Starting phenix.real_space_refine
on Sat Aug 23 08:06:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6off_20044/08_2025/6off_20044_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6off_20044/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6off_20044/08_2025/6off_20044_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6off_20044/08_2025/6off_20044_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6off_20044/08_2025/6off_20044.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6off_20044/08_2025/6off_20044.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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:
    B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
  Time building chain proxies: 0.95, per 1000 atoms: 0.09
  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: 0.68
  Conformation dependent library (CDL) restraints added in 290.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.29
  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: 1.47

  Time building geometry restraints manager: 0.90 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  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:             1.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.510
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.230
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.004   0.001   ARG I  58 
 TYR   0.011   0.002   TYR O  57 
 PHE   0.012   0.003   PHE O  79 
 TRP   0.014   0.003   TRP H   5 

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

*********************** 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  : 0.406 
Fit side-chains
REVERT: A   66 LYS cc_start: 0.8617 (tptp) cc_final: 0.7190 (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: 0.7986 (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: 0.7935 (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: 0.8481 (t80)
REVERT: M   29 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7069 (mt-10)
REVERT: M   69 LYS cc_start: 0.8962 (tmtt) cc_final: 0.7840 (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: 0.0887
  time to fit residues: 48.9515
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  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 123 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   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
G  61 GLN
H  61 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.101386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.091398 restraints weight = 18274.828|
|-----------------------------------------------------------------------------|
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: 0.8511
moved from start:          0.2806

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= 0.135
  Angle     :  0.476   3.990  15264  Z= 0.264
  Chirality :  0.033   0.118   1746
  Planarity :  0.005   0.029   1998
  Dihedral  :  4.078  18.164   1512
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  9.34 %
    Favored  : 89.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.51 (0.20), residues: 1368
  helix: -0.02 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -1.75 (0.51), residues: 162

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (11214)
  covalent geometry    : angle       0.47567 (15264)
  hydrogen bonds       : bond        0.03769 (  900)
  hydrogen bonds       : angle       3.47149 ( 2700)

*********************** 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
  360 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 346
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ASP cc_start: 0.8646 (m-30) cc_final: 0.8276 (m-30)
REVERT: A   39 SER cc_start: 0.8634 (m) cc_final: 0.8389 (p)
REVERT: B   37 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7001 (tptt)
REVERT: B   66 LYS cc_start: 0.8391 (tptp) cc_final: 0.7028 (ttmm)
REVERT: C    4 PRO cc_start: 0.8118 (Cg_endo) cc_final: 0.7899 (Cg_exo)
REVERT: C   10 ASP cc_start: 0.8577 (m-30) cc_final: 0.8370 (m-30)
REVERT: C   37 LYS cc_start: 0.9070 (ttmt) cc_final: 0.7602 (tptt)
REVERT: C   69 LYS cc_start: 0.9075 (tmtt) cc_final: 0.8752 (tttm)
REVERT: D   10 ASP cc_start: 0.8436 (m-30) cc_final: 0.7652 (m-30)
REVERT: D   69 LYS cc_start: 0.8917 (tmtt) cc_final: 0.8578 (tptp)
REVERT: D   72 ASP cc_start: 0.9149 (m-30) cc_final: 0.8801 (m-30)
REVERT: E   10 ASP cc_start: 0.8399 (m-30) cc_final: 0.7915 (m-30)
REVERT: E   37 LYS cc_start: 0.9094 (ttmt) cc_final: 0.7852 (tptt)
REVERT: E   57 TYR cc_start: 0.9297 (t80) cc_final: 0.9013 (t80)
REVERT: F   10 ASP cc_start: 0.8549 (m-30) cc_final: 0.8114 (m-30)
REVERT: F   37 LYS cc_start: 0.9076 (ttmt) cc_final: 0.7537 (tptt)
REVERT: G   33 LYS cc_start: 0.8787 (mttt) cc_final: 0.8433 (mtpp)
REVERT: G   37 LYS cc_start: 0.8672 (ttmt) cc_final: 0.6934 (tptp)
REVERT: H   37 LYS cc_start: 0.9011 (ttmt) cc_final: 0.7497 (tptt)
REVERT: H   72 ASP cc_start: 0.9117 (m-30) cc_final: 0.8701 (m-30)
REVERT: I    8 TYR cc_start: 0.8776 (t80) cc_final: 0.8341 (t80)
REVERT: J   10 ASP cc_start: 0.8563 (m-30) cc_final: 0.8204 (m-30)
REVERT: J   37 LYS cc_start: 0.8977 (ttmm) cc_final: 0.8769 (ttmt)
REVERT: K   10 ASP cc_start: 0.8403 (m-30) cc_final: 0.7950 (m-30)
REVERT: K   31 LEU cc_start: 0.9277 (tp) cc_final: 0.9021 (tp)
REVERT: L   10 ASP cc_start: 0.8699 (m-30) cc_final: 0.8421 (m-30)
REVERT: M    8 TYR cc_start: 0.8885 (t80) cc_final: 0.8575 (t80)
REVERT: M   69 LYS cc_start: 0.9184 (tmtt) cc_final: 0.7834 (ttmt)
REVERT: N   25 THR cc_start: 0.8894 (m) cc_final: 0.8606 (p)
REVERT: N   29 GLU cc_start: 0.7731 (tp30) cc_final: 0.7452 (tp30)
REVERT: N   69 LYS cc_start: 0.9115 (tmtt) cc_final: 0.8000 (ttmt)
REVERT: N   70 ASP cc_start: 0.8533 (m-30) cc_final: 0.8021 (m-30)
REVERT: O   15 LYS cc_start: 0.8616 (ttmm) cc_final: 0.7350 (tttt)
REVERT: O   29 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7984 (tp30)
REVERT: Q   15 LYS cc_start: 0.8822 (mttp) cc_final: 0.7710 (ttpt)
REVERT: Q   25 THR cc_start: 0.9143 (m) cc_final: 0.8745 (p)
REVERT: Q   32 ASP cc_start: 0.8464 (m-30) cc_final: 0.8213 (m-30)
REVERT: Q   53 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7665 (mt-10)
REVERT: R   15 LYS cc_start: 0.8524 (mttp) cc_final: 0.7437 (ttpt)
REVERT: R   69 LYS cc_start: 0.9124 (tmtt) cc_final: 0.7930 (ttmt)
  outliers start: 14
  outliers final: 3
  residues processed: 349
  average time/residue: 0.0895
  time to fit residues: 45.4380
Evaluate side-chains
  289 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 286
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 124 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.0582

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.094898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.084989 restraints weight = 18793.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 1.74
r_work: 0.2912 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.3601

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= 0.140
  Angle     :  0.448   5.599  15264  Z= 0.243
  Chirality :  0.034   0.113   1746
  Planarity :  0.003   0.025   1998
  Dihedral  :  3.720  16.500   1512
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 12.04 %
    Favored  : 87.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.21), residues: 1368
  helix:  1.55 (0.14), residues: 1206
  sheet:  None (None), residues: 0
  loop : -1.70 (0.52), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG P  80 
 TYR   0.013   0.001   TYR B  47 
 PHE   0.007   0.001   PHE O  68 
 TRP   0.007   0.001   TRP M   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (11214)
  covalent geometry    : angle       0.44797 (15264)
  hydrogen bonds       : bond        0.03793 (  900)
  hydrogen bonds       : angle       3.08644 ( 2700)

*********************** 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
  344 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 334
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 LYS cc_start: 0.8649 (ttmt) cc_final: 0.7392 (tptt)
REVERT: B   56 LEU cc_start: 0.9446 (mt) cc_final: 0.9099 (mt)
REVERT: B   66 LYS cc_start: 0.8814 (tptp) cc_final: 0.7627 (ttmt)
REVERT: B   69 LYS cc_start: 0.8799 (tptp) cc_final: 0.8595 (tttm)
REVERT: C   10 ASP cc_start: 0.8581 (m-30) cc_final: 0.7884 (m-30)
REVERT: C   24 GLN cc_start: 0.8219 (mp10) cc_final: 0.8008 (mp10)
REVERT: C   37 LYS cc_start: 0.8977 (ttmt) cc_final: 0.7509 (tptt)
REVERT: C   69 LYS cc_start: 0.9062 (tmtt) cc_final: 0.8768 (tttm)
REVERT: C   72 ASP cc_start: 0.9262 (m-30) cc_final: 0.8875 (m-30)
REVERT: D   10 ASP cc_start: 0.8615 (m-30) cc_final: 0.7997 (m-30)
REVERT: D   66 LYS cc_start: 0.8666 (tptp) cc_final: 0.7860 (ttmt)
REVERT: D   69 LYS cc_start: 0.9006 (tmtt) cc_final: 0.8686 (tptp)
REVERT: D   72 ASP cc_start: 0.9200 (m-30) cc_final: 0.8988 (m-30)
REVERT: E   37 LYS cc_start: 0.9181 (ttmt) cc_final: 0.7915 (tptt)
REVERT: F   10 ASP cc_start: 0.8545 (m-30) cc_final: 0.8097 (m-30)
REVERT: F   37 LYS cc_start: 0.9106 (ttmt) cc_final: 0.7520 (tptt)
REVERT: G   33 LYS cc_start: 0.8887 (mttt) cc_final: 0.8609 (mtpp)
REVERT: G   52 SER cc_start: 0.9000 (m) cc_final: 0.8531 (p)
REVERT: G   53 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7965 (mm-30)
REVERT: H   37 LYS cc_start: 0.9133 (ttmt) cc_final: 0.7494 (tptt)
REVERT: H   72 ASP cc_start: 0.9270 (m-30) cc_final: 0.8955 (m-30)
REVERT: I    8 TYR cc_start: 0.8756 (t80) cc_final: 0.8367 (t80)
REVERT: I   77 GLN cc_start: 0.9143 (tp40) cc_final: 0.8715 (tp40)
REVERT: J   10 ASP cc_start: 0.8624 (m-30) cc_final: 0.8374 (m-30)
REVERT: J   37 LYS cc_start: 0.8964 (ttmm) cc_final: 0.8722 (ttmt)
REVERT: J   72 ASP cc_start: 0.8581 (m-30) cc_final: 0.8099 (m-30)
REVERT: K   10 ASP cc_start: 0.8560 (m-30) cc_final: 0.8087 (m-30)
REVERT: K   31 LEU cc_start: 0.9315 (tp) cc_final: 0.9086 (tp)
REVERT: L   39 SER cc_start: 0.8887 (m) cc_final: 0.7927 (m)
REVERT: M   69 LYS cc_start: 0.9255 (tmtt) cc_final: 0.7927 (ttmt)
REVERT: N   15 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.7516 (ttpt)
REVERT: N   29 GLU cc_start: 0.7782 (tp30) cc_final: 0.7527 (tp30)
REVERT: N   69 LYS cc_start: 0.9138 (tmtt) cc_final: 0.8012 (ttmt)
REVERT: N   70 ASP cc_start: 0.8574 (m-30) cc_final: 0.8133 (m-30)
REVERT: O   69 LYS cc_start: 0.9156 (tmtt) cc_final: 0.8285 (ttmt)
REVERT: O   72 ASP cc_start: 0.8693 (m-30) cc_final: 0.8472 (m-30)
REVERT: P   69 LYS cc_start: 0.9059 (tmtt) cc_final: 0.8095 (ttmt)
REVERT: Q   15 LYS cc_start: 0.8786 (mttp) cc_final: 0.7852 (ttpt)
REVERT: Q   25 THR cc_start: 0.9113 (m) cc_final: 0.8775 (p)
REVERT: Q   32 ASP cc_start: 0.8507 (m-30) cc_final: 0.8133 (m-30)
REVERT: Q   69 LYS cc_start: 0.9036 (tmtt) cc_final: 0.7630 (tttt)
REVERT: R   15 LYS cc_start: 0.8524 (mttp) cc_final: 0.7464 (ttpt)
REVERT: R   69 LYS cc_start: 0.9181 (tmtt) cc_final: 0.7994 (ttmt)
REVERT: R   77 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8495 (tm-30)
  outliers start: 10
  outliers final: 4
  residues processed: 339
  average time/residue: 0.1061
  time to fit residues: 50.8091
Evaluate side-chains
  301 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 296
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain D residue   32 ASP
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 16 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 111 optimal weight:    4.9990
   chunk 120 optimal weight:    4.9990
   chunk 119 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 89 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
B  61 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.089728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.079888 restraints weight = 19039.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 1.76
r_work: 0.2832 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  11214  Z= 0.225
  Angle     :  0.502   5.286  15264  Z= 0.271
  Chirality :  0.037   0.112   1746
  Planarity :  0.003   0.028   1998
  Dihedral  :  3.945  20.113   1512
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 13.22 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.19 (0.21), residues: 1368
  helix:  1.88 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -1.85 (0.50), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG O  80 
 TYR   0.013   0.001   TYR J  57 
 PHE   0.011   0.001   PHE O  68 
 TRP   0.006   0.001   TRP G   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 (11214)
  covalent geometry    : angle       0.50234 (15264)
  hydrogen bonds       : bond        0.04023 (  900)
  hydrogen bonds       : angle       3.20351 ( 2700)

*********************** 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
  335 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 319
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ASP cc_start: 0.8841 (m-30) cc_final: 0.8484 (m-30)
REVERT: A   37 LYS cc_start: 0.9032 (ttmm) cc_final: 0.8824 (ttmt)
REVERT: B   37 LYS cc_start: 0.9025 (ttmt) cc_final: 0.7685 (tptt)
REVERT: B   40 ASP cc_start: 0.8423 (t0) cc_final: 0.8210 (t0)
REVERT: B   56 LEU cc_start: 0.9455 (mt) cc_final: 0.9184 (mt)
REVERT: B   61 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8786 (tt0)
REVERT: B   66 LYS cc_start: 0.8838 (tptp) cc_final: 0.7124 (mttm)
REVERT: C   10 ASP cc_start: 0.8853 (m-30) cc_final: 0.8413 (m-30)
REVERT: C   37 LYS cc_start: 0.9003 (ttmt) cc_final: 0.7514 (tptt)
REVERT: C   53 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8418 (mm-30)
REVERT: C   69 LYS cc_start: 0.9127 (tmtt) cc_final: 0.8849 (tttm)
REVERT: C   72 ASP cc_start: 0.9293 (m-30) cc_final: 0.8949 (m-30)
REVERT: D   10 ASP cc_start: 0.8760 (m-30) cc_final: 0.8042 (m-30)
REVERT: D   66 LYS cc_start: 0.8906 (tptp) cc_final: 0.7924 (ttmt)
REVERT: D   69 LYS cc_start: 0.9040 (tmtt) cc_final: 0.8600 (tptp)
REVERT: D   72 ASP cc_start: 0.9230 (m-30) cc_final: 0.9028 (m-30)
REVERT: E   37 LYS cc_start: 0.9165 (ttmt) cc_final: 0.7849 (tptt)
REVERT: E   66 LYS cc_start: 0.8574 (tptp) cc_final: 0.7682 (tppt)
REVERT: F   10 ASP cc_start: 0.8613 (m-30) cc_final: 0.8247 (m-30)
REVERT: F   37 LYS cc_start: 0.9126 (ttmt) cc_final: 0.7528 (tptt)
REVERT: G   32 ASP cc_start: 0.8436 (m-30) cc_final: 0.8111 (m-30)
REVERT: G   33 LYS cc_start: 0.8921 (mttt) cc_final: 0.8713 (mtpp)
REVERT: H   10 ASP cc_start: 0.8864 (m-30) cc_final: 0.8639 (m-30)
REVERT: H   72 ASP cc_start: 0.9327 (m-30) cc_final: 0.8992 (m-30)
REVERT: I    8 TYR cc_start: 0.8817 (t80) cc_final: 0.8348 (t80)
REVERT: I   69 LYS cc_start: 0.9026 (tmtt) cc_final: 0.8606 (tttp)
REVERT: J   37 LYS cc_start: 0.9064 (ttmm) cc_final: 0.8818 (ttmt)
REVERT: J   53 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8047 (mt-10)
REVERT: K   53 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8536 (mt-10)
REVERT: M   59 ASN cc_start: 0.8968 (OUTLIER) cc_final: 0.8683 (m110)
REVERT: N   15 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.7608 (ttpt)
REVERT: N   69 LYS cc_start: 0.9163 (tmtt) cc_final: 0.8017 (ttmt)
REVERT: N   70 ASP cc_start: 0.8637 (m-30) cc_final: 0.8437 (m-30)
REVERT: O   69 LYS cc_start: 0.9210 (tmtt) cc_final: 0.8048 (ttmt)
REVERT: O   72 ASP cc_start: 0.8825 (m-30) cc_final: 0.8531 (m-30)
REVERT: P   54 TYR cc_start: 0.9302 (t80) cc_final: 0.9013 (t80)
REVERT: P   69 LYS cc_start: 0.9135 (tmtt) cc_final: 0.8130 (ttmt)
REVERT: P   77 GLN cc_start: 0.8820 (tt0) cc_final: 0.8553 (tm-30)
REVERT: Q   25 THR cc_start: 0.9119 (m) cc_final: 0.8706 (p)
REVERT: Q   69 LYS cc_start: 0.9069 (tmtt) cc_final: 0.7718 (tttt)
REVERT: R   69 LYS cc_start: 0.9209 (tmtt) cc_final: 0.8033 (ttmt)
REVERT: R   77 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8402 (tm-30)
  outliers start: 16
  outliers final: 10
  residues processed: 328
  average time/residue: 0.1027
  time to fit residues: 47.4349
Evaluate side-chains
  303 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 290
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   61 GLN
Chi-restraints excluded: chain C residue   25 THR
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 F residue   25 THR
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain M residue   59 ASN
Chi-restraints excluded: chain N residue   15 LYS
Chi-restraints excluded: chain P residue   59 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 125 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9990
   chunk 113 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B  61 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.092105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.082331 restraints weight = 18908.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 1.73
r_work: 0.2879 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2768 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.4186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  11214  Z= 0.120
  Angle     :  0.421   5.188  15264  Z= 0.226
  Chirality :  0.034   0.104   1746
  Planarity :  0.003   0.023   1998
  Dihedral  :  3.688  17.572   1512
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 14.81 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.72 (0.22), residues: 1368
  helix:  2.30 (0.13), residues: 1224
  sheet:  None (None), residues: 0
  loop : -2.88 (0.49), residues: 144

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (11214)
  covalent geometry    : angle       0.42075 (15264)
  hydrogen bonds       : bond        0.03294 (  900)
  hydrogen bonds       : angle       2.99711 ( 2700)

*********************** 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
  329 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 319
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ASP cc_start: 0.8646 (m-30) cc_final: 0.8241 (m-30)
REVERT: A   37 LYS cc_start: 0.8999 (ttmm) cc_final: 0.8796 (ttmt)
REVERT: B   37 LYS cc_start: 0.8999 (ttmt) cc_final: 0.7718 (tptt)
REVERT: B   40 ASP cc_start: 0.8463 (t0) cc_final: 0.8208 (t0)
REVERT: B   56 LEU cc_start: 0.9410 (mt) cc_final: 0.9080 (mt)
REVERT: B   61 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8881 (tt0)
REVERT: B   66 LYS cc_start: 0.8839 (tptp) cc_final: 0.7723 (ttmt)
REVERT: B   69 LYS cc_start: 0.8985 (tttm) cc_final: 0.8737 (tttm)
REVERT: C   10 ASP cc_start: 0.8670 (m-30) cc_final: 0.8114 (m-30)
REVERT: C   37 LYS cc_start: 0.8980 (ttmt) cc_final: 0.7543 (tptt)
REVERT: C   53 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8211 (mm-30)
REVERT: C   69 LYS cc_start: 0.9103 (tmtt) cc_final: 0.8820 (tttm)
REVERT: C   72 ASP cc_start: 0.9200 (m-30) cc_final: 0.8810 (m-30)
REVERT: D   10 ASP cc_start: 0.8663 (m-30) cc_final: 0.7996 (m-30)
REVERT: D   66 LYS cc_start: 0.8884 (tptp) cc_final: 0.7829 (ttmt)
REVERT: D   69 LYS cc_start: 0.8991 (tmtt) cc_final: 0.8731 (tttm)
REVERT: E   37 LYS cc_start: 0.9168 (ttmt) cc_final: 0.7872 (tptt)
REVERT: E   66 LYS cc_start: 0.8539 (tptp) cc_final: 0.7725 (tppt)
REVERT: F   10 ASP cc_start: 0.8591 (m-30) cc_final: 0.8184 (m-30)
REVERT: F   37 LYS cc_start: 0.9076 (ttmt) cc_final: 0.7492 (tptt)
REVERT: G   10 ASP cc_start: 0.9016 (m-30) cc_final: 0.8654 (m-30)
REVERT: G   33 LYS cc_start: 0.8836 (mttt) cc_final: 0.8619 (mtpp)
REVERT: H   72 ASP cc_start: 0.9288 (m-30) cc_final: 0.8950 (m-30)
REVERT: I    8 TYR cc_start: 0.8729 (t80) cc_final: 0.8302 (t80)
REVERT: I   69 LYS cc_start: 0.8951 (tmtt) cc_final: 0.8553 (tttp)
REVERT: I   77 GLN cc_start: 0.9084 (tp40) cc_final: 0.8852 (tp40)
REVERT: J   37 LYS cc_start: 0.8953 (ttmm) cc_final: 0.8749 (ttmt)
REVERT: M   53 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8279 (mt-10)
REVERT: N   15 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.7531 (ttpt)
REVERT: N   69 LYS cc_start: 0.9141 (tmtt) cc_final: 0.7971 (ttmt)
REVERT: O   69 LYS cc_start: 0.9250 (tmtt) cc_final: 0.8111 (ttmt)
REVERT: P   54 TYR cc_start: 0.9289 (t80) cc_final: 0.9003 (t80)
REVERT: P   69 LYS cc_start: 0.9181 (tmtt) cc_final: 0.8087 (ttmt)
REVERT: Q   25 THR cc_start: 0.9115 (m) cc_final: 0.8792 (p)
REVERT: Q   69 LYS cc_start: 0.9073 (tmtt) cc_final: 0.7605 (tttt)
REVERT: R   69 LYS cc_start: 0.9221 (tmtt) cc_final: 0.8010 (ttmt)
REVERT: R   77 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8384 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 323
  average time/residue: 0.1011
  time to fit residues: 46.3509
Evaluate side-chains
  308 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 300
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   61 GLN
Chi-restraints excluded: chain D residue   21 ASP
Chi-restraints excluded: chain D residue   32 ASP
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain N residue   15 LYS
Chi-restraints excluded: chain P residue   59 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 120 optimal weight:    0.1980
   chunk 34 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 116 optimal weight:    0.5980
   chunk 77 optimal weight:    5.9990
   chunk 94 optimal weight:    0.3980
   chunk 73 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B  61 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.093283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.083559 restraints weight = 18800.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 1.73
r_work: 0.2903 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2794 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.4295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  11214  Z= 0.098
  Angle     :  0.397   3.873  15264  Z= 0.213
  Chirality :  0.033   0.103   1746
  Planarity :  0.003   0.022   1998
  Dihedral  :  3.555  15.852   1512
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 15.07 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.49 (0.21), residues: 1368
  helix:  2.82 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -2.06 (0.48), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG O  80 
 TYR   0.011   0.001   TYR K  47 
 PHE   0.005   0.001   PHE D  16 
 TRP   0.003   0.000   TRP G   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 (11214)
  covalent geometry    : angle       0.39712 (15264)
  hydrogen bonds       : bond        0.03015 (  900)
  hydrogen bonds       : angle       2.91644 ( 2700)

*********************** 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
  333 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 320
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ASP cc_start: 0.8502 (m-30) cc_final: 0.8017 (m-30)
REVERT: A   37 LYS cc_start: 0.8984 (ttmm) cc_final: 0.8779 (ttmt)
REVERT: B   37 LYS cc_start: 0.8987 (ttmt) cc_final: 0.7677 (tptt)
REVERT: B   40 ASP cc_start: 0.8428 (t0) cc_final: 0.8164 (t0)
REVERT: B   56 LEU cc_start: 0.9389 (mt) cc_final: 0.9036 (mt)
REVERT: B   61 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8856 (tt0)
REVERT: B   66 LYS cc_start: 0.8821 (tptp) cc_final: 0.7715 (ttmt)
REVERT: B   69 LYS cc_start: 0.8950 (tttm) cc_final: 0.8708 (tttm)
REVERT: C   10 ASP cc_start: 0.8491 (m-30) cc_final: 0.7875 (m-30)
REVERT: C   53 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7906 (mm-30)
REVERT: C   69 LYS cc_start: 0.9073 (tmtt) cc_final: 0.8796 (tttm)
REVERT: C   72 ASP cc_start: 0.9169 (m-30) cc_final: 0.8761 (m-30)
REVERT: D   10 ASP cc_start: 0.8588 (m-30) cc_final: 0.7928 (m-30)
REVERT: D   66 LYS cc_start: 0.8843 (tptp) cc_final: 0.7772 (ttmt)
REVERT: D   69 LYS cc_start: 0.8951 (tmtt) cc_final: 0.8706 (tttm)
REVERT: E   37 LYS cc_start: 0.9168 (ttmt) cc_final: 0.7891 (tptt)
REVERT: E   66 LYS cc_start: 0.8608 (tptp) cc_final: 0.7723 (tppt)
REVERT: F   10 ASP cc_start: 0.8538 (m-30) cc_final: 0.8160 (m-30)
REVERT: F   37 LYS cc_start: 0.9039 (ttmt) cc_final: 0.7452 (tptt)
REVERT: G   10 ASP cc_start: 0.9016 (m-30) cc_final: 0.8616 (m-30)
REVERT: G   33 LYS cc_start: 0.8829 (mttt) cc_final: 0.8614 (mtpp)
REVERT: H   72 ASP cc_start: 0.9264 (m-30) cc_final: 0.8942 (m-30)
REVERT: I    8 TYR cc_start: 0.8715 (t80) cc_final: 0.8341 (t80)
REVERT: I   69 LYS cc_start: 0.8940 (tmtt) cc_final: 0.8517 (tttp)
REVERT: I   77 GLN cc_start: 0.9141 (tp40) cc_final: 0.8899 (tp40)
REVERT: J   10 ASP cc_start: 0.8778 (m-30) cc_final: 0.8335 (m-30)
REVERT: J   37 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8703 (ttmt)
REVERT: K   53 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8516 (mt-10)
REVERT: M   53 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8250 (mt-10)
REVERT: N   15 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7515 (ttpt)
REVERT: N   69 LYS cc_start: 0.9093 (tmtt) cc_final: 0.7933 (ttmt)
REVERT: O   69 LYS cc_start: 0.9241 (tmtt) cc_final: 0.8082 (ttmt)
REVERT: P   53 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7833 (mt-10)
REVERT: P   69 LYS cc_start: 0.9168 (tmtt) cc_final: 0.8051 (ttmt)
REVERT: P   77 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8539 (tm-30)
REVERT: Q   25 THR cc_start: 0.9130 (m) cc_final: 0.8837 (p)
REVERT: Q   32 ASP cc_start: 0.8331 (m-30) cc_final: 0.7897 (m-30)
REVERT: Q   69 LYS cc_start: 0.9066 (tmtt) cc_final: 0.7562 (tttt)
REVERT: R   15 LYS cc_start: 0.8544 (mttp) cc_final: 0.7513 (ttpt)
REVERT: R   69 LYS cc_start: 0.9186 (tmtt) cc_final: 0.7965 (ttmt)
REVERT: R   77 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8453 (tm-30)
  outliers start: 13
  outliers final: 8
  residues processed: 327
  average time/residue: 0.0920
  time to fit residues: 42.7113
Evaluate side-chains
  309 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 299
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   61 GLN
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain F residue   69 LYS
Chi-restraints excluded: chain G residue   25 THR
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain K residue   57 TYR
Chi-restraints excluded: chain N residue   15 LYS
Chi-restraints excluded: chain O residue   57 TYR
Chi-restraints excluded: chain P residue   59 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 105 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 43 optimal weight:    6.9990
   chunk 96 optimal weight:    0.8980
   chunk 103 optimal weight:    0.6980
   chunk 106 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 94 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.092811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.083132 restraints weight = 18751.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 1.73
r_work: 0.2895 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.4329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  11214  Z= 0.111
  Angle     :  0.410   3.880  15264  Z= 0.218
  Chirality :  0.034   0.104   1746
  Planarity :  0.003   0.022   1998
  Dihedral  :  3.532  15.790   1512
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 15.40 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.72 (0.21), residues: 1368
  helix:  2.99 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -2.18 (0.47), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  58 
 TYR   0.013   0.001   TYR K  47 
 PHE   0.006   0.001   PHE N  68 
 TRP   0.003   0.000   TRP G   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (11214)
  covalent geometry    : angle       0.40977 (15264)
  hydrogen bonds       : bond        0.03058 (  900)
  hydrogen bonds       : angle       2.91348 ( 2700)

*********************** 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
  324 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 311
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ASP cc_start: 0.8521 (m-30) cc_final: 0.7999 (m-30)
REVERT: B   37 LYS cc_start: 0.8989 (ttmt) cc_final: 0.7672 (tptt)
REVERT: B   40 ASP cc_start: 0.8410 (t0) cc_final: 0.8126 (t0)
REVERT: B   56 LEU cc_start: 0.9396 (mt) cc_final: 0.9030 (mt)
REVERT: B   66 LYS cc_start: 0.8823 (tptp) cc_final: 0.7717 (ttmt)
REVERT: B   69 LYS cc_start: 0.8969 (tttm) cc_final: 0.8746 (tttm)
REVERT: C   10 ASP cc_start: 0.8489 (m-30) cc_final: 0.7813 (m-30)
REVERT: C   53 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7921 (mm-30)
REVERT: C   69 LYS cc_start: 0.9073 (tmtt) cc_final: 0.8806 (tttm)
REVERT: C   72 ASP cc_start: 0.9179 (m-30) cc_final: 0.8780 (m-30)
REVERT: D   10 ASP cc_start: 0.8598 (m-30) cc_final: 0.7984 (m-30)
REVERT: D   66 LYS cc_start: 0.8881 (tptp) cc_final: 0.7790 (ttmt)
REVERT: D   69 LYS cc_start: 0.8961 (tmtt) cc_final: 0.8702 (tttm)
REVERT: E   37 LYS cc_start: 0.9173 (ttmt) cc_final: 0.7897 (tptt)
REVERT: E   66 LYS cc_start: 0.8614 (tptp) cc_final: 0.7677 (tppt)
REVERT: F   10 ASP cc_start: 0.8515 (m-30) cc_final: 0.8121 (m-30)
REVERT: F   37 LYS cc_start: 0.9042 (ttmt) cc_final: 0.7506 (tptt)
REVERT: G   10 ASP cc_start: 0.9025 (m-30) cc_final: 0.8640 (m-30)
REVERT: G   33 LYS cc_start: 0.8847 (mttt) cc_final: 0.8633 (mtpp)
REVERT: H   72 ASP cc_start: 0.9271 (m-30) cc_final: 0.8965 (m-30)
REVERT: I    8 TYR cc_start: 0.8709 (t80) cc_final: 0.8301 (t80)
REVERT: I   53 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7752 (mt-10)
REVERT: I   69 LYS cc_start: 0.8951 (tmtt) cc_final: 0.8535 (tttp)
REVERT: I   77 GLN cc_start: 0.9138 (tp40) cc_final: 0.8886 (tp40)
REVERT: J   10 ASP cc_start: 0.8780 (m-30) cc_final: 0.8307 (m-30)
REVERT: K   53 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8454 (mt-10)
REVERT: M   53 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8289 (mt-10)
REVERT: N   15 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7513 (ttpt)
REVERT: N   69 LYS cc_start: 0.9124 (tmtt) cc_final: 0.7868 (ttmt)
REVERT: O   69 LYS cc_start: 0.9251 (tmtt) cc_final: 0.8083 (ttmt)
REVERT: P   53 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7748 (mt-10)
REVERT: P   69 LYS cc_start: 0.9161 (tmtt) cc_final: 0.8022 (ttmt)
REVERT: P   77 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8522 (tm-30)
REVERT: Q   15 LYS cc_start: 0.8842 (mttp) cc_final: 0.7631 (ttpt)
REVERT: Q   25 THR cc_start: 0.9123 (m) cc_final: 0.8829 (p)
REVERT: Q   32 ASP cc_start: 0.8347 (m-30) cc_final: 0.7917 (m-30)
REVERT: Q   69 LYS cc_start: 0.9049 (tmtt) cc_final: 0.7557 (tttt)
REVERT: R   15 LYS cc_start: 0.8480 (mttp) cc_final: 0.7442 (ttpt)
REVERT: R   69 LYS cc_start: 0.9191 (tmtt) cc_final: 0.7971 (ttmt)
  outliers start: 13
  outliers final: 8
  residues processed: 319
  average time/residue: 0.0961
  time to fit residues: 43.7593
Evaluate side-chains
  312 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 303
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 LYS
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 H residue   33 LYS
Chi-restraints excluded: chain K residue   57 TYR
Chi-restraints excluded: chain N residue   15 LYS
Chi-restraints excluded: chain O residue   57 TYR
Chi-restraints excluded: chain P residue   59 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 81 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 115 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 108 optimal weight:    2.9990
   overall best weight:    1.0184

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.092168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.082433 restraints weight = 18720.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 1.73
r_work: 0.2883 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2773 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.4343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11214  Z= 0.127
  Angle     :  0.426   5.943  15264  Z= 0.226
  Chirality :  0.034   0.109   1746
  Planarity :  0.003   0.027   1998
  Dihedral  :  3.565  15.684   1512
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 15.66 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.78 (0.21), residues: 1368
  helix:  3.06 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -2.39 (0.46), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  80 
 TYR   0.014   0.001   TYR K  47 
 PHE   0.007   0.001   PHE N  68 
 TRP   0.004   0.001   TRP G   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (11214)
  covalent geometry    : angle       0.42604 (15264)
  hydrogen bonds       : bond        0.03186 (  900)
  hydrogen bonds       : angle       2.96306 ( 2700)

*********************** 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
  333 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 318
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ASP cc_start: 0.8600 (m-30) cc_final: 0.8106 (m-30)
REVERT: B   37 LYS cc_start: 0.9016 (ttmt) cc_final: 0.7675 (tptt)
REVERT: B   40 ASP cc_start: 0.8432 (t0) cc_final: 0.8185 (t0)
REVERT: B   56 LEU cc_start: 0.9398 (mt) cc_final: 0.9034 (mt)
REVERT: B   61 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8845 (tt0)
REVERT: B   66 LYS cc_start: 0.8832 (tptp) cc_final: 0.7729 (ttmt)
REVERT: B   69 LYS cc_start: 0.8980 (tttm) cc_final: 0.8762 (tttm)
REVERT: C   10 ASP cc_start: 0.8578 (m-30) cc_final: 0.7865 (m-30)
REVERT: C   53 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7922 (mm-30)
REVERT: C   69 LYS cc_start: 0.9089 (tmtt) cc_final: 0.8823 (tttm)
REVERT: C   72 ASP cc_start: 0.9214 (m-30) cc_final: 0.8817 (m-30)
REVERT: D   10 ASP cc_start: 0.8636 (m-30) cc_final: 0.7954 (m-30)
REVERT: D   66 LYS cc_start: 0.8868 (tptp) cc_final: 0.7337 (mttt)
REVERT: D   69 LYS cc_start: 0.8994 (tmtt) cc_final: 0.8733 (tttm)
REVERT: E   37 LYS cc_start: 0.9154 (ttmt) cc_final: 0.7874 (tptt)
REVERT: E   66 LYS cc_start: 0.8675 (tptp) cc_final: 0.7721 (tppt)
REVERT: F   10 ASP cc_start: 0.8549 (m-30) cc_final: 0.8145 (m-30)
REVERT: F   37 LYS cc_start: 0.9058 (ttmt) cc_final: 0.7527 (tptt)
REVERT: G   10 ASP cc_start: 0.9013 (m-30) cc_final: 0.8645 (m-30)
REVERT: G   33 LYS cc_start: 0.8894 (mttt) cc_final: 0.8676 (mtpp)
REVERT: H   72 ASP cc_start: 0.9294 (m-30) cc_final: 0.8964 (m-30)
REVERT: I    8 TYR cc_start: 0.8726 (t80) cc_final: 0.8366 (t80)
REVERT: I   53 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7708 (mt-10)
REVERT: I   69 LYS cc_start: 0.8989 (tmtt) cc_final: 0.8540 (tttp)
REVERT: I   77 GLN cc_start: 0.9100 (tp40) cc_final: 0.8842 (tp40)
REVERT: J   10 ASP cc_start: 0.8794 (m-30) cc_final: 0.8522 (m-30)
REVERT: K   53 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8474 (mt-10)
REVERT: M   53 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8286 (mt-10)
REVERT: N   15 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.7500 (ttpt)
REVERT: N   69 LYS cc_start: 0.9134 (tmtt) cc_final: 0.7968 (ttmt)
REVERT: O   69 LYS cc_start: 0.9222 (tmtt) cc_final: 0.8079 (ttmt)
REVERT: P   53 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8070 (mt-10)
REVERT: P   69 LYS cc_start: 0.9152 (tmtt) cc_final: 0.8021 (ttmt)
REVERT: P   77 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8536 (tm-30)
REVERT: Q   23 LEU cc_start: 0.9117 (tp) cc_final: 0.8912 (tp)
REVERT: Q   25 THR cc_start: 0.9098 (m) cc_final: 0.8813 (p)
REVERT: Q   32 ASP cc_start: 0.8368 (m-30) cc_final: 0.7974 (m-30)
REVERT: Q   69 LYS cc_start: 0.9056 (tmtt) cc_final: 0.7554 (tttt)
REVERT: R   69 LYS cc_start: 0.9203 (tmtt) cc_final: 0.8027 (ttmt)
  outliers start: 15
  outliers final: 10
  residues processed: 325
  average time/residue: 0.0966
  time to fit residues: 44.6583
Evaluate side-chains
  320 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 307
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   61 GLN
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 I 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   59 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 112 optimal weight:    6.9990
   chunk 106 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.9384

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.092398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.082651 restraints weight = 18764.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 1.74
r_work: 0.2881 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2771 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.4366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11214  Z= 0.123
  Angle     :  0.426   4.855  15264  Z= 0.228
  Chirality :  0.034   0.119   1746
  Planarity :  0.003   0.025   1998
  Dihedral  :  3.565  15.689   1512
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 15.91 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.92 (0.21), residues: 1368
  helix:  3.15 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -2.41 (0.46), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG N  58 
 TYR   0.019   0.001   TYR K  47 
 PHE   0.006   0.001   PHE N  68 
 TRP   0.004   0.001   TRP G   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (11214)
  covalent geometry    : angle       0.42630 (15264)
  hydrogen bonds       : bond        0.03142 (  900)
  hydrogen bonds       : angle       2.95983 ( 2700)

*********************** 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
  324 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 308
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ASP cc_start: 0.8573 (m-30) cc_final: 0.8065 (m-30)
REVERT: B   37 LYS cc_start: 0.9024 (ttmt) cc_final: 0.7684 (tptt)
REVERT: B   40 ASP cc_start: 0.8488 (t0) cc_final: 0.8184 (t0)
REVERT: B   56 LEU cc_start: 0.9392 (mt) cc_final: 0.9017 (mt)
REVERT: B   61 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8872 (tt0)
REVERT: B   66 LYS cc_start: 0.8830 (tptp) cc_final: 0.7729 (ttmt)
REVERT: B   69 LYS cc_start: 0.8956 (tttm) cc_final: 0.8728 (tttm)
REVERT: C   10 ASP cc_start: 0.8508 (m-30) cc_final: 0.7769 (m-30)
REVERT: C   53 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7932 (mm-30)
REVERT: C   69 LYS cc_start: 0.9076 (tmtt) cc_final: 0.8814 (tttm)
REVERT: C   72 ASP cc_start: 0.9176 (m-30) cc_final: 0.8783 (m-30)
REVERT: D   10 ASP cc_start: 0.8634 (m-30) cc_final: 0.7945 (m-30)
REVERT: D   66 LYS cc_start: 0.8862 (tptp) cc_final: 0.7848 (ttmt)
REVERT: D   69 LYS cc_start: 0.8968 (tmtt) cc_final: 0.8707 (tttm)
REVERT: E   37 LYS cc_start: 0.9147 (ttmt) cc_final: 0.7865 (tptt)
REVERT: E   66 LYS cc_start: 0.8651 (tptp) cc_final: 0.7686 (tppt)
REVERT: F   10 ASP cc_start: 0.8544 (m-30) cc_final: 0.8134 (m-30)
REVERT: F   37 LYS cc_start: 0.9039 (ttmt) cc_final: 0.7493 (tptt)
REVERT: G   10 ASP cc_start: 0.8989 (m-30) cc_final: 0.8622 (m-30)
REVERT: G   33 LYS cc_start: 0.8902 (mttt) cc_final: 0.8686 (mtpp)
REVERT: H   72 ASP cc_start: 0.9289 (m-30) cc_final: 0.8991 (m-30)
REVERT: I    8 TYR cc_start: 0.8726 (t80) cc_final: 0.8382 (t80)
REVERT: I   53 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7700 (mt-10)
REVERT: I   69 LYS cc_start: 0.8979 (tmtt) cc_final: 0.8527 (tttp)
REVERT: I   77 GLN cc_start: 0.9097 (tp40) cc_final: 0.8838 (tp40)
REVERT: J   10 ASP cc_start: 0.8784 (m-30) cc_final: 0.8520 (m-30)
REVERT: K   53 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8463 (mt-10)
REVERT: N   15 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.7491 (ttpt)
REVERT: N   69 LYS cc_start: 0.9130 (tmtt) cc_final: 0.7958 (ttmt)
REVERT: O   69 LYS cc_start: 0.9224 (tmtt) cc_final: 0.8074 (ttmt)
REVERT: P   53 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8078 (mt-10)
REVERT: P   69 LYS cc_start: 0.9152 (tmtt) cc_final: 0.8012 (ttmt)
REVERT: P   77 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8518 (tm-30)
REVERT: Q   25 THR cc_start: 0.9103 (m) cc_final: 0.8818 (p)
REVERT: Q   32 ASP cc_start: 0.8362 (m-30) cc_final: 0.7924 (m-30)
REVERT: Q   69 LYS cc_start: 0.9052 (tmtt) cc_final: 0.7544 (tttt)
REVERT: R   69 LYS cc_start: 0.9200 (tmtt) cc_final: 0.8029 (ttmt)
  outliers start: 16
  outliers final: 12
  residues processed: 317
  average time/residue: 0.0925
  time to fit residues: 42.2025
Evaluate side-chains
  320 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 305
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   61 GLN
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 F residue   69 LYS
Chi-restraints excluded: chain G residue   25 THR
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain I residue   53 GLU
Chi-restraints excluded: chain K residue   57 TYR
Chi-restraints excluded: chain N residue   15 LYS
Chi-restraints excluded: chain O residue   57 TYR
Chi-restraints excluded: chain P residue   59 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 105 optimal weight:    6.9990
   chunk 68 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 29 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
B  61 GLN
D  55 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 = 0.090891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.081180 restraints weight = 18967.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 1.72
r_work: 0.2850 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2738 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.4329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11214  Z= 0.166
  Angle     :  0.460   5.749  15264  Z= 0.245
  Chirality :  0.036   0.132   1746
  Planarity :  0.003   0.029   1998
  Dihedral  :  3.667  16.990   1512
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 16.25 %
    Favored  : 82.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.70 (0.21), residues: 1368
  helix:  3.02 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -2.58 (0.45), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG N  58 
 TYR   0.016   0.001   TYR K  47 
 PHE   0.008   0.001   PHE O  68 
 TRP   0.004   0.001   TRP G   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (11214)
  covalent geometry    : angle       0.45992 (15264)
  hydrogen bonds       : bond        0.03463 (  900)
  hydrogen bonds       : angle       3.04630 ( 2700)

********************** 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
  311 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 295
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ASP cc_start: 0.8697 (m-30) cc_final: 0.8173 (m-30)
REVERT: B   37 LYS cc_start: 0.9035 (ttmt) cc_final: 0.7665 (tptt)
REVERT: B   40 ASP cc_start: 0.8503 (t0) cc_final: 0.8224 (t0)
REVERT: B   56 LEU cc_start: 0.9402 (mt) cc_final: 0.9037 (mt)
REVERT: B   61 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8940 (tt0)
REVERT: B   66 LYS cc_start: 0.8851 (tptp) cc_final: 0.7749 (ttmt)
REVERT: C   10 ASP cc_start: 0.8671 (m-30) cc_final: 0.7993 (m-30)
REVERT: C   53 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8015 (mm-30)
REVERT: C   69 LYS cc_start: 0.9108 (tmtt) cc_final: 0.8849 (tttm)
REVERT: C   72 ASP cc_start: 0.9233 (m-30) cc_final: 0.8866 (m-30)
REVERT: D   10 ASP cc_start: 0.8687 (m-30) cc_final: 0.7977 (m-30)
REVERT: D   66 LYS cc_start: 0.8914 (tptp) cc_final: 0.7359 (mttt)
REVERT: D   69 LYS cc_start: 0.9034 (tmtt) cc_final: 0.8763 (tttm)
REVERT: E   37 LYS cc_start: 0.9173 (ttmt) cc_final: 0.7870 (tptt)
REVERT: E   66 LYS cc_start: 0.8646 (tptp) cc_final: 0.7716 (tppt)
REVERT: F   10 ASP cc_start: 0.8579 (m-30) cc_final: 0.8181 (m-30)
REVERT: F   37 LYS cc_start: 0.9077 (ttmt) cc_final: 0.7486 (tptt)
REVERT: G   33 LYS cc_start: 0.8909 (mttt) cc_final: 0.8692 (mtpp)
REVERT: H   72 ASP cc_start: 0.9310 (m-30) cc_final: 0.8999 (m-30)
REVERT: I    8 TYR cc_start: 0.8755 (t80) cc_final: 0.8387 (t80)
REVERT: I   53 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7741 (mt-10)
REVERT: I   69 LYS cc_start: 0.8994 (tmtt) cc_final: 0.8546 (tttp)
REVERT: I   77 GLN cc_start: 0.9096 (tp40) cc_final: 0.8819 (tp40)
REVERT: K   53 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8426 (mt-10)
REVERT: N   15 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.7516 (ttpt)
REVERT: N   69 LYS cc_start: 0.9147 (tmtt) cc_final: 0.7978 (ttmt)
REVERT: O   69 LYS cc_start: 0.9229 (tmtt) cc_final: 0.8063 (ttmt)
REVERT: P   69 LYS cc_start: 0.9177 (tmtt) cc_final: 0.8029 (ttmt)
REVERT: P   77 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8533 (tm-30)
REVERT: Q   25 THR cc_start: 0.9101 (m) cc_final: 0.8741 (p)
REVERT: Q   32 ASP cc_start: 0.8371 (m-30) cc_final: 0.7918 (m-30)
REVERT: Q   69 LYS cc_start: 0.9079 (tmtt) cc_final: 0.7551 (tttt)
REVERT: R   69 LYS cc_start: 0.9213 (tmtt) cc_final: 0.8039 (ttmt)
  outliers start: 16
  outliers final: 13
  residues processed: 303
  average time/residue: 0.0839
  time to fit residues: 36.4475
Evaluate side-chains
  308 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 292
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   61 GLN
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 F residue   69 LYS
Chi-restraints excluded: chain G residue   25 THR
Chi-restraints excluded: chain H residue   21 ASP
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain I residue   53 GLU
Chi-restraints excluded: chain K residue   57 TYR
Chi-restraints excluded: chain N residue   15 LYS
Chi-restraints excluded: chain O residue   57 TYR
Chi-restraints excluded: chain P residue   59 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 112 optimal weight:    6.9990
   chunk 114 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 120 optimal weight:    3.9990
   chunk 89 optimal weight:    0.5980
   chunk 104 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 17 optimal weight:    0.4980
   overall best weight:    0.7782

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.092061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.082373 restraints weight = 18925.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 1.73
r_work: 0.2884 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2774 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.4415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11214  Z= 0.115
  Angle     :  0.436   6.894  15264  Z= 0.232
  Chirality :  0.034   0.122   1746
  Planarity :  0.003   0.027   1998
  Dihedral  :  3.611  15.683   1512
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.67 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.94 (0.21), residues: 1368
  helix:  3.18 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -2.48 (0.46), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG O  80 
 TYR   0.017   0.001   TYR K  47 
 PHE   0.006   0.001   PHE N  68 
 TRP   0.005   0.001   TRP L   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (11214)
  covalent geometry    : angle       0.43640 (15264)
  hydrogen bonds       : bond        0.03114 (  900)
  hydrogen bonds       : angle       2.98936 ( 2700)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2150.19 seconds
wall clock time: 37 minutes 53.68 seconds (2273.68 seconds total)