resid 78 through 80'
    Processing helix  chain 'B' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE B  16 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 37
      removed outlier: 3.819A  pdb=" N   THR B  28 " --> pdb=" O   GLN B  24 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA B  36 " --> pdb=" O   ASP B  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS B  37 " --> pdb=" O   LYS B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU B  56 " --> pdb=" O   SER B  52 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   VAL B  65 " --> pdb=" O   GLN B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 80
      No H-bonds generated for 'chain 'B' and resid 78 through 80'
    Processing helix  chain 'C' and resid 7 through 20
      removed outlier: 3.884A  pdb=" N   PHE C  16 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 22 through 37
      removed outlier: 3.821A  pdb=" N   THR C  28 " --> pdb=" O   GLN C  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA C  36 " --> pdb=" O   ASP C  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS C  37 " --> pdb=" O   LYS C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU C  56 " --> pdb=" O   SER C  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL C  65 " --> pdb=" O   GLN C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 80
      No H-bonds generated for 'chain 'C' and resid 78 through 80'
    Processing helix  chain 'D' and resid 7 through 20
      removed outlier: 3.884A  pdb=" N   PHE D  16 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR D  28 " --> pdb=" O   GLN D  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA D  36 " --> pdb=" O   ASP D  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS D  37 " --> pdb=" O   LYS D  33 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU D  56 " --> pdb=" O   SER D  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL D  65 " --> pdb=" O   GLN D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 80
      No H-bonds generated for 'chain 'D' and resid 78 through 80'
    Processing helix  chain 'E' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE E  16 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR E  28 " --> pdb=" O   GLN E  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA E  36 " --> pdb=" O   ASP E  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS E  37 " --> pdb=" O   LYS E  33 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU E  56 " --> pdb=" O   SER E  52 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   VAL E  65 " --> pdb=" O   GLN E  61 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 78 through 80
      No H-bonds generated for 'chain 'E' and resid 78 through 80'
    Processing helix  chain 'F' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE F  16 " --> pdb=" O   VAL F  12 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR F  28 " --> pdb=" O   GLN F  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA F  36 " --> pdb=" O   ASP F  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS F  37 " --> pdb=" O   LYS F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU F  56 " --> pdb=" O   SER F  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL F  65 " --> pdb=" O   GLN F  61 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 78 through 80
      No H-bonds generated for 'chain 'F' and resid 78 through 80'
    Processing helix  chain 'G' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE G  16 " --> pdb=" O   VAL G  12 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 22 through 37
      removed outlier: 3.819A  pdb=" N   THR G  28 " --> pdb=" O   GLN G  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA G  36 " --> pdb=" O   ASP G  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS G  37 " --> pdb=" O   LYS G  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU G  56 " --> pdb=" O   SER G  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL G  65 " --> pdb=" O   GLN G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 78 through 80
      No H-bonds generated for 'chain 'G' and resid 78 through 80'
    Processing helix  chain 'H' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE H  16 " --> pdb=" O   VAL H  12 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 22 through 37
      removed outlier: 3.819A  pdb=" N   THR H  28 " --> pdb=" O   GLN H  24 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA H  36 " --> pdb=" O   ASP H  32 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS H  37 " --> pdb=" O   LYS H  33 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 40 through 77
      removed outlier: 3.699A  pdb=" N   LEU H  56 " --> pdb=" O   SER H  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL H  65 " --> pdb=" O   GLN H  61 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 78 through 80
      No H-bonds generated for 'chain 'H' and resid 78 through 80'
    Processing helix  chain 'I' and resid 7 through 20
      removed outlier: 3.884A  pdb=" N   PHE I  16 " --> pdb=" O   VAL I  12 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR I  28 " --> pdb=" O   GLN I  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA I  36 " --> pdb=" O   ASP I  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS I  37 " --> pdb=" O   LYS I  33 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU I  56 " --> pdb=" O   SER I  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL I  65 " --> pdb=" O   GLN I  61 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 78 through 80
      No H-bonds generated for 'chain 'I' and resid 78 through 80'
    Processing helix  chain 'J' and resid 7 through 20
      removed outlier: 3.884A  pdb=" N   PHE J  16 " --> pdb=" O   VAL J  12 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 22 through 37
      removed outlier: 3.819A  pdb=" N   THR J  28 " --> pdb=" O   GLN J  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA J  36 " --> pdb=" O   ASP J  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS J  37 " --> pdb=" O   LYS J  33 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 40 through 77
      removed outlier: 3.701A  pdb=" N   LEU J  56 " --> pdb=" O   SER J  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL J  65 " --> pdb=" O   GLN J  61 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 78 through 80
      No H-bonds generated for 'chain 'J' and resid 78 through 80'
    Processing helix  chain 'K' and resid 7 through 20
      removed outlier: 3.884A  pdb=" N   PHE K  16 " --> pdb=" O   VAL K  12 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 22 through 37
      removed outlier: 3.821A  pdb=" N   THR K  28 " --> pdb=" O   GLN K  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA K  36 " --> pdb=" O   ASP K  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS K  37 " --> pdb=" O   LYS K  33 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU K  56 " --> pdb=" O   SER K  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL K  65 " --> pdb=" O   GLN K  61 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 78 through 80
      No H-bonds generated for 'chain 'K' and resid 78 through 80'
    Processing helix  chain 'L' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE L  16 " --> pdb=" O   VAL L  12 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR L  28 " --> pdb=" O   GLN L  24 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA L  36 " --> pdb=" O   ASP L  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS L  37 " --> pdb=" O   LYS L  33 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU L  56 " --> pdb=" O   SER L  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL L  65 " --> pdb=" O   GLN L  61 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 78 through 80
      No H-bonds generated for 'chain 'L' and resid 78 through 80'
    Processing helix  chain 'M' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE M  16 " --> pdb=" O   VAL M  12 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 37
      removed outlier: 3.821A  pdb=" N   THR M  28 " --> pdb=" O   GLN M  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA M  36 " --> pdb=" O   ASP M  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS M  37 " --> pdb=" O   LYS M  33 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU M  56 " --> pdb=" O   SER M  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL M  65 " --> pdb=" O   GLN M  61 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 78 through 80
      No H-bonds generated for 'chain 'M' and resid 78 through 80'
    Processing helix  chain 'N' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE N  16 " --> pdb=" O   VAL N  12 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR N  28 " --> pdb=" O   GLN N  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA N  36 " --> pdb=" O   ASP N  32 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS N  37 " --> pdb=" O   LYS N  33 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 40 through 77
      removed outlier: 3.699A  pdb=" N   LEU N  56 " --> pdb=" O   SER N  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL N  65 " --> pdb=" O   GLN N  61 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 78 through 80
      No H-bonds generated for 'chain 'N' and resid 78 through 80'
    Processing helix  chain 'O' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE O  16 " --> pdb=" O   VAL O  12 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR O  28 " --> pdb=" O   GLN O  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA O  36 " --> pdb=" O   ASP O  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS O  37 " --> pdb=" O   LYS O  33 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU O  56 " --> pdb=" O   SER O  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL O  65 " --> pdb=" O   GLN O  61 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 78 through 80
      No H-bonds generated for 'chain 'O' and resid 78 through 80'
    Processing helix  chain 'P' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE P  16 " --> pdb=" O   VAL P  12 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR P  28 " --> pdb=" O   GLN P  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA P  36 " --> pdb=" O   ASP P  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS P  37 " --> pdb=" O   LYS P  33 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU P  56 " --> pdb=" O   SER P  52 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   VAL P  65 " --> pdb=" O   GLN P  61 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 78 through 80
      No H-bonds generated for 'chain 'P' and resid 78 through 80'
    Processing helix  chain 'Q' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE Q  16 " --> pdb=" O   VAL Q  12 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR Q  28 " --> pdb=" O   GLN Q  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA Q  36 " --> pdb=" O   ASP Q  32 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LYS Q  37 " --> pdb=" O   LYS Q  33 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 40 through 77
      removed outlier: 3.699A  pdb=" N   LEU Q  56 " --> pdb=" O   SER Q  52 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   VAL Q  65 " --> pdb=" O   GLN Q  61 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 78 through 80
      No H-bonds generated for 'chain 'Q' and resid 78 through 80'
    Processing helix  chain 'R' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE R  16 " --> pdb=" O   VAL R  12 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 22 through 37
      removed outlier: 3.821A  pdb=" N   THR R  28 " --> pdb=" O   GLN R  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA R  36 " --> pdb=" O   ASP R  32 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS R  37 " --> pdb=" O   LYS R  33 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU R  56 " --> pdb=" O   SER R  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL R  65 " --> pdb=" O   GLN R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 78 through 80
      No H-bonds generated for 'chain 'R' and resid 78 through 80'

    900 hydrogen bonds defined for protein.
    2700 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.01

  Time building geometry restraints manager: 3.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 1962
        1.29 -     1.35: 1674
        1.35 -     1.41: 1088
        1.41 -     1.48: 1669
        1.48 -     1.54: 4821
  Bond restraints: 11214
  Sorted by residual:
  bond pdb=" CG  LEU Q   9 "
       pdb=" CD2 LEU Q   9 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.61e+00
  bond pdb=" CG  LEU L   9 "
       pdb=" CD2 LEU L   9 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.61e+00
  bond pdb=" CG  LEU R   9 "
       pdb=" CD2 LEU R   9 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.60e+00
  bond pdb=" CG  LEU B   9 "
       pdb=" CD2 LEU B   9 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.59e+00
  bond pdb=" CG  LEU H   9 "
       pdb=" CD2 LEU H   9 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.59e+00
  ... (remaining 11209 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 12885
        1.06 -     2.11: 1956
        2.11 -     3.17: 332
        3.17 -     4.23: 55
        4.23 -     5.28: 36
  Bond angle restraints: 15264
  Sorted by residual:
  angle pdb=" CA  GLN N  61 "
        pdb=" CB  GLN N  61 "
        pdb=" CG  GLN N  61 "
      ideal   model   delta    sigma   weight residual
     114.10  119.38   -5.28 2.00e+00 2.50e-01 6.97e+00
  angle pdb=" CA  GLN M  61 "
        pdb=" CB  GLN M  61 "
        pdb=" CG  GLN M  61 "
      ideal   model   delta    sigma   weight residual
     114.10  119.37   -5.27 2.00e+00 2.50e-01 6.95e+00
  angle pdb=" CA  GLN B  61 "
        pdb=" CB  GLN B  61 "
        pdb=" CG  GLN B  61 "
      ideal   model   delta    sigma   weight residual
     114.10  119.37   -5.27 2.00e+00 2.50e-01 6.95e+00
  angle pdb=" CA  GLN G  61 "
        pdb=" CB  GLN G  61 "
        pdb=" CG  GLN G  61 "
      ideal   model   delta    sigma   weight residual
     114.10  119.37   -5.27 2.00e+00 2.50e-01 6.94e+00
  angle pdb=" CA  GLN O  61 "
        pdb=" CB  GLN O  61 "
        pdb=" CG  GLN O  61 "
      ideal   model   delta    sigma   weight residual
     114.10  119.36   -5.26 2.00e+00 2.50e-01 6.91e+00
  ... (remaining 15259 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.01: 6462
       15.01 -    30.03: 252
       30.03 -    45.04: 54
       45.04 -    60.05: 18
       60.05 -    75.06: 18
  Dihedral angle restraints: 6804
    sinusoidal: 2610
      harmonic: 4194
  Sorted by residual:
  dihedral pdb=" CA  GLY A  19 "
           pdb=" C   GLY A  19 "
           pdb=" N   VAL A  20 "
           pdb=" CA  VAL A  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.34   15.66     0      5.00e+00 4.00e-02 9.81e+00
  dihedral pdb=" CA  GLY P  19 "
           pdb=" C   GLY P  19 "
           pdb=" N   VAL P  20 "
           pdb=" CA  VAL P  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.36   15.64     0      5.00e+00 4.00e-02 9.79e+00
  dihedral pdb=" CA  GLY B  19 "
           pdb=" C   GLY B  19 "
           pdb=" N   VAL B  20 "
           pdb=" CA  VAL B  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.36   15.64     0      5.00e+00 4.00e-02 9.78e+00
  ... (remaining 6801 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.020: 471
       0.020 -    0.041: 597
       0.041 -    0.061: 317
       0.061 -    0.081: 305
       0.081 -    0.101: 56
  Chirality restraints: 1746
  Sorted by residual:
  chirality pdb=" CA  PRO N  41 "
            pdb=" N   PRO N  41 "
            pdb=" C   PRO N  41 "
            pdb=" CB  PRO N  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.62    0.10 2.00e-01 2.50e+01 2.56e-01
  chirality pdb=" CA  PRO H  41 "
            pdb=" N   PRO H  41 "
            pdb=" C   PRO H  41 "
            pdb=" CB  PRO H  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.62    0.10 2.00e-01 2.50e+01 2.42e-01
  chirality pdb=" CA  PRO J  41 "
            pdb=" N   PRO J  41 "
            pdb=" C   PRO J  41 "
            pdb=" CB  PRO J  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.62    0.10 2.00e-01 2.50e+01 2.42e-01
  ... (remaining 1743 not shown)

  Planarity restraints: 1998
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL K  20 "    0.008 2.00e-02 2.50e+03   1.56e-02 2.44e+00
        pdb=" C   VAL K  20 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   VAL K  20 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASP K  21 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  20 "    0.008 2.00e-02 2.50e+03   1.56e-02 2.43e+00
        pdb=" C   VAL A  20 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   VAL A  20 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASP A  21 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL Q  20 "    0.008 2.00e-02 2.50e+03   1.56e-02 2.43e+00
        pdb=" C   VAL Q  20 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   VAL Q  20 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASP Q  21 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1995 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 248
        2.70 -     3.25: 11456
        3.25 -     3.80: 17333
        3.80 -     4.35: 23717
        4.35 -     4.90: 40635
  Nonbonded interactions: 93389
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP I  10 "
            pdb=" OG  SER O  49 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" OD1 ASP J  10 "
            pdb=" OG  SER P  49 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" OD1 ASP D  10 "
            pdb=" OG  SER J  49 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" N   ASP A  10 "
            pdb=" OE2 GLU G  53 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" OD1 ASP E  17 "
            pdb=" OH  TYR E  57 "
     model   vdw
     2.310 3.040
  ... (remaining 93384 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: 0.11
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'L'
  selection = chain 'O'
  selection = chain 'N'
  selection = chain 'Q'
  selection = chain 'P'
  selection = chain 'R'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     24.170
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
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      :  0.009   0.042  11214  Z= 0.398
  Angle     :  0.831   5.282  15264  Z= 0.500
  Chirality :  0.045   0.101   1746
  Planarity :  0.005   0.031   1998
  Dihedral  : 10.880  75.065   4068
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.21 (0.13), residues: 1368
  helix: -3.28 (0.09), residues: 1152
  sheet:  None (None), residues: 0
  loop : -2.57 (0.28), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP H   5 
 PHE   0.012   0.003   PHE O  79 
 TYR   0.011   0.002   TYR O  57 
 ARG   0.004   0.001   ARG I  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24560 (  900)
  hydrogen bonds       : angle       8.50853 ( 2700)
  covalent geometry    : bond        0.00917 (11214)
  covalent geometry    : angle       0.83090 (15264)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  389 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 389
  time to evaluate  : 1.377 
Fit side-chains
REVERT: A   66 LYS cc_start: 0.8617 (tptp) cc_final: 0.7191 (mttm)
REVERT: B   37 LYS cc_start: 0.7539 (ttmt) cc_final: 0.6639 (tptt)
REVERT: C    4 PRO cc_start: 0.7523 (Cg_endo) cc_final: 0.7248 (Cg_exo)
REVERT: C   10 ASP cc_start: 0.8562 (m-30) cc_final: 0.7963 (m-30)
REVERT: C   37 LYS cc_start: 0.9078 (ttmt) cc_final: 0.7713 (tptt)
REVERT: C   72 ASP cc_start: 0.9174 (m-30) cc_final: 0.8948 (m-30)
REVERT: D   10 ASP cc_start: 0.7896 (m-30) cc_final: 0.7502 (m-30)
REVERT: E   10 ASP cc_start: 0.8060 (m-30) cc_final: 0.7723 (m-30)
REVERT: E   37 LYS cc_start: 0.9093 (ttmt) cc_final: 0.7985 (tptt)
REVERT: E   52 SER cc_start: 0.8568 (m) cc_final: 0.8250 (p)
REVERT: E   70 ASP cc_start: 0.8333 (m-30) cc_final: 0.7939 (m-30)
REVERT: F   10 ASP cc_start: 0.8421 (m-30) cc_final: 0.8061 (m-30)
REVERT: F   37 LYS cc_start: 0.9074 (ttmt) cc_final: 0.7655 (tptt)
REVERT: G   33 LYS cc_start: 0.8397 (mttt) cc_final: 0.7936 (mtpp)
REVERT: G   37 LYS cc_start: 0.8503 (ttmt) cc_final: 0.6720 (tptp)
REVERT: H   37 LYS cc_start: 0.8965 (ttmt) cc_final: 0.7269 (tptt)
REVERT: H   72 ASP cc_start: 0.9104 (m-30) cc_final: 0.8750 (m-30)
REVERT: I   53 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7514 (mt-10)
REVERT: K   10 ASP cc_start: 0.7953 (m-30) cc_final: 0.7545 (m-30)
REVERT: L   53 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7571 (mt-10)
REVERT: M    8 TYR cc_start: 0.8717 (t80) cc_final: 0.8480 (t80)
REVERT: M   29 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7068 (mt-10)
REVERT: M   69 LYS cc_start: 0.8962 (tmtt) cc_final: 0.7838 (ttmt)
REVERT: N   25 THR cc_start: 0.8717 (m) cc_final: 0.8353 (p)
REVERT: N   69 LYS cc_start: 0.8770 (tmtt) cc_final: 0.8159 (ttmt)
REVERT: O   28 THR cc_start: 0.8751 (m) cc_final: 0.8371 (p)
REVERT: O   33 LYS cc_start: 0.7967 (mttt) cc_final: 0.7095 (mttm)
REVERT: R   33 LYS cc_start: 0.8610 (mttt) cc_final: 0.7864 (mttm)
REVERT: R   69 LYS cc_start: 0.9078 (tmtt) cc_final: 0.7908 (ttmt)
REVERT: R   72 ASP cc_start: 0.8863 (m-30) cc_final: 0.8630 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 389
  average time/residue: 0.2219
  time to fit residues: 121.3780
Evaluate side-chains
  275 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 275
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 98 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  61 GLN
B  61 GLN
F  78 ASN
G  61 GLN
H  61 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.101836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.091799 restraints weight = 18062.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 1.71
r_work: 0.3025 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  11214  Z= 0.131
  Angle     :  0.471   3.738  15264  Z= 0.263
  Chirality :  0.033   0.114   1746
  Planarity :  0.005   0.028   1998
  Dihedral  :  4.059  17.480   1512
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  9.09 %
    Favored  : 89.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.20), residues: 1368
  helix: -0.08 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -1.76 (0.50), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP N   5 
 PHE   0.007   0.001   PHE B  79 
 TYR   0.015   0.001   TYR B  47 
 ARG   0.001   0.000   ARG B  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04021 (  900)
  hydrogen bonds       : angle       3.49296 ( 2700)
  covalent geometry    : bond        0.00270 (11214)
  covalent geometry    : angle       0.47063 (15264)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 341
  time to evaluate  : 1.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ASP cc_start: 0.8625 (m-30) cc_final: 0.8280 (m-30)
REVERT: A   39 SER cc_start: 0.8619 (m) cc_final: 0.8370 (p)
REVERT: B   37 LYS cc_start: 0.8166 (ttmt) cc_final: 0.6961 (tptt)
REVERT: B   66 LYS cc_start: 0.8335 (tptp) cc_final: 0.6967 (ttmm)
REVERT: C    4 PRO cc_start: 0.8120 (Cg_endo) cc_final: 0.7909 (Cg_exo)
REVERT: C   10 ASP cc_start: 0.8543 (m-30) cc_final: 0.8057 (m-30)
REVERT: C   37 LYS cc_start: 0.9074 (ttmt) cc_final: 0.7614 (tptt)
REVERT: C   69 LYS cc_start: 0.9077 (tmtt) cc_final: 0.8723 (tttm)
REVERT: D   10 ASP cc_start: 0.8383 (m-30) cc_final: 0.7594 (m-30)
REVERT: D   72 ASP cc_start: 0.9221 (m-30) cc_final: 0.8926 (m-30)
REVERT: E   10 ASP cc_start: 0.8378 (m-30) cc_final: 0.7904 (m-30)
REVERT: E   37 LYS cc_start: 0.9133 (ttmt) cc_final: 0.7922 (tptt)
REVERT: E   52 SER cc_start: 0.8675 (m) cc_final: 0.8278 (p)
REVERT: E   57 TYR cc_start: 0.9303 (t80) cc_final: 0.9025 (t80)
REVERT: F   10 ASP cc_start: 0.8560 (m-30) cc_final: 0.8147 (m-30)
REVERT: F   37 LYS cc_start: 0.9082 (ttmt) cc_final: 0.7554 (tptt)
REVERT: G   33 LYS cc_start: 0.8793 (mttt) cc_final: 0.8445 (mtpp)
REVERT: G   37 LYS cc_start: 0.8657 (ttmt) cc_final: 0.6929 (tptp)
REVERT: H   10 ASP cc_start: 0.8708 (m-30) cc_final: 0.8499 (m-30)
REVERT: H   37 LYS cc_start: 0.8995 (ttmt) cc_final: 0.7444 (tptt)
REVERT: H   72 ASP cc_start: 0.9126 (m-30) cc_final: 0.8665 (m-30)
REVERT: I    8 TYR cc_start: 0.8790 (t80) cc_final: 0.8414 (t80)
REVERT: J   10 ASP cc_start: 0.8535 (m-30) cc_final: 0.8175 (m-30)
REVERT: J   24 GLN cc_start: 0.8017 (mp10) cc_final: 0.7797 (mp10)
REVERT: J   37 LYS cc_start: 0.8990 (ttmm) cc_final: 0.8745 (ttmt)
REVERT: K   31 LEU cc_start: 0.9251 (tp) cc_final: 0.8991 (tp)
REVERT: L   10 ASP cc_start: 0.8683 (m-30) cc_final: 0.8391 (m-30)
REVERT: M    8 TYR cc_start: 0.8878 (t80) cc_final: 0.8573 (t80)
REVERT: M   29 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7557 (mt-10)
REVERT: M   69 LYS cc_start: 0.9195 (tmtt) cc_final: 0.7924 (ttmt)
REVERT: N   15 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.7519 (ttpt)
REVERT: N   25 THR cc_start: 0.8900 (m) cc_final: 0.8613 (p)
REVERT: N   29 GLU cc_start: 0.7728 (tp30) cc_final: 0.7447 (tp30)
REVERT: N   69 LYS cc_start: 0.9088 (tmtt) cc_final: 0.8016 (ttmt)
REVERT: N   70 ASP cc_start: 0.8556 (m-30) cc_final: 0.8033 (m-30)
REVERT: N   72 ASP cc_start: 0.8570 (m-30) cc_final: 0.8314 (m-30)
REVERT: O   15 LYS cc_start: 0.8620 (ttmm) cc_final: 0.7353 (tttt)
REVERT: O   29 GLU cc_start: 0.8247 (tm-30) cc_final: 0.8003 (tp30)
REVERT: O   33 LYS cc_start: 0.8632 (mttt) cc_final: 0.8394 (mttm)
REVERT: Q   32 ASP cc_start: 0.8474 (m-30) cc_final: 0.8191 (m-30)
REVERT: Q   53 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7680 (mt-10)
REVERT: R   69 LYS cc_start: 0.9153 (tmtt) cc_final: 0.7988 (ttmt)
REVERT: R   77 GLN cc_start: 0.8760 (tt0) cc_final: 0.8550 (tm-30)
  outliers start: 14
  outliers final: 3
  residues processed: 345
  average time/residue: 0.2082
  time to fit residues: 102.9739
Evaluate side-chains
  294 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 290
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain J residue   33 LYS
Chi-restraints excluded: chain N residue   15 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 94 optimal weight:    6.9990
   chunk 89 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0060
   chunk 37 optimal weight:    0.9980
   chunk 91 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
D  55 ASN
I  78 ASN
J  78 ASN
K  63 ASN
N  63 ASN
O  61 GLN
O  63 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.098166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.088207 restraints weight = 18533.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 1.73
r_work: 0.2970 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.3444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019  11214  Z= 0.109
  Angle     :  0.412   4.347  15264  Z= 0.224
  Chirality :  0.032   0.111   1746
  Planarity :  0.003   0.023   1998
  Dihedral  :  3.596  15.700   1512
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 12.54 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.21), residues: 1368
  helix:  1.58 (0.14), residues: 1206
  sheet:  None (None), residues: 0
  loop : -1.68 (0.52), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP N   5 
 PHE   0.005   0.001   PHE O  68 
 TYR   0.011   0.001   TYR B  47 
 ARG   0.001   0.000   ARG E  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03432 (  900)
  hydrogen bonds       : angle       2.98929 ( 2700)
  covalent geometry    : bond        0.00222 (11214)
  covalent geometry    : angle       0.41230 (15264)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 332
  time to evaluate  : 1.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 LYS cc_start: 0.8430 (ttmt) cc_final: 0.7242 (tptt)
REVERT: B   66 LYS cc_start: 0.8715 (tptp) cc_final: 0.7421 (ttmt)
REVERT: C   10 ASP cc_start: 0.8545 (m-30) cc_final: 0.8108 (m-30)
REVERT: C   37 LYS cc_start: 0.8964 (ttmt) cc_final: 0.7513 (tptt)
REVERT: C   69 LYS cc_start: 0.9104 (tmtt) cc_final: 0.8788 (tttm)
REVERT: C   72 ASP cc_start: 0.9237 (m-30) cc_final: 0.8958 (m-30)
REVERT: D   10 ASP cc_start: 0.8445 (m-30) cc_final: 0.7871 (m-30)
REVERT: D   69 LYS cc_start: 0.8986 (tmtt) cc_final: 0.8647 (tptp)
REVERT: D   72 ASP cc_start: 0.9190 (m-30) cc_final: 0.8908 (m-30)
REVERT: E   10 ASP cc_start: 0.8403 (m-30) cc_final: 0.8005 (m-30)
REVERT: E   24 GLN cc_start: 0.8503 (mp10) cc_final: 0.8290 (mp10)
REVERT: E   37 LYS cc_start: 0.9168 (ttmt) cc_final: 0.7922 (tptt)
REVERT: F   10 ASP cc_start: 0.8459 (m-30) cc_final: 0.7957 (m-30)
REVERT: F   25 THR cc_start: 0.8826 (m) cc_final: 0.8570 (p)
REVERT: F   37 LYS cc_start: 0.9101 (ttmt) cc_final: 0.7553 (tptt)
REVERT: G   10 ASP cc_start: 0.8895 (m-30) cc_final: 0.8565 (m-30)
REVERT: G   33 LYS cc_start: 0.8861 (mttt) cc_final: 0.8563 (mtpp)
REVERT: G   77 GLN cc_start: 0.9033 (tp-100) cc_final: 0.8815 (tp40)
REVERT: H   10 ASP cc_start: 0.8696 (m-30) cc_final: 0.8463 (m-30)
REVERT: H   37 LYS cc_start: 0.9046 (ttmt) cc_final: 0.7434 (tptt)
REVERT: H   72 ASP cc_start: 0.9195 (m-30) cc_final: 0.8738 (m-30)
REVERT: I    8 TYR cc_start: 0.8717 (t80) cc_final: 0.8312 (t80)
REVERT: I   53 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7878 (mt-10)
REVERT: J   10 ASP cc_start: 0.8574 (m-30) cc_final: 0.8226 (m-30)
REVERT: J   72 ASP cc_start: 0.8567 (m-30) cc_final: 0.8101 (m-30)
REVERT: K   31 LEU cc_start: 0.9301 (tp) cc_final: 0.9057 (tp)
REVERT: L   39 SER cc_start: 0.8922 (m) cc_final: 0.7968 (m)
REVERT: M   69 LYS cc_start: 0.9235 (tmtt) cc_final: 0.7959 (ttmt)
REVERT: N   15 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.7483 (ttpt)
REVERT: N   29 GLU cc_start: 0.7765 (tp30) cc_final: 0.7533 (tp30)
REVERT: N   69 LYS cc_start: 0.9128 (tmtt) cc_final: 0.8041 (ttmt)
REVERT: N   70 ASP cc_start: 0.8504 (m-30) cc_final: 0.8115 (m-30)
REVERT: N   72 ASP cc_start: 0.8645 (m-30) cc_final: 0.8371 (m-30)
REVERT: O   10 ASP cc_start: 0.8564 (m-30) cc_final: 0.8348 (m-30)
REVERT: O   32 ASP cc_start: 0.8340 (m-30) cc_final: 0.8124 (m-30)
REVERT: O   69 LYS cc_start: 0.9047 (tmtt) cc_final: 0.8050 (ttmt)
REVERT: O   72 ASP cc_start: 0.8766 (m-30) cc_final: 0.8522 (m-30)
REVERT: P   32 ASP cc_start: 0.8283 (m-30) cc_final: 0.7934 (m-30)
REVERT: Q   15 LYS cc_start: 0.8719 (mttp) cc_final: 0.7658 (tttt)
REVERT: Q   25 THR cc_start: 0.9101 (m) cc_final: 0.8792 (p)
REVERT: Q   69 LYS cc_start: 0.8987 (tmtt) cc_final: 0.7612 (tttt)
REVERT: R   15 LYS cc_start: 0.8579 (mttp) cc_final: 0.7537 (ttpt)
REVERT: R   69 LYS cc_start: 0.9195 (tmtt) cc_final: 0.7988 (ttmt)
REVERT: R   72 ASP cc_start: 0.8915 (m-30) cc_final: 0.8672 (m-30)
  outliers start: 7
  outliers final: 2
  residues processed: 335
  average time/residue: 0.2823
  time to fit residues: 133.6739
Evaluate side-chains
  297 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 294
  time to evaluate  : 1.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain N residue   15 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 68 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   chunk 123 optimal weight:    0.6980
   chunk 122 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   chunk 102 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
D  55 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.095476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.085621 restraints weight = 18550.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3032 rms_B_bonded: 1.72
r_work: 0.2933 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2821 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.3815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019  11214  Z= 0.111
  Angle     :  0.413   4.013  15264  Z= 0.221
  Chirality :  0.033   0.105   1746
  Planarity :  0.003   0.025   1998
  Dihedral  :  3.532  15.518   1512
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 13.38 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.78 (0.21), residues: 1368
  helix:  2.28 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -1.71 (0.51), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP M   5 
 PHE   0.006   0.001   PHE N  68 
 TYR   0.010   0.001   TYR B  47 
 ARG   0.001   0.000   ARG E  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03141 (  900)
  hydrogen bonds       : angle       2.92430 ( 2700)
  covalent geometry    : bond        0.00234 (11214)
  covalent geometry    : angle       0.41307 (15264)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 306
  time to evaluate  : 1.347 
Fit side-chains
   revert: symmetry clash
REVERT: B   37 LYS cc_start: 0.8666 (ttmt) cc_final: 0.7399 (tptt)
REVERT: B   56 LEU cc_start: 0.9415 (mt) cc_final: 0.9049 (mt)
REVERT: B   66 LYS cc_start: 0.8851 (tptp) cc_final: 0.7687 (ttmt)
REVERT: B   69 LYS cc_start: 0.8903 (tmtt) cc_final: 0.8544 (tttm)
REVERT: C   10 ASP cc_start: 0.8617 (m-30) cc_final: 0.8144 (m-30)
REVERT: C   37 LYS cc_start: 0.8961 (ttmt) cc_final: 0.7482 (tptt)
REVERT: C   69 LYS cc_start: 0.9112 (tmtt) cc_final: 0.8821 (tttm)
REVERT: C   72 ASP cc_start: 0.9278 (m-30) cc_final: 0.8893 (m-30)
REVERT: D   10 ASP cc_start: 0.8515 (m-30) cc_final: 0.7889 (m-30)
REVERT: D   66 LYS cc_start: 0.8787 (tptp) cc_final: 0.7846 (ttmt)
REVERT: D   69 LYS cc_start: 0.9022 (tmtt) cc_final: 0.8785 (tttm)
REVERT: E   10 ASP cc_start: 0.8579 (m-30) cc_final: 0.8136 (m-30)
REVERT: E   37 LYS cc_start: 0.9165 (ttmt) cc_final: 0.7919 (tptt)
REVERT: F   10 ASP cc_start: 0.8471 (m-30) cc_final: 0.8082 (m-30)
REVERT: F   25 THR cc_start: 0.8816 (m) cc_final: 0.8610 (p)
REVERT: F   37 LYS cc_start: 0.9058 (ttmt) cc_final: 0.7527 (tptt)
REVERT: G   10 ASP cc_start: 0.8732 (m-30) cc_final: 0.8511 (m-30)
REVERT: G   33 LYS cc_start: 0.8840 (mttt) cc_final: 0.8626 (mtpp)
REVERT: G   53 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8049 (mm-30)
REVERT: H   10 ASP cc_start: 0.8732 (m-30) cc_final: 0.8496 (m-30)
REVERT: H   37 LYS cc_start: 0.9069 (ttmt) cc_final: 0.7412 (tptt)
REVERT: H   72 ASP cc_start: 0.9230 (m-30) cc_final: 0.8839 (m-30)
REVERT: I    8 TYR cc_start: 0.8716 (t80) cc_final: 0.8404 (t80)
REVERT: I   21 ASP cc_start: 0.8600 (m-30) cc_final: 0.8316 (t70)
REVERT: I   53 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8011 (mt-10)
REVERT: J   72 ASP cc_start: 0.8647 (m-30) cc_final: 0.8123 (m-30)
REVERT: K   31 LEU cc_start: 0.9325 (tp) cc_final: 0.9081 (tp)
REVERT: L   39 SER cc_start: 0.8837 (m) cc_final: 0.8216 (m)
REVERT: M   69 LYS cc_start: 0.9241 (tmtt) cc_final: 0.7818 (ttmt)
REVERT: N   15 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7445 (ttpt)
REVERT: N   24 GLN cc_start: 0.7816 (mp10) cc_final: 0.7584 (mp10)
REVERT: N   69 LYS cc_start: 0.9126 (tmtt) cc_final: 0.7993 (ttmt)
REVERT: N   70 ASP cc_start: 0.8550 (m-30) cc_final: 0.8181 (m-30)
REVERT: N   72 ASP cc_start: 0.8682 (m-30) cc_final: 0.8363 (m-30)
REVERT: O   69 LYS cc_start: 0.9160 (tmtt) cc_final: 0.8236 (ttmt)
REVERT: O   72 ASP cc_start: 0.8822 (m-30) cc_final: 0.8520 (m-30)
REVERT: P   32 ASP cc_start: 0.8292 (m-30) cc_final: 0.8085 (m-30)
REVERT: P   69 LYS cc_start: 0.9009 (tmtt) cc_final: 0.8046 (ttmt)
REVERT: P   77 GLN cc_start: 0.8767 (tt0) cc_final: 0.8534 (tm-30)
REVERT: Q   15 LYS cc_start: 0.8788 (mttp) cc_final: 0.7593 (ttpt)
REVERT: Q   25 THR cc_start: 0.9095 (m) cc_final: 0.8786 (p)
REVERT: Q   69 LYS cc_start: 0.9060 (tmtt) cc_final: 0.7600 (tttt)
REVERT: R   15 LYS cc_start: 0.8515 (mttp) cc_final: 0.7457 (ttpt)
REVERT: R   69 LYS cc_start: 0.9193 (tmtt) cc_final: 0.7976 (ttmt)
REVERT: R   77 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8401 (tm-30)
  outliers start: 7
  outliers final: 4
  residues processed: 308
  average time/residue: 0.2333
  time to fit residues: 100.7105
Evaluate side-chains
  288 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 283
  time to evaluate  : 1.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain M residue   53 GLU
Chi-restraints excluded: chain N residue   15 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 111 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0000
   chunk 121 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 82 optimal weight:    0.6980
   chunk 98 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.5390

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

Flipped N/Q/H residues before XYZ refinement:
B  61 GLN
C  63 ASN
D  55 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.091105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.081380 restraints weight = 18817.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 1.72
r_work: 0.2858 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2747 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.4019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  11214  Z= 0.173
  Angle     :  0.460   5.017  15264  Z= 0.247
  Chirality :  0.036   0.107   1746
  Planarity :  0.003   0.026   1998
  Dihedral  :  3.673  17.996   1512
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 13.72 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.00 (0.21), residues: 1368
  helix:  2.46 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -1.92 (0.49), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP M   5 
 PHE   0.008   0.001   PHE O  68 
 TYR   0.012   0.001   TYR J  57 
 ARG   0.002   0.000   ARG K  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03690 (  900)
  hydrogen bonds       : angle       3.05551 ( 2700)
  covalent geometry    : bond        0.00387 (11214)
  covalent geometry    : angle       0.46030 (15264)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 320
  time to evaluate  : 1.359 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8811 (ttmt)
REVERT: B   37 LYS cc_start: 0.8906 (ttmt) cc_final: 0.7696 (tptt)
REVERT: B   56 LEU cc_start: 0.9421 (mt) cc_final: 0.9106 (mt)
REVERT: B   66 LYS cc_start: 0.8886 (tptp) cc_final: 0.7734 (ttmt)
REVERT: B   69 LYS cc_start: 0.9035 (tmtt) cc_final: 0.8778 (tttm)
REVERT: C   10 ASP cc_start: 0.8742 (m-30) cc_final: 0.8245 (m-30)
REVERT: C   37 LYS cc_start: 0.8987 (ttmt) cc_final: 0.7496 (tptt)
REVERT: C   69 LYS cc_start: 0.9139 (tmtt) cc_final: 0.8854 (tttm)
REVERT: C   72 ASP cc_start: 0.9264 (m-30) cc_final: 0.8887 (m-30)
REVERT: D   10 ASP cc_start: 0.8687 (m-30) cc_final: 0.7976 (m-30)
REVERT: D   66 LYS cc_start: 0.8876 (tptp) cc_final: 0.7262 (mttm)
REVERT: E   37 LYS cc_start: 0.9181 (ttmt) cc_final: 0.7889 (tptt)
REVERT: F   10 ASP cc_start: 0.8612 (m-30) cc_final: 0.8231 (m-30)
REVERT: F   25 THR cc_start: 0.8839 (m) cc_final: 0.8615 (p)
REVERT: F   37 LYS cc_start: 0.9102 (ttmt) cc_final: 0.7513 (tptt)
REVERT: G   10 ASP cc_start: 0.8721 (m-30) cc_final: 0.8519 (m-30)
REVERT: G   33 LYS cc_start: 0.8882 (mttt) cc_final: 0.8669 (mtpp)
REVERT: G   53 GLU cc_start: 0.8258 (mm-30) cc_final: 0.8033 (mm-30)
REVERT: H   10 ASP cc_start: 0.8816 (m-30) cc_final: 0.8573 (m-30)
REVERT: H   64 THR cc_start: 0.9535 (m) cc_final: 0.9303 (m)
REVERT: H   72 ASP cc_start: 0.9303 (m-30) cc_final: 0.8908 (m-30)
REVERT: I    8 TYR cc_start: 0.8769 (t80) cc_final: 0.8425 (t80)
REVERT: I   53 GLU cc_start: 0.8501 (mt-10) cc_final: 0.7980 (mt-10)
REVERT: I   69 LYS cc_start: 0.9009 (tmtt) cc_final: 0.8598 (tttp)
REVERT: J   10 ASP cc_start: 0.8680 (m-30) cc_final: 0.8325 (m-30)
REVERT: K   31 LEU cc_start: 0.9362 (tp) cc_final: 0.9152 (tp)
REVERT: L   39 SER cc_start: 0.8867 (m) cc_final: 0.8287 (m)
REVERT: M   69 LYS cc_start: 0.9220 (tmtt) cc_final: 0.7920 (ttmt)
REVERT: N   15 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.7538 (ttpt)
REVERT: N   69 LYS cc_start: 0.9172 (tmtt) cc_final: 0.8031 (ttmt)
REVERT: N   70 ASP cc_start: 0.8596 (m-30) cc_final: 0.8383 (m-30)
REVERT: O   69 LYS cc_start: 0.9186 (tmtt) cc_final: 0.8172 (ttmt)
REVERT: O   72 ASP cc_start: 0.8777 (m-30) cc_final: 0.8482 (m-30)
REVERT: P   54 TYR cc_start: 0.9296 (t80) cc_final: 0.8985 (t80)
REVERT: P   69 LYS cc_start: 0.9134 (tmtt) cc_final: 0.8141 (ttmt)
REVERT: Q   25 THR cc_start: 0.9117 (m) cc_final: 0.8799 (p)
REVERT: Q   32 ASP cc_start: 0.8409 (m-30) cc_final: 0.7977 (m-30)
REVERT: Q   69 LYS cc_start: 0.9065 (tmtt) cc_final: 0.7593 (tttt)
REVERT: R   15 LYS cc_start: 0.8497 (mttp) cc_final: 0.7461 (ttpt)
REVERT: R   69 LYS cc_start: 0.9224 (tmtt) cc_final: 0.8045 (ttmt)
REVERT: R   72 ASP cc_start: 0.8990 (m-30) cc_final: 0.8746 (m-30)
REVERT: R   77 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8370 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 326
  average time/residue: 0.2444
  time to fit residues: 111.3059
Evaluate side-chains
  301 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 291
  time to evaluate  : 1.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain D residue   32 ASP
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain E residue   39 SER
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain M residue   53 GLU
Chi-restraints excluded: chain N residue   15 LYS
Chi-restraints excluded: chain O residue   27 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 38 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   chunk 13 optimal weight:    0.7980
   chunk 14 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 118 optimal weight:    2.9990
   chunk 115 optimal weight:    0.9990
   chunk 110 optimal weight:    3.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
D  55 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.092873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.083139 restraints weight = 18956.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 1.73
r_work: 0.2886 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.4210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  11214  Z= 0.118
  Angle     :  0.420   5.749  15264  Z= 0.223
  Chirality :  0.034   0.110   1746
  Planarity :  0.003   0.027   1998
  Dihedral  :  3.559  16.324   1512
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 14.81 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.47 (0.21), residues: 1368
  helix:  2.81 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -2.17 (0.47), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP N   5 
 PHE   0.006   0.001   PHE N  68 
 TYR   0.008   0.001   TYR B  47 
 ARG   0.001   0.000   ARG A  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03152 (  900)
  hydrogen bonds       : angle       2.97635 ( 2700)
  covalent geometry    : bond        0.00252 (11214)
  covalent geometry    : angle       0.41965 (15264)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 311
  time to evaluate  : 2.238 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 LYS cc_start: 0.9002 (ttmm) cc_final: 0.8793 (ttmt)
REVERT: B   37 LYS cc_start: 0.9012 (ttmt) cc_final: 0.7704 (tptt)
REVERT: B   56 LEU cc_start: 0.9406 (mt) cc_final: 0.9041 (mt)
REVERT: B   66 LYS cc_start: 0.8858 (tptp) cc_final: 0.7734 (ttmt)
REVERT: B   69 LYS cc_start: 0.8936 (tmtt) cc_final: 0.8676 (tttm)
REVERT: C   10 ASP cc_start: 0.8694 (m-30) cc_final: 0.8143 (m-30)
REVERT: C   37 LYS cc_start: 0.8971 (ttmt) cc_final: 0.7539 (tptt)
REVERT: C   69 LYS cc_start: 0.9127 (tmtt) cc_final: 0.8854 (tttm)
REVERT: C   72 ASP cc_start: 0.9222 (m-30) cc_final: 0.8831 (m-30)
REVERT: D   10 ASP cc_start: 0.8628 (m-30) cc_final: 0.7948 (m-30)
REVERT: D   66 LYS cc_start: 0.8852 (tptp) cc_final: 0.7257 (mttm)
REVERT: D   69 LYS cc_start: 0.8919 (ttpp) cc_final: 0.8566 (tttm)
REVERT: E   37 LYS cc_start: 0.9170 (ttmt) cc_final: 0.7910 (tptt)
REVERT: E   66 LYS cc_start: 0.8667 (tptp) cc_final: 0.7781 (tppt)
REVERT: F   10 ASP cc_start: 0.8583 (m-30) cc_final: 0.8206 (m-30)
REVERT: F   37 LYS cc_start: 0.9060 (ttmt) cc_final: 0.7498 (tptt)
REVERT: G   10 ASP cc_start: 0.8706 (m-30) cc_final: 0.8488 (m-30)
REVERT: G   33 LYS cc_start: 0.8817 (mttt) cc_final: 0.8606 (mtpp)
REVERT: H   10 ASP cc_start: 0.8815 (m-30) cc_final: 0.8615 (m-30)
REVERT: H   72 ASP cc_start: 0.9267 (m-30) cc_final: 0.8882 (m-30)
REVERT: I    8 TYR cc_start: 0.8703 (t80) cc_final: 0.8336 (t80)
REVERT: I   53 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7889 (mt-10)
REVERT: I   69 LYS cc_start: 0.8986 (tmtt) cc_final: 0.8526 (tttp)
REVERT: J   10 ASP cc_start: 0.8614 (m-30) cc_final: 0.8399 (m-30)
REVERT: K   31 LEU cc_start: 0.9331 (tp) cc_final: 0.9107 (tp)
REVERT: L   39 SER cc_start: 0.8890 (m) cc_final: 0.8211 (m)
REVERT: M   69 LYS cc_start: 0.9241 (tmtt) cc_final: 0.7937 (ttmt)
REVERT: N   15 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.7573 (ttpt)
REVERT: N   24 GLN cc_start: 0.7761 (mp10) cc_final: 0.7526 (mp10)
REVERT: N   69 LYS cc_start: 0.9147 (tmtt) cc_final: 0.7978 (ttmt)
REVERT: O   69 LYS cc_start: 0.9212 (tmtt) cc_final: 0.8076 (ttmt)
REVERT: P   54 TYR cc_start: 0.9282 (t80) cc_final: 0.9059 (t80)
REVERT: P   69 LYS cc_start: 0.9156 (tmtt) cc_final: 0.8112 (ttmt)
REVERT: P   77 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8062 (tm-30)
REVERT: Q   25 THR cc_start: 0.9150 (m) cc_final: 0.8813 (p)
REVERT: Q   32 ASP cc_start: 0.8373 (m-30) cc_final: 0.7929 (m-30)
REVERT: Q   69 LYS cc_start: 0.9057 (tmtt) cc_final: 0.7534 (tttt)
REVERT: R   15 LYS cc_start: 0.8490 (mttp) cc_final: 0.7478 (ttpt)
REVERT: R   69 LYS cc_start: 0.9189 (tmtt) cc_final: 0.7989 (ttmt)
REVERT: R   77 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8416 (tm-30)
  outliers start: 8
  outliers final: 4
  residues processed: 314
  average time/residue: 0.3527
  time to fit residues: 156.6754
Evaluate side-chains
  300 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 295
  time to evaluate  : 1.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain M residue   53 GLU
Chi-restraints excluded: chain N residue   15 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 7 optimal weight:    6.9990
   chunk 98 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
D  55 ASN
O  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.091068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.081382 restraints weight = 19168.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.2957 rms_B_bonded: 1.73
r_work: 0.2856 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2746 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.4241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  11214  Z= 0.157
  Angle     :  0.447   4.902  15264  Z= 0.239
  Chirality :  0.035   0.107   1746
  Planarity :  0.003   0.023   1998
  Dihedral  :  3.637  16.511   1512
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 14.98 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.50 (0.21), residues: 1368
  helix:  2.86 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -2.37 (0.46), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G   5 
 PHE   0.007   0.001   PHE O  68 
 TYR   0.010   0.001   TYR J  57 
 ARG   0.001   0.000   ARG A  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03443 (  900)
  hydrogen bonds       : angle       3.02257 ( 2700)
  covalent geometry    : bond        0.00351 (11214)
  covalent geometry    : angle       0.44669 (15264)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 306
  time to evaluate  : 1.368 
Fit side-chains
   revert: symmetry clash
REVERT: B   37 LYS cc_start: 0.9024 (ttmt) cc_final: 0.7687 (tptt)
REVERT: B   56 LEU cc_start: 0.9412 (mt) cc_final: 0.9059 (mt)
REVERT: B   66 LYS cc_start: 0.8797 (tptp) cc_final: 0.7606 (ttmt)
REVERT: B   69 LYS cc_start: 0.8983 (tmtt) cc_final: 0.8734 (tttm)
REVERT: C   10 ASP cc_start: 0.8730 (m-30) cc_final: 0.8179 (m-30)
REVERT: C   37 LYS cc_start: 0.8987 (ttmt) cc_final: 0.7546 (tptt)
REVERT: C   69 LYS cc_start: 0.9125 (tmtt) cc_final: 0.8843 (tttm)
REVERT: C   72 ASP cc_start: 0.9239 (m-30) cc_final: 0.8862 (m-30)
REVERT: D   10 ASP cc_start: 0.8653 (m-30) cc_final: 0.7966 (m-30)
REVERT: D   66 LYS cc_start: 0.8853 (tptp) cc_final: 0.7871 (ttmt)
REVERT: D   69 LYS cc_start: 0.8931 (ttpp) cc_final: 0.8571 (tttm)
REVERT: E   37 LYS cc_start: 0.9178 (ttmt) cc_final: 0.7874 (tptt)
REVERT: E   66 LYS cc_start: 0.8649 (tptp) cc_final: 0.7763 (tppt)
REVERT: F   10 ASP cc_start: 0.8593 (m-30) cc_final: 0.8208 (m-30)
REVERT: F   37 LYS cc_start: 0.9071 (ttmt) cc_final: 0.7499 (tptt)
REVERT: G   10 ASP cc_start: 0.8738 (m-30) cc_final: 0.8535 (m-30)
REVERT: G   32 ASP cc_start: 0.8432 (m-30) cc_final: 0.7939 (m-30)
REVERT: G   33 LYS cc_start: 0.8856 (mttt) cc_final: 0.8653 (mtpp)
REVERT: G   53 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8093 (mm-30)
REVERT: H   72 ASP cc_start: 0.9301 (m-30) cc_final: 0.8940 (m-30)
REVERT: I    8 TYR cc_start: 0.8749 (t80) cc_final: 0.8449 (t80)
REVERT: I   53 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7908 (mt-10)
REVERT: I   69 LYS cc_start: 0.8983 (tmtt) cc_final: 0.8542 (tttp)
REVERT: J   10 ASP cc_start: 0.8607 (m-30) cc_final: 0.8070 (m-30)
REVERT: K   31 LEU cc_start: 0.9346 (tp) cc_final: 0.9142 (tp)
REVERT: L   39 SER cc_start: 0.8799 (m) cc_final: 0.8328 (m)
REVERT: M   69 LYS cc_start: 0.9229 (tmtt) cc_final: 0.7919 (ttmt)
REVERT: N   15 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.7551 (ttpt)
REVERT: N   24 GLN cc_start: 0.7699 (mp10) cc_final: 0.7476 (mp10)
REVERT: N   69 LYS cc_start: 0.9139 (tmtt) cc_final: 0.7983 (ttmt)
REVERT: O   69 LYS cc_start: 0.9169 (tmtt) cc_final: 0.8050 (ttmt)
REVERT: P   53 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7950 (mt-10)
REVERT: P   54 TYR cc_start: 0.9310 (t80) cc_final: 0.9055 (t80)
REVERT: P   69 LYS cc_start: 0.9160 (tmtt) cc_final: 0.8086 (ttmt)
REVERT: P   77 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8102 (tm-30)
REVERT: Q   25 THR cc_start: 0.9119 (m) cc_final: 0.8799 (p)
REVERT: Q   32 ASP cc_start: 0.8363 (m-30) cc_final: 0.7910 (m-30)
REVERT: Q   69 LYS cc_start: 0.9082 (tmtt) cc_final: 0.7571 (tttt)
REVERT: R   69 LYS cc_start: 0.9213 (tmtt) cc_final: 0.8043 (ttmt)
REVERT: R   77 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8454 (tm-30)
  outliers start: 13
  outliers final: 9
  residues processed: 314
  average time/residue: 0.2255
  time to fit residues: 99.2280
Evaluate side-chains
  310 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 300
  time to evaluate  : 1.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   32 ASP
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain E residue   39 SER
Chi-restraints excluded: chain G residue   25 THR
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain M residue   53 GLU
Chi-restraints excluded: chain N residue   15 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 64 optimal weight:    0.2980
   chunk 101 optimal weight:    0.8980
   chunk 84 optimal weight:    5.9990
   chunk 120 optimal weight:    4.9990
   chunk 95 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 114 optimal weight:    4.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
D  55 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.091428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.081806 restraints weight = 18892.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 1.72
r_work: 0.2863 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.4322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  11214  Z= 0.142
  Angle     :  0.441   6.466  15264  Z= 0.234
  Chirality :  0.035   0.109   1746
  Planarity :  0.003   0.023   1998
  Dihedral  :  3.609  15.941   1512
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 15.49 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.65 (0.21), residues: 1368
  helix:  2.98 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -2.57 (0.45), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G   5 
 PHE   0.007   0.001   PHE O  68 
 TYR   0.009   0.001   TYR J  57 
 ARG   0.001   0.000   ARG A  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03287 (  900)
  hydrogen bonds       : angle       3.01581 ( 2700)
  covalent geometry    : bond        0.00314 (11214)
  covalent geometry    : angle       0.44108 (15264)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 302
  time to evaluate  : 2.426 
Fit side-chains
   revert: symmetry clash
REVERT: B   37 LYS cc_start: 0.9016 (ttmt) cc_final: 0.7654 (tptt)
REVERT: B   56 LEU cc_start: 0.9417 (mt) cc_final: 0.9051 (mt)
REVERT: B   66 LYS cc_start: 0.8791 (tptp) cc_final: 0.7615 (ttmt)
REVERT: B   69 LYS cc_start: 0.8982 (tmtt) cc_final: 0.8737 (tttm)
REVERT: C   10 ASP cc_start: 0.8728 (m-30) cc_final: 0.8191 (m-30)
REVERT: C   37 LYS cc_start: 0.8998 (ttmt) cc_final: 0.7561 (tptt)
REVERT: C   69 LYS cc_start: 0.9122 (tmtt) cc_final: 0.8846 (tttm)
REVERT: C   72 ASP cc_start: 0.9208 (m-30) cc_final: 0.8822 (m-30)
REVERT: D   10 ASP cc_start: 0.8634 (m-30) cc_final: 0.7946 (m-30)
REVERT: D   66 LYS cc_start: 0.8857 (tptp) cc_final: 0.7825 (ttmt)
REVERT: D   69 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8568 (tttm)
REVERT: E   37 LYS cc_start: 0.9167 (ttmt) cc_final: 0.7866 (tptt)
REVERT: E   66 LYS cc_start: 0.8658 (tptp) cc_final: 0.7795 (tppt)
REVERT: F   10 ASP cc_start: 0.8588 (m-30) cc_final: 0.8164 (m-30)
REVERT: F   37 LYS cc_start: 0.9067 (ttmt) cc_final: 0.7506 (tptt)
REVERT: G   10 ASP cc_start: 0.8726 (m-30) cc_final: 0.8513 (m-30)
REVERT: G   33 LYS cc_start: 0.8914 (mttt) cc_final: 0.8699 (mtpp)
REVERT: H   10 ASP cc_start: 0.8878 (m-30) cc_final: 0.8661 (m-30)
REVERT: H   72 ASP cc_start: 0.9280 (m-30) cc_final: 0.8947 (m-30)
REVERT: I    8 TYR cc_start: 0.8730 (t80) cc_final: 0.8364 (t80)
REVERT: I   53 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7914 (mt-10)
REVERT: I   69 LYS cc_start: 0.8981 (tmtt) cc_final: 0.8534 (tttp)
REVERT: J   10 ASP cc_start: 0.8602 (m-30) cc_final: 0.8042 (m-30)
REVERT: K   31 LEU cc_start: 0.9342 (tp) cc_final: 0.9125 (tp)
REVERT: L   39 SER cc_start: 0.8806 (m) cc_final: 0.8544 (p)
REVERT: M   69 LYS cc_start: 0.9223 (tmtt) cc_final: 0.7920 (ttmt)
REVERT: N   15 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.7553 (ttpt)
REVERT: N   24 GLN cc_start: 0.7744 (mp10) cc_final: 0.7508 (mp10)
REVERT: N   69 LYS cc_start: 0.9138 (tmtt) cc_final: 0.7972 (ttmt)
REVERT: O   69 LYS cc_start: 0.9170 (tmtt) cc_final: 0.8050 (ttmt)
REVERT: P   21 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7956 (t0)
REVERT: P   53 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7924 (mt-10)
REVERT: P   54 TYR cc_start: 0.9302 (t80) cc_final: 0.9099 (t80)
REVERT: P   69 LYS cc_start: 0.9150 (tmtt) cc_final: 0.8039 (ttmt)
REVERT: P   77 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8496 (tm-30)
REVERT: Q   25 THR cc_start: 0.9129 (m) cc_final: 0.8816 (p)
REVERT: Q   32 ASP cc_start: 0.8359 (m-30) cc_final: 0.7945 (m-30)
REVERT: Q   69 LYS cc_start: 0.9080 (tmtt) cc_final: 0.7565 (tttt)
REVERT: R   69 LYS cc_start: 0.9214 (tmtt) cc_final: 0.8039 (ttmt)
  outliers start: 13
  outliers final: 11
  residues processed: 310
  average time/residue: 0.2355
  time to fit residues: 102.5179
Evaluate side-chains
  308 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 295
  time to evaluate  : 1.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   32 ASP
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain E residue   39 SER
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain M residue   53 GLU
Chi-restraints excluded: chain N residue   15 LYS
Chi-restraints excluded: chain O residue   57 TYR
Chi-restraints excluded: chain P residue   21 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 107 optimal weight:    4.9990
   chunk 93 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 105 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 108 optimal weight:    0.4980
   chunk 2 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 121 optimal weight:    1.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
D  55 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.090478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.080869 restraints weight = 19014.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 1.72
r_work: 0.2843 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2733 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.4325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  11214  Z= 0.165
  Angle     :  0.461   4.381  15264  Z= 0.245
  Chirality :  0.036   0.111   1746
  Planarity :  0.003   0.022   1998
  Dihedral  :  3.670  16.986   1512
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 15.49 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.59 (0.21), residues: 1368
  helix:  2.95 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -2.70 (0.45), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G   5 
 PHE   0.008   0.001   PHE O  68 
 TYR   0.011   0.001   TYR J  57 
 ARG   0.001   0.000   ARG N  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03442 (  900)
  hydrogen bonds       : angle       3.04554 ( 2700)
  covalent geometry    : bond        0.00373 (11214)
  covalent geometry    : angle       0.46055 (15264)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 302
  time to evaluate  : 1.333 
Fit side-chains
   revert: symmetry clash
REVERT: B   37 LYS cc_start: 0.8997 (ttmt) cc_final: 0.7612 (tptt)
REVERT: B   56 LEU cc_start: 0.9415 (mt) cc_final: 0.9110 (mt)
REVERT: B   66 LYS cc_start: 0.8801 (tptp) cc_final: 0.7620 (ttmt)
REVERT: B   69 LYS cc_start: 0.8989 (tmtt) cc_final: 0.8740 (tttm)
REVERT: C   10 ASP cc_start: 0.8736 (m-30) cc_final: 0.8140 (m-30)
REVERT: C   37 LYS cc_start: 0.9007 (ttmt) cc_final: 0.7560 (tptt)
REVERT: C   69 LYS cc_start: 0.9126 (tmtt) cc_final: 0.8849 (tttm)
REVERT: C   72 ASP cc_start: 0.9232 (m-30) cc_final: 0.8853 (m-30)
REVERT: D   10 ASP cc_start: 0.8671 (m-30) cc_final: 0.7943 (m-30)
REVERT: D   66 LYS cc_start: 0.8846 (tptp) cc_final: 0.7861 (ttmt)
REVERT: D   69 LYS cc_start: 0.8893 (ttpp) cc_final: 0.8573 (tttm)
REVERT: E   37 LYS cc_start: 0.9176 (ttmt) cc_final: 0.7869 (tptt)
REVERT: E   66 LYS cc_start: 0.8672 (tptp) cc_final: 0.7792 (tppt)
REVERT: F   10 ASP cc_start: 0.8602 (m-30) cc_final: 0.8222 (m-30)
REVERT: F   24 GLN cc_start: 0.8023 (mp10) cc_final: 0.7804 (mp10)
REVERT: F   37 LYS cc_start: 0.9100 (ttmt) cc_final: 0.7511 (tptt)
REVERT: G   10 ASP cc_start: 0.8744 (m-30) cc_final: 0.8533 (m-30)
REVERT: G   32 ASP cc_start: 0.8438 (m-30) cc_final: 0.7982 (m-30)
REVERT: G   33 LYS cc_start: 0.8934 (mttt) cc_final: 0.8711 (mtpp)
REVERT: H   72 ASP cc_start: 0.9307 (m-30) cc_final: 0.8994 (m-30)
REVERT: I    8 TYR cc_start: 0.8761 (t80) cc_final: 0.8433 (t80)
REVERT: I   53 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7878 (mt-10)
REVERT: I   69 LYS cc_start: 0.8991 (tmtt) cc_final: 0.8559 (tttp)
REVERT: J   10 ASP cc_start: 0.8597 (m-30) cc_final: 0.8315 (m-30)
REVERT: M   69 LYS cc_start: 0.9230 (tmtt) cc_final: 0.7916 (ttmt)
REVERT: N   15 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.7532 (ttpt)
REVERT: N   24 GLN cc_start: 0.7668 (mp10) cc_final: 0.7434 (mp10)
REVERT: N   69 LYS cc_start: 0.9140 (tmtt) cc_final: 0.7979 (ttmt)
REVERT: O   69 LYS cc_start: 0.9170 (tmtt) cc_final: 0.8037 (ttmt)
REVERT: O   72 ASP cc_start: 0.8805 (m-30) cc_final: 0.8514 (m-30)
REVERT: P   21 ASP cc_start: 0.8324 (t0) cc_final: 0.8075 (t0)
REVERT: P   53 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8268 (mt-10)
REVERT: P   54 TYR cc_start: 0.9290 (t80) cc_final: 0.9030 (t80)
REVERT: P   69 LYS cc_start: 0.9166 (tmtt) cc_final: 0.8031 (ttmt)
REVERT: P   77 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8495 (tm-30)
REVERT: Q   25 THR cc_start: 0.9128 (m) cc_final: 0.8801 (p)
REVERT: Q   32 ASP cc_start: 0.8367 (m-30) cc_final: 0.7903 (m-30)
REVERT: Q   69 LYS cc_start: 0.9085 (tmtt) cc_final: 0.7569 (tttt)
REVERT: R   69 LYS cc_start: 0.9214 (tmtt) cc_final: 0.8039 (ttmt)
  outliers start: 15
  outliers final: 11
  residues processed: 312
  average time/residue: 0.2586
  time to fit residues: 113.7301
Evaluate side-chains
  306 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 294
  time to evaluate  : 1.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   32 ASP
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain E residue   39 SER
Chi-restraints excluded: chain G residue   25 THR
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain M residue   53 GLU
Chi-restraints excluded: chain N residue   15 LYS
Chi-restraints excluded: chain O residue   57 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 91 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 70 optimal weight:    6.9990
   chunk 81 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
D  55 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.092792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.083338 restraints weight = 18816.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 1.67
r_work: 0.2891 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2783 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.4443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  11214  Z= 0.110
  Angle     :  0.424   4.390  15264  Z= 0.226
  Chirality :  0.034   0.110   1746
  Planarity :  0.003   0.022   1998
  Dihedral  :  3.558  14.099   1512
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 16.33 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.89 (0.21), residues: 1368
  helix:  3.16 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -2.67 (0.45), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K   5 
 PHE   0.005   0.001   PHE N  68 
 TYR   0.010   0.001   TYR K  47 
 ARG   0.001   0.000   ARG P  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02988 (  900)
  hydrogen bonds       : angle       2.97324 ( 2700)
  covalent geometry    : bond        0.00234 (11214)
  covalent geometry    : angle       0.42358 (15264)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 309
  time to evaluate  : 1.383 
Fit side-chains
   revert: symmetry clash
REVERT: B   37 LYS cc_start: 0.9009 (ttmt) cc_final: 0.7637 (tptt)
REVERT: B   56 LEU cc_start: 0.9394 (mt) cc_final: 0.9033 (mt)
REVERT: B   66 LYS cc_start: 0.8776 (tptp) cc_final: 0.7598 (ttmt)
REVERT: B   69 LYS cc_start: 0.8961 (tmtt) cc_final: 0.8717 (tttm)
REVERT: C   10 ASP cc_start: 0.8650 (m-30) cc_final: 0.8108 (m-30)
REVERT: C   69 LYS cc_start: 0.9101 (tmtt) cc_final: 0.8824 (tttm)
REVERT: C   72 ASP cc_start: 0.9144 (m-30) cc_final: 0.8732 (m-30)
REVERT: D   10 ASP cc_start: 0.8589 (m-30) cc_final: 0.7962 (m-30)
REVERT: D   66 LYS cc_start: 0.8834 (tptp) cc_final: 0.7248 (mttm)
REVERT: D   69 LYS cc_start: 0.8912 (ttpp) cc_final: 0.8655 (tttm)
REVERT: E   37 LYS cc_start: 0.9158 (ttmt) cc_final: 0.7858 (tptt)
REVERT: E   66 LYS cc_start: 0.8671 (tptp) cc_final: 0.7741 (tppt)
REVERT: F   10 ASP cc_start: 0.8565 (m-30) cc_final: 0.8147 (m-30)
REVERT: F   24 GLN cc_start: 0.8004 (mp10) cc_final: 0.7785 (mp10)
REVERT: F   37 LYS cc_start: 0.9032 (ttmt) cc_final: 0.7516 (tptt)
REVERT: G   10 ASP cc_start: 0.8675 (m-30) cc_final: 0.8456 (m-30)
REVERT: G   33 LYS cc_start: 0.8853 (mttt) cc_final: 0.8646 (mtpp)
REVERT: H   72 ASP cc_start: 0.9256 (m-30) cc_final: 0.8950 (m-30)
REVERT: I    8 TYR cc_start: 0.8659 (t80) cc_final: 0.8304 (t80)
REVERT: I   53 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7839 (mt-10)
REVERT: I   69 LYS cc_start: 0.8980 (tmtt) cc_final: 0.8528 (tttp)
REVERT: J   10 ASP cc_start: 0.8607 (m-30) cc_final: 0.8390 (m-30)
REVERT: M   69 LYS cc_start: 0.9243 (tmtt) cc_final: 0.8244 (ttmt)
REVERT: N   15 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.7580 (ttpt)
REVERT: N   24 GLN cc_start: 0.7745 (mp10) cc_final: 0.7509 (mp10)
REVERT: N   69 LYS cc_start: 0.9133 (tmtt) cc_final: 0.7975 (ttmt)
REVERT: O   69 LYS cc_start: 0.9209 (tmtt) cc_final: 0.8071 (ttmt)
REVERT: P   21 ASP cc_start: 0.8182 (t0) cc_final: 0.7908 (t0)
REVERT: P   54 TYR cc_start: 0.9295 (t80) cc_final: 0.9082 (t80)
REVERT: P   69 LYS cc_start: 0.9177 (tmtt) cc_final: 0.8037 (ttmt)
REVERT: P   77 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8436 (tm-30)
REVERT: Q   25 THR cc_start: 0.9102 (m) cc_final: 0.8822 (p)
REVERT: Q   32 ASP cc_start: 0.8329 (m-30) cc_final: 0.7886 (m-30)
REVERT: Q   69 LYS cc_start: 0.9057 (tmtt) cc_final: 0.7567 (tttt)
REVERT: R   21 ASP cc_start: 0.8068 (m-30) cc_final: 0.7842 (m-30)
REVERT: R   69 LYS cc_start: 0.9211 (tmtt) cc_final: 0.8042 (ttmt)
REVERT: R   77 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8241 (tm-30)
  outliers start: 11
  outliers final: 9
  residues processed: 316
  average time/residue: 0.2205
  time to fit residues: 98.4920
Evaluate side-chains
  311 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 301
  time to evaluate  : 1.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   32 ASP
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain E residue   39 SER
Chi-restraints excluded: chain G residue   25 THR
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain N residue   15 LYS
Chi-restraints excluded: chain O residue   57 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 91 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 114 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
D  55 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.090277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.080577 restraints weight = 18832.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 1.75
r_work: 0.2835 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2725 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.4370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11214  Z= 0.177
  Angle     :  0.474   5.039  15264  Z= 0.253
  Chirality :  0.036   0.117   1746
  Planarity :  0.003   0.021   1998
  Dihedral  :  3.699  17.905   1512
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 16.67 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.63 (0.21), residues: 1368
  helix:  2.99 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -2.74 (0.45), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G   5 
 PHE   0.008   0.001   PHE O  68 
 TYR   0.011   0.001   TYR J  57 
 ARG   0.001   0.000   ARG N  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03505 (  900)
  hydrogen bonds       : angle       3.07850 ( 2700)
  covalent geometry    : bond        0.00400 (11214)
  covalent geometry    : angle       0.47442 (15264)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5501.43 seconds
wall clock time: 99 minutes 32.82 seconds (5972.82 seconds total)