Starting phenix.real_space_refine
on Fri Feb 14 22:45:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6off_20044/02_2025/6off_20044_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6off_20044/02_2025/6off_20044.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6off_20044/02_2025/6off_20044.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6off_20044/02_2025/6off_20044.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6off_20044/02_2025/6off_20044_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6off_20044/02_2025/6off_20044_neut.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    6966      2.51       5
     N    1818      2.21       5
     O    2232      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 11016
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 612
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 74}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, R
  Time building chain proxies: 3.10, per 1000 atoms: 0.28
  Number of scatterers: 11016
  At special positions: 0
  Unit cell: (90.915, 90.915, 145.255, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O    2232      8.00
     N    1818      7.00
     C    6966      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.85
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 0 sheets defined
      91.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE A  16 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA A  36 " --> pdb=" O   ASP A  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS A  37 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU A  56 " --> pdb=" O   SER A  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL A  65 " --> pdb=" O   GLN A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 80
      No H-bonds generated for 'chain 'A' and resid 78 through 80'
    Processing helix  chain 'B' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE B  16 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 37
      removed outlier: 3.819A  pdb=" N   THR B  28 " --> pdb=" O   GLN B  24 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA B  36 " --> pdb=" O   ASP B  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS B  37 " --> pdb=" O   LYS B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU B  56 " --> pdb=" O   SER B  52 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   VAL B  65 " --> pdb=" O   GLN B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 80
      No H-bonds generated for 'chain 'B' and resid 78 through 80'
    Processing helix  chain 'C' and resid 7 through 20
      removed outlier: 3.884A  pdb=" N   PHE C  16 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 22 through 37
      removed outlier: 3.821A  pdb=" N   THR C  28 " --> pdb=" O   GLN C  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA C  36 " --> pdb=" O   ASP C  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS C  37 " --> pdb=" O   LYS C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU C  56 " --> pdb=" O   SER C  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL C  65 " --> pdb=" O   GLN C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 80
      No H-bonds generated for 'chain 'C' and resid 78 through 80'
    Processing helix  chain 'D' and resid 7 through 20
      removed outlier: 3.884A  pdb=" N   PHE D  16 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR D  28 " --> pdb=" O   GLN D  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA D  36 " --> pdb=" O   ASP D  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS D  37 " --> pdb=" O   LYS D  33 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU D  56 " --> pdb=" O   SER D  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL D  65 " --> pdb=" O   GLN D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 80
      No H-bonds generated for 'chain 'D' and resid 78 through 80'
    Processing helix  chain 'E' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE E  16 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR E  28 " --> pdb=" O   GLN E  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA E  36 " --> pdb=" O   ASP E  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS E  37 " --> pdb=" O   LYS E  33 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU E  56 " --> pdb=" O   SER E  52 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   VAL E  65 " --> pdb=" O   GLN E  61 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 78 through 80
      No H-bonds generated for 'chain 'E' and resid 78 through 80'
    Processing helix  chain 'F' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE F  16 " --> pdb=" O   VAL F  12 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR F  28 " --> pdb=" O   GLN F  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA F  36 " --> pdb=" O   ASP F  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS F  37 " --> pdb=" O   LYS F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU F  56 " --> pdb=" O   SER F  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL F  65 " --> pdb=" O   GLN F  61 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 78 through 80
      No H-bonds generated for 'chain 'F' and resid 78 through 80'
    Processing helix  chain 'G' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE G  16 " --> pdb=" O   VAL G  12 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 22 through 37
      removed outlier: 3.819A  pdb=" N   THR G  28 " --> pdb=" O   GLN G  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA G  36 " --> pdb=" O   ASP G  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS G  37 " --> pdb=" O   LYS G  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU G  56 " --> pdb=" O   SER G  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL G  65 " --> pdb=" O   GLN G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 78 through 80
      No H-bonds generated for 'chain 'G' and resid 78 through 80'
    Processing helix  chain 'H' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE H  16 " --> pdb=" O   VAL H  12 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 22 through 37
      removed outlier: 3.819A  pdb=" N   THR H  28 " --> pdb=" O   GLN H  24 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA H  36 " --> pdb=" O   ASP H  32 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS H  37 " --> pdb=" O   LYS H  33 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 40 through 77
      removed outlier: 3.699A  pdb=" N   LEU H  56 " --> pdb=" O   SER H  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL H  65 " --> pdb=" O   GLN H  61 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 78 through 80
      No H-bonds generated for 'chain 'H' and resid 78 through 80'
    Processing helix  chain 'I' and resid 7 through 20
      removed outlier: 3.884A  pdb=" N   PHE I  16 " --> pdb=" O   VAL I  12 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR I  28 " --> pdb=" O   GLN I  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA I  36 " --> pdb=" O   ASP I  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS I  37 " --> pdb=" O   LYS I  33 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU I  56 " --> pdb=" O   SER I  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL I  65 " --> pdb=" O   GLN I  61 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 78 through 80
      No H-bonds generated for 'chain 'I' and resid 78 through 80'
    Processing helix  chain 'J' and resid 7 through 20
      removed outlier: 3.884A  pdb=" N   PHE J  16 " --> pdb=" O   VAL J  12 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 22 through 37
      removed outlier: 3.819A  pdb=" N   THR J  28 " --> pdb=" O   GLN J  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA J  36 " --> pdb=" O   ASP J  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS J  37 " --> pdb=" O   LYS J  33 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 40 through 77
      removed outlier: 3.701A  pdb=" N   LEU J  56 " --> pdb=" O   SER J  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL J  65 " --> pdb=" O   GLN J  61 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 78 through 80
      No H-bonds generated for 'chain 'J' and resid 78 through 80'
    Processing helix  chain 'K' and resid 7 through 20
      removed outlier: 3.884A  pdb=" N   PHE K  16 " --> pdb=" O   VAL K  12 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 22 through 37
      removed outlier: 3.821A  pdb=" N   THR K  28 " --> pdb=" O   GLN K  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA K  36 " --> pdb=" O   ASP K  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS K  37 " --> pdb=" O   LYS K  33 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU K  56 " --> pdb=" O   SER K  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL K  65 " --> pdb=" O   GLN K  61 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 78 through 80
      No H-bonds generated for 'chain 'K' and resid 78 through 80'
    Processing helix  chain 'L' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE L  16 " --> pdb=" O   VAL L  12 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR L  28 " --> pdb=" O   GLN L  24 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA L  36 " --> pdb=" O   ASP L  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS L  37 " --> pdb=" O   LYS L  33 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU L  56 " --> pdb=" O   SER L  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL L  65 " --> pdb=" O   GLN L  61 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 78 through 80
      No H-bonds generated for 'chain 'L' and resid 78 through 80'
    Processing helix  chain 'M' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE M  16 " --> pdb=" O   VAL M  12 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 37
      removed outlier: 3.821A  pdb=" N   THR M  28 " --> pdb=" O   GLN M  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA M  36 " --> pdb=" O   ASP M  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS M  37 " --> pdb=" O   LYS M  33 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU M  56 " --> pdb=" O   SER M  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL M  65 " --> pdb=" O   GLN M  61 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 78 through 80
      No H-bonds generated for 'chain 'M' and resid 78 through 80'
    Processing helix  chain 'N' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE N  16 " --> pdb=" O   VAL N  12 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR N  28 " --> pdb=" O   GLN N  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA N  36 " --> pdb=" O   ASP N  32 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS N  37 " --> pdb=" O   LYS N  33 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 40 through 77
      removed outlier: 3.699A  pdb=" N   LEU N  56 " --> pdb=" O   SER N  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL N  65 " --> pdb=" O   GLN N  61 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 78 through 80
      No H-bonds generated for 'chain 'N' and resid 78 through 80'
    Processing helix  chain 'O' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE O  16 " --> pdb=" O   VAL O  12 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR O  28 " --> pdb=" O   GLN O  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA O  36 " --> pdb=" O   ASP O  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS O  37 " --> pdb=" O   LYS O  33 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU O  56 " --> pdb=" O   SER O  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL O  65 " --> pdb=" O   GLN O  61 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 78 through 80
      No H-bonds generated for 'chain 'O' and resid 78 through 80'
    Processing helix  chain 'P' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE P  16 " --> pdb=" O   VAL P  12 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR P  28 " --> pdb=" O   GLN P  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA P  36 " --> pdb=" O   ASP P  32 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS P  37 " --> pdb=" O   LYS P  33 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU P  56 " --> pdb=" O   SER P  52 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   VAL P  65 " --> pdb=" O   GLN P  61 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 78 through 80
      No H-bonds generated for 'chain 'P' and resid 78 through 80'
    Processing helix  chain 'Q' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE Q  16 " --> pdb=" O   VAL Q  12 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 22 through 37
      removed outlier: 3.820A  pdb=" N   THR Q  28 " --> pdb=" O   GLN Q  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA Q  36 " --> pdb=" O   ASP Q  32 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LYS Q  37 " --> pdb=" O   LYS Q  33 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 40 through 77
      removed outlier: 3.699A  pdb=" N   LEU Q  56 " --> pdb=" O   SER Q  52 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   VAL Q  65 " --> pdb=" O   GLN Q  61 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 78 through 80
      No H-bonds generated for 'chain 'Q' and resid 78 through 80'
    Processing helix  chain 'R' and resid 7 through 20
      removed outlier: 3.883A  pdb=" N   PHE R  16 " --> pdb=" O   VAL R  12 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 22 through 37
      removed outlier: 3.821A  pdb=" N   THR R  28 " --> pdb=" O   GLN R  24 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA R  36 " --> pdb=" O   ASP R  32 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS R  37 " --> pdb=" O   LYS R  33 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 40 through 77
      removed outlier: 3.700A  pdb=" N   LEU R  56 " --> pdb=" O   SER R  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL R  65 " --> pdb=" O   GLN R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 78 through 80
      No H-bonds generated for 'chain 'R' and resid 78 through 80'

    900 hydrogen bonds defined for protein.
    2700 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.30

  Time building geometry restraints manager: 3.26 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 248
        2.70 -     3.25: 11456
        3.25 -     3.80: 17333
        3.80 -     4.35: 23717
        4.35 -     4.90: 40635
  Nonbonded interactions: 93389
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP I  10 "
            pdb=" OG  SER O  49 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" OD1 ASP J  10 "
            pdb=" OG  SER P  49 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" OD1 ASP D  10 "
            pdb=" OG  SER J  49 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" N   ASP A  10 "
            pdb=" OE2 GLU G  53 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" OD1 ASP E  17 "
            pdb=" OH  TYR E  57 "
     model   vdw
     2.310 3.040
  ... (remaining 93384 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.11
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'L'
  selection = chain 'O'
  selection = chain 'N'
  selection = chain 'Q'
  selection = chain 'P'
  selection = chain 'R'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     23.270
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.730
-------------------------------------------------------------------------------
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= 0.565
  Angle     :  0.831   5.282  15264  Z= 0.500
  Chirality :  0.045   0.101   1746
  Planarity :  0.005   0.031   1998
  Dihedral  : 10.880  75.065   4068
  Min Nonbonded Distance : 2.147

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

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

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

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

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  389 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 389
  time to evaluate  : 1.406 
Fit side-chains
REVERT: A   66 LYS cc_start: 0.8617 (tptp) cc_final: 0.7191 (mttm)
REVERT: B   37 LYS cc_start: 0.7539 (ttmt) cc_final: 0.6639 (tptt)
REVERT: C    4 PRO cc_start: 0.7523 (Cg_endo) cc_final: 0.7248 (Cg_exo)
REVERT: C   10 ASP cc_start: 0.8562 (m-30) cc_final: 0.7963 (m-30)
REVERT: C   37 LYS cc_start: 0.9078 (ttmt) cc_final: 0.7713 (tptt)
REVERT: C   72 ASP cc_start: 0.9174 (m-30) cc_final: 0.8948 (m-30)
REVERT: D   10 ASP cc_start: 0.7896 (m-30) cc_final: 0.7502 (m-30)
REVERT: E   10 ASP cc_start: 0.8060 (m-30) cc_final: 0.7723 (m-30)
REVERT: E   37 LYS cc_start: 0.9093 (ttmt) cc_final: 0.7985 (tptt)
REVERT: E   52 SER cc_start: 0.8568 (m) cc_final: 0.8250 (p)
REVERT: E   70 ASP cc_start: 0.8333 (m-30) cc_final: 0.7939 (m-30)
REVERT: F   10 ASP cc_start: 0.8421 (m-30) cc_final: 0.8061 (m-30)
REVERT: F   37 LYS cc_start: 0.9074 (ttmt) cc_final: 0.7655 (tptt)
REVERT: G   33 LYS cc_start: 0.8397 (mttt) cc_final: 0.7936 (mtpp)
REVERT: G   37 LYS cc_start: 0.8503 (ttmt) cc_final: 0.6720 (tptp)
REVERT: H   37 LYS cc_start: 0.8965 (ttmt) cc_final: 0.7269 (tptt)
REVERT: H   72 ASP cc_start: 0.9104 (m-30) cc_final: 0.8750 (m-30)
REVERT: I   53 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7514 (mt-10)
REVERT: K   10 ASP cc_start: 0.7953 (m-30) cc_final: 0.7545 (m-30)
REVERT: L   53 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7571 (mt-10)
REVERT: M    8 TYR cc_start: 0.8717 (t80) cc_final: 0.8480 (t80)
REVERT: M   29 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7068 (mt-10)
REVERT: M   69 LYS cc_start: 0.8962 (tmtt) cc_final: 0.7838 (ttmt)
REVERT: N   25 THR cc_start: 0.8717 (m) cc_final: 0.8353 (p)
REVERT: N   69 LYS cc_start: 0.8770 (tmtt) cc_final: 0.8159 (ttmt)
REVERT: O   28 THR cc_start: 0.8751 (m) cc_final: 0.8371 (p)
REVERT: O   33 LYS cc_start: 0.7967 (mttt) cc_final: 0.7095 (mttm)
REVERT: R   33 LYS cc_start: 0.8610 (mttt) cc_final: 0.7864 (mttm)
REVERT: R   69 LYS cc_start: 0.9078 (tmtt) cc_final: 0.7908 (ttmt)
REVERT: R   72 ASP cc_start: 0.8863 (m-30) cc_final: 0.8630 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 389
  average time/residue: 0.2284
  time to fit residues: 124.4601
Evaluate side-chains
  275 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 275
  time to evaluate  : 1.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 98 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9980
   overall best weight:    0.8180

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.101837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.091787 restraints weight = 18062.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 1.71
r_work: 0.3024 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  11214  Z= 0.167
  Angle     :  0.471   3.738  15264  Z= 0.263
  Chirality :  0.033   0.114   1746
  Planarity :  0.005   0.028   1998
  Dihedral  :  4.059  17.480   1512
  Min Nonbonded Distance : 2.495

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

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

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

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

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 341
  time to evaluate  : 1.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ASP cc_start: 0.8626 (m-30) cc_final: 0.8282 (m-30)
REVERT: A   39 SER cc_start: 0.8620 (m) cc_final: 0.8371 (p)
REVERT: B   37 LYS cc_start: 0.8167 (ttmt) cc_final: 0.6965 (tptt)
REVERT: B   66 LYS cc_start: 0.8335 (tptp) cc_final: 0.6968 (ttmm)
REVERT: C    4 PRO cc_start: 0.8112 (Cg_endo) cc_final: 0.7900 (Cg_exo)
REVERT: C   10 ASP cc_start: 0.8547 (m-30) cc_final: 0.8060 (m-30)
REVERT: C   37 LYS cc_start: 0.9074 (ttmt) cc_final: 0.7615 (tptt)
REVERT: C   69 LYS cc_start: 0.9077 (tmtt) cc_final: 0.8723 (tttm)
REVERT: D   10 ASP cc_start: 0.8385 (m-30) cc_final: 0.7595 (m-30)
REVERT: D   72 ASP cc_start: 0.9220 (m-30) cc_final: 0.8925 (m-30)
REVERT: E   10 ASP cc_start: 0.8378 (m-30) cc_final: 0.7904 (m-30)
REVERT: E   37 LYS cc_start: 0.9134 (ttmt) cc_final: 0.7922 (tptt)
REVERT: E   52 SER cc_start: 0.8675 (m) cc_final: 0.8279 (p)
REVERT: E   57 TYR cc_start: 0.9301 (t80) cc_final: 0.9024 (t80)
REVERT: F   10 ASP cc_start: 0.8561 (m-30) cc_final: 0.8151 (m-30)
REVERT: F   37 LYS cc_start: 0.9082 (ttmt) cc_final: 0.7553 (tptt)
REVERT: G   33 LYS cc_start: 0.8795 (mttt) cc_final: 0.8448 (mtpp)
REVERT: G   37 LYS cc_start: 0.8658 (ttmt) cc_final: 0.6930 (tptp)
REVERT: H   10 ASP cc_start: 0.8708 (m-30) cc_final: 0.8501 (m-30)
REVERT: H   37 LYS cc_start: 0.8995 (ttmt) cc_final: 0.7443 (tptt)
REVERT: H   72 ASP cc_start: 0.9126 (m-30) cc_final: 0.8666 (m-30)
REVERT: I    8 TYR cc_start: 0.8790 (t80) cc_final: 0.8414 (t80)
REVERT: J   10 ASP cc_start: 0.8535 (m-30) cc_final: 0.8175 (m-30)
REVERT: J   24 GLN cc_start: 0.8014 (mp10) cc_final: 0.7795 (mp10)
REVERT: J   37 LYS cc_start: 0.8991 (ttmm) cc_final: 0.8746 (ttmt)
REVERT: K   31 LEU cc_start: 0.9251 (tp) cc_final: 0.8992 (tp)
REVERT: L   10 ASP cc_start: 0.8686 (m-30) cc_final: 0.8394 (m-30)
REVERT: M    8 TYR cc_start: 0.8878 (t80) cc_final: 0.8574 (t80)
REVERT: M   69 LYS cc_start: 0.9196 (tmtt) cc_final: 0.7927 (ttmt)
REVERT: N   15 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.7522 (ttpt)
REVERT: N   25 THR cc_start: 0.8899 (m) cc_final: 0.8613 (p)
REVERT: N   29 GLU cc_start: 0.7728 (tp30) cc_final: 0.7448 (tp30)
REVERT: N   69 LYS cc_start: 0.9088 (tmtt) cc_final: 0.8019 (ttmt)
REVERT: N   70 ASP cc_start: 0.8559 (m-30) cc_final: 0.8035 (m-30)
REVERT: N   72 ASP cc_start: 0.8571 (m-30) cc_final: 0.8316 (m-30)
REVERT: O   15 LYS cc_start: 0.8621 (ttmm) cc_final: 0.7354 (tttt)
REVERT: O   29 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8006 (tp30)
REVERT: O   33 LYS cc_start: 0.8636 (mttt) cc_final: 0.8399 (mttm)
REVERT: Q   32 ASP cc_start: 0.8475 (m-30) cc_final: 0.8193 (m-30)
REVERT: Q   53 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7683 (mt-10)
REVERT: R   69 LYS cc_start: 0.9155 (tmtt) cc_final: 0.7991 (ttmt)
REVERT: R   77 GLN cc_start: 0.8762 (tt0) cc_final: 0.8554 (tm-30)
  outliers start: 14
  outliers final: 3
  residues processed: 345
  average time/residue: 0.2234
  time to fit residues: 110.1650
Evaluate side-chains
  294 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 290
  time to evaluate  : 1.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain J residue   33 LYS
Chi-restraints excluded: chain N residue   15 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 94 optimal weight:    6.9990
   chunk 89 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0970
   chunk 37 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 55 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:
D  55 ASN
I  78 ASN
J  78 ASN
K  63 ASN
N  63 ASN
O  61 GLN
O  63 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.097506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.087521 restraints weight = 18573.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 1.73
r_work: 0.2958 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2846 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.3400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019  11214  Z= 0.149
  Angle     :  0.420   4.642  15264  Z= 0.228
  Chirality :  0.033   0.110   1746
  Planarity :  0.003   0.023   1998
  Dihedral  :  3.630  15.822   1512
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 12.46 %
    Favored  : 86.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.21), residues: 1368
  helix:  1.55 (0.14), residues: 1206
  sheet:  None (None), residues: 0
  loop : -1.68 (0.52), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP N   5 
 PHE   0.005   0.001   PHE O  68 
 TYR   0.011   0.001   TYR B  47 
 ARG   0.001   0.000   ARG B  80 

*********************** 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
  337 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 330
  time to evaluate  : 1.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 LYS cc_start: 0.8441 (ttmt) cc_final: 0.7257 (tptt)
REVERT: B   66 LYS cc_start: 0.8723 (tptp) cc_final: 0.7424 (ttmt)
REVERT: C   10 ASP cc_start: 0.8579 (m-30) cc_final: 0.8133 (m-30)
REVERT: C   37 LYS cc_start: 0.8989 (ttmt) cc_final: 0.7501 (tptt)
REVERT: C   69 LYS cc_start: 0.9060 (tmtt) cc_final: 0.8769 (tttm)
REVERT: C   72 ASP cc_start: 0.9242 (m-30) cc_final: 0.8958 (m-30)
REVERT: D   10 ASP cc_start: 0.8442 (m-30) cc_final: 0.7855 (m-30)
REVERT: D   69 LYS cc_start: 0.8984 (tmtt) cc_final: 0.8646 (tptp)
REVERT: D   72 ASP cc_start: 0.9194 (m-30) cc_final: 0.8910 (m-30)
REVERT: E   10 ASP cc_start: 0.8416 (m-30) cc_final: 0.8018 (m-30)
REVERT: E   37 LYS cc_start: 0.9171 (ttmt) cc_final: 0.7920 (tptt)
REVERT: F   10 ASP cc_start: 0.8480 (m-30) cc_final: 0.7975 (m-30)
REVERT: F   37 LYS cc_start: 0.9113 (ttmt) cc_final: 0.7534 (tptt)
REVERT: G   10 ASP cc_start: 0.8895 (m-30) cc_final: 0.8545 (m-30)
REVERT: G   33 LYS cc_start: 0.8867 (mttt) cc_final: 0.8564 (mtpp)
REVERT: H   10 ASP cc_start: 0.8712 (m-30) cc_final: 0.8458 (m-30)
REVERT: H   37 LYS cc_start: 0.9074 (ttmt) cc_final: 0.7448 (tptt)
REVERT: H   72 ASP cc_start: 0.9206 (m-30) cc_final: 0.8756 (m-30)
REVERT: I    8 TYR cc_start: 0.8733 (t80) cc_final: 0.8335 (t80)
REVERT: I   53 GLU cc_start: 0.8421 (mt-10) cc_final: 0.7926 (mt-10)
REVERT: J   10 ASP cc_start: 0.8547 (m-30) cc_final: 0.8194 (m-30)
REVERT: J   37 LYS cc_start: 0.8947 (ttmm) cc_final: 0.8739 (ttmt)
REVERT: J   72 ASP cc_start: 0.8571 (m-30) cc_final: 0.8102 (m-30)
REVERT: K   31 LEU cc_start: 0.9305 (tp) cc_final: 0.9055 (tp)
REVERT: L   39 SER cc_start: 0.8933 (m) cc_final: 0.7975 (m)
REVERT: M   26 GLN cc_start: 0.8675 (mt0) cc_final: 0.8410 (mt0)
REVERT: M   69 LYS cc_start: 0.9241 (tmtt) cc_final: 0.7964 (ttmt)
REVERT: N   15 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.7535 (ttpt)
REVERT: N   29 GLU cc_start: 0.7788 (tp30) cc_final: 0.7562 (tp30)
REVERT: N   69 LYS cc_start: 0.9138 (tmtt) cc_final: 0.8061 (ttmt)
REVERT: N   70 ASP cc_start: 0.8522 (m-30) cc_final: 0.8127 (m-30)
REVERT: N   72 ASP cc_start: 0.8676 (m-30) cc_final: 0.8356 (m-30)
REVERT: O   69 LYS cc_start: 0.9054 (tmtt) cc_final: 0.8063 (ttmt)
REVERT: O   72 ASP cc_start: 0.8789 (m-30) cc_final: 0.8548 (m-30)
REVERT: P   32 ASP cc_start: 0.8294 (m-30) cc_final: 0.7951 (m-30)
REVERT: P   77 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8492 (tt0)
REVERT: Q   15 LYS cc_start: 0.8738 (mttp) cc_final: 0.7749 (ttpt)
REVERT: Q   25 THR cc_start: 0.9106 (m) cc_final: 0.8765 (p)
REVERT: Q   69 LYS cc_start: 0.8989 (tmtt) cc_final: 0.7732 (tttt)
REVERT: R   15 LYS cc_start: 0.8540 (mttp) cc_final: 0.7487 (ttpt)
REVERT: R   69 LYS cc_start: 0.9194 (tmtt) cc_final: 0.7986 (ttmt)
REVERT: R   72 ASP cc_start: 0.8921 (m-30) cc_final: 0.8681 (m-30)
  outliers start: 7
  outliers final: 2
  residues processed: 333
  average time/residue: 0.2299
  time to fit residues: 107.9987
Evaluate side-chains
  295 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 292
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain N residue   15 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0040
   chunk 50 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 123 optimal weight:    0.6980
   chunk 122 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.6592

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.096247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.086372 restraints weight = 18502.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 1.73
r_work: 0.2946 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2836 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.3778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018  11214  Z= 0.132
  Angle     :  0.401   3.982  15264  Z= 0.215
  Chirality :  0.033   0.105   1746
  Planarity :  0.003   0.022   1998
  Dihedral  :  3.507  15.349   1512
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 13.38 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.21), residues: 1368
  helix:  2.29 (0.14), residues: 1206
  sheet:  None (None), residues: 0
  loop : -1.70 (0.51), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP M   5 
 PHE   0.005   0.001   PHE N  68 
 TYR   0.009   0.001   TYR B  47 
 ARG   0.001   0.000   ARG E  58 

*********************** 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
  314 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 308
  time to evaluate  : 1.307 
Fit side-chains
   revert: symmetry clash
REVERT: B   37 LYS cc_start: 0.8628 (ttmt) cc_final: 0.7364 (tptt)
REVERT: B   61 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8648 (tt0)
REVERT: B   66 LYS cc_start: 0.8827 (tptp) cc_final: 0.7633 (ttmt)
REVERT: B   69 LYS cc_start: 0.8855 (tmtt) cc_final: 0.8480 (tttm)
REVERT: C   10 ASP cc_start: 0.8500 (m-30) cc_final: 0.7984 (m-30)
REVERT: C   37 LYS cc_start: 0.8956 (ttmt) cc_final: 0.7483 (tptt)
REVERT: C   69 LYS cc_start: 0.9112 (tmtt) cc_final: 0.8824 (tttm)
REVERT: C   72 ASP cc_start: 0.9258 (m-30) cc_final: 0.8873 (m-30)
REVERT: D   10 ASP cc_start: 0.8488 (m-30) cc_final: 0.7863 (m-30)
REVERT: D   66 LYS cc_start: 0.8786 (tptp) cc_final: 0.7848 (ttmt)
REVERT: D   69 LYS cc_start: 0.9014 (tmtt) cc_final: 0.8776 (tttm)
REVERT: E   10 ASP cc_start: 0.8548 (m-30) cc_final: 0.8132 (m-30)
REVERT: E   37 LYS cc_start: 0.9171 (ttmt) cc_final: 0.7921 (tptt)
REVERT: F   10 ASP cc_start: 0.8474 (m-30) cc_final: 0.8100 (m-30)
REVERT: F   37 LYS cc_start: 0.9058 (ttmt) cc_final: 0.7532 (tptt)
REVERT: G   10 ASP cc_start: 0.8753 (m-30) cc_final: 0.8542 (m-30)
REVERT: G   33 LYS cc_start: 0.8833 (mttt) cc_final: 0.8615 (mtpp)
REVERT: G   53 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8085 (mm-30)
REVERT: H   10 ASP cc_start: 0.8711 (m-30) cc_final: 0.8469 (m-30)
REVERT: H   37 LYS cc_start: 0.9064 (ttmt) cc_final: 0.7390 (tptt)
REVERT: H   72 ASP cc_start: 0.9213 (m-30) cc_final: 0.8767 (m-30)
REVERT: I    8 TYR cc_start: 0.8710 (t80) cc_final: 0.8405 (t80)
REVERT: I   21 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8309 (t70)
REVERT: I   53 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7988 (mt-10)
REVERT: K   31 LEU cc_start: 0.9312 (tp) cc_final: 0.9081 (tp)
REVERT: L   39 SER cc_start: 0.8805 (m) cc_final: 0.8271 (m)
REVERT: M   69 LYS cc_start: 0.9243 (tmtt) cc_final: 0.7887 (ttmt)
REVERT: N   15 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.7394 (ttpt)
REVERT: N   69 LYS cc_start: 0.9126 (tmtt) cc_final: 0.8007 (ttmt)
REVERT: N   70 ASP cc_start: 0.8553 (m-30) cc_final: 0.8222 (m-30)
REVERT: O   32 ASP cc_start: 0.8304 (m-30) cc_final: 0.8022 (m-30)
REVERT: O   69 LYS cc_start: 0.9134 (tmtt) cc_final: 0.8094 (ttmt)
REVERT: O   72 ASP cc_start: 0.8775 (m-30) cc_final: 0.8502 (m-30)
REVERT: P   32 ASP cc_start: 0.8286 (m-30) cc_final: 0.8073 (m-30)
REVERT: P   69 LYS cc_start: 0.9021 (tmtt) cc_final: 0.8078 (ttmt)
REVERT: Q   15 LYS cc_start: 0.8788 (mttp) cc_final: 0.7596 (ttpt)
REVERT: Q   25 THR cc_start: 0.9088 (m) cc_final: 0.8799 (p)
REVERT: Q   69 LYS cc_start: 0.9048 (tmtt) cc_final: 0.7602 (tttt)
REVERT: R   15 LYS cc_start: 0.8505 (mttp) cc_final: 0.7466 (ttpt)
REVERT: R   69 LYS cc_start: 0.9186 (tmtt) cc_final: 0.7965 (ttmt)
REVERT: R   77 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8473 (tm-30)
  outliers start: 6
  outliers final: 3
  residues processed: 310
  average time/residue: 0.2336
  time to fit residues: 102.0550
Evaluate side-chains
  292 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 287
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain I residue   21 ASP
Chi-restraints excluded: chain N residue   15 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 111 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0000
   chunk 121 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   chunk 98 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.6184

-------------------------------------------------------------------------------
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 = 0.3187 r_free = 0.3187 target = 0.095817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.085999 restraints weight = 18574.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 1.73
r_work: 0.2939 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.3992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017  11214  Z= 0.128
  Angle     :  0.398   4.933  15264  Z= 0.211
  Chirality :  0.033   0.103   1746
  Planarity :  0.003   0.025   1998
  Dihedral  :  3.427  14.890   1512
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 14.14 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.41 (0.21), residues: 1368
  helix:  2.73 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -1.75 (0.51), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP M   5 
 PHE   0.005   0.001   PHE N  68 
 TYR   0.008   0.001   TYR B  47 
 ARG   0.001   0.000   ARG E  58 

*********************** 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
  321 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 312
  time to evaluate  : 1.227 
Fit side-chains
   revert: symmetry clash
REVERT: B   37 LYS cc_start: 0.8747 (ttmt) cc_final: 0.7482 (tptt)
REVERT: B   40 ASP cc_start: 0.8083 (t0) cc_final: 0.7856 (t0)
REVERT: B   66 LYS cc_start: 0.8859 (tptp) cc_final: 0.7599 (ttmt)
REVERT: B   69 LYS cc_start: 0.8879 (tmtt) cc_final: 0.8561 (tttm)
REVERT: C   10 ASP cc_start: 0.8515 (m-30) cc_final: 0.8005 (m-30)
REVERT: C   37 LYS cc_start: 0.8954 (ttmt) cc_final: 0.7477 (tptt)
REVERT: C   69 LYS cc_start: 0.9085 (tmtt) cc_final: 0.8806 (tttm)
REVERT: C   72 ASP cc_start: 0.9219 (m-30) cc_final: 0.8842 (m-30)
REVERT: D   10 ASP cc_start: 0.8486 (m-30) cc_final: 0.7862 (m-30)
REVERT: D   66 LYS cc_start: 0.8795 (tptp) cc_final: 0.7858 (ttmt)
REVERT: D   69 LYS cc_start: 0.8972 (tmtt) cc_final: 0.8765 (tttm)
REVERT: E   37 LYS cc_start: 0.9164 (ttmt) cc_final: 0.7903 (tptt)
REVERT: F   10 ASP cc_start: 0.8447 (m-30) cc_final: 0.8061 (m-30)
REVERT: F   37 LYS cc_start: 0.9033 (ttmt) cc_final: 0.7538 (tptt)
REVERT: G   10 ASP cc_start: 0.8712 (m-30) cc_final: 0.8480 (m-30)
REVERT: G   33 LYS cc_start: 0.8791 (mttt) cc_final: 0.8579 (mtpp)
REVERT: G   52 SER cc_start: 0.8967 (m) cc_final: 0.8476 (p)
REVERT: H   10 ASP cc_start: 0.8709 (m-30) cc_final: 0.8467 (m-30)
REVERT: H   37 LYS cc_start: 0.9069 (ttmt) cc_final: 0.7414 (tptt)
REVERT: H   72 ASP cc_start: 0.9224 (m-30) cc_final: 0.8817 (m-30)
REVERT: I    8 TYR cc_start: 0.8667 (t80) cc_final: 0.8368 (t80)
REVERT: I   21 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8353 (t70)
REVERT: I   53 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7912 (mt-10)
REVERT: J   72 ASP cc_start: 0.8603 (m-30) cc_final: 0.8083 (m-30)
REVERT: K   31 LEU cc_start: 0.9325 (tp) cc_final: 0.9093 (tp)
REVERT: L   39 SER cc_start: 0.8826 (m) cc_final: 0.8112 (m)
REVERT: M   69 LYS cc_start: 0.9244 (tmtt) cc_final: 0.7825 (ttmt)
REVERT: N   15 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.7377 (ttpt)
REVERT: N   69 LYS cc_start: 0.9141 (tmtt) cc_final: 0.8023 (ttmt)
REVERT: O   32 ASP cc_start: 0.8280 (m-30) cc_final: 0.8023 (m-30)
REVERT: O   69 LYS cc_start: 0.9207 (tmtt) cc_final: 0.8230 (ttmt)
REVERT: O   72 ASP cc_start: 0.8832 (m-30) cc_final: 0.8523 (m-30)
REVERT: P   69 LYS cc_start: 0.9033 (tmtt) cc_final: 0.8038 (ttmt)
REVERT: Q   15 LYS cc_start: 0.8778 (mttp) cc_final: 0.7549 (ttpt)
REVERT: Q   25 THR cc_start: 0.9105 (m) cc_final: 0.8838 (p)
REVERT: Q   32 ASP cc_start: 0.8425 (m-30) cc_final: 0.8026 (m-30)
REVERT: Q   69 LYS cc_start: 0.9066 (tmtt) cc_final: 0.7586 (tttt)
REVERT: R   15 LYS cc_start: 0.8493 (mttp) cc_final: 0.7455 (ttpt)
REVERT: R   69 LYS cc_start: 0.9191 (tmtt) cc_final: 0.7936 (ttmt)
REVERT: R   72 ASP cc_start: 0.8934 (m-30) cc_final: 0.8713 (m-30)
REVERT: R   77 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8448 (tm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 315
  average time/residue: 0.2342
  time to fit residues: 103.9987
Evaluate side-chains
  298 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 289
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain D residue   32 ASP
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain I residue   21 ASP
Chi-restraints excluded: chain M residue   53 GLU
Chi-restraints excluded: chain N residue   15 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 42 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   chunk 118 optimal weight:    2.9990
   chunk 115 optimal weight:    0.6980
   chunk 110 optimal weight:    1.9990
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.094591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.084758 restraints weight = 18843.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 1.73
r_work: 0.2912 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2803 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.4129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  11214  Z= 0.147
  Angle     :  0.405   3.994  15264  Z= 0.215
  Chirality :  0.034   0.101   1746
  Planarity :  0.003   0.026   1998
  Dihedral  :  3.456  14.720   1512
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 14.65 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.75 (0.21), residues: 1368
  helix:  2.97 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -1.81 (0.50), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP M   5 
 PHE   0.006   0.001   PHE N  68 
 TYR   0.009   0.001   TYR B  47 
 ARG   0.002   0.000   ARG I  80 

*********************** 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
  312 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 301
  time to evaluate  : 1.221 
Fit side-chains
   revert: symmetry clash
REVERT: B   37 LYS cc_start: 0.8841 (ttmt) cc_final: 0.7595 (tptt)
REVERT: B   56 LEU cc_start: 0.9393 (mt) cc_final: 0.8997 (mt)
REVERT: B   66 LYS cc_start: 0.8862 (tptp) cc_final: 0.7626 (ttmt)
REVERT: B   69 LYS cc_start: 0.8916 (tmtt) cc_final: 0.8639 (tttm)
REVERT: C   10 ASP cc_start: 0.8558 (m-30) cc_final: 0.8002 (m-30)
REVERT: C   37 LYS cc_start: 0.8963 (ttmt) cc_final: 0.7527 (tptt)
REVERT: C   69 LYS cc_start: 0.9103 (tmtt) cc_final: 0.8826 (tttm)
REVERT: C   72 ASP cc_start: 0.9213 (m-30) cc_final: 0.8852 (m-30)
REVERT: D   10 ASP cc_start: 0.8562 (m-30) cc_final: 0.7884 (m-30)
REVERT: D   66 LYS cc_start: 0.8805 (tptp) cc_final: 0.7829 (ttmt)
REVERT: E   37 LYS cc_start: 0.9165 (ttmt) cc_final: 0.7910 (tptt)
REVERT: E   66 LYS cc_start: 0.8616 (tptp) cc_final: 0.7677 (tppt)
REVERT: F   10 ASP cc_start: 0.8479 (m-30) cc_final: 0.8112 (m-30)
REVERT: F   37 LYS cc_start: 0.9024 (ttmt) cc_final: 0.7511 (tptt)
REVERT: G   10 ASP cc_start: 0.8730 (m-30) cc_final: 0.8367 (m-30)
REVERT: G   33 LYS cc_start: 0.8798 (mttt) cc_final: 0.8580 (mtpp)
REVERT: H   37 LYS cc_start: 0.9132 (ttmt) cc_final: 0.7505 (tptt)
REVERT: H   72 ASP cc_start: 0.9245 (m-30) cc_final: 0.8853 (m-30)
REVERT: I    8 TYR cc_start: 0.8697 (t80) cc_final: 0.8407 (t80)
REVERT: I   21 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8321 (t70)
REVERT: I   53 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7905 (mt-10)
REVERT: I   69 LYS cc_start: 0.8925 (tmtt) cc_final: 0.8514 (tttp)
REVERT: K   31 LEU cc_start: 0.9330 (tp) cc_final: 0.9121 (tp)
REVERT: L   39 SER cc_start: 0.8838 (m) cc_final: 0.8571 (m)
REVERT: M   69 LYS cc_start: 0.9259 (tmtt) cc_final: 0.7831 (ttmt)
REVERT: N   15 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.7462 (ttpt)
REVERT: N   69 LYS cc_start: 0.9112 (tmtt) cc_final: 0.7990 (ttmt)
REVERT: O   32 ASP cc_start: 0.8267 (m-30) cc_final: 0.7740 (m-30)
REVERT: O   69 LYS cc_start: 0.9220 (tmtt) cc_final: 0.8082 (ttmt)
REVERT: P   69 LYS cc_start: 0.9101 (tmtt) cc_final: 0.8103 (ttmt)
REVERT: Q   15 LYS cc_start: 0.8780 (mttp) cc_final: 0.7521 (ttpt)
REVERT: Q   25 THR cc_start: 0.9105 (m) cc_final: 0.8835 (p)
REVERT: Q   32 ASP cc_start: 0.8409 (m-30) cc_final: 0.8050 (m-30)
REVERT: Q   69 LYS cc_start: 0.9076 (tmtt) cc_final: 0.7551 (tttt)
REVERT: R   15 LYS cc_start: 0.8544 (mttp) cc_final: 0.7489 (ttpt)
REVERT: R   69 LYS cc_start: 0.9191 (tmtt) cc_final: 0.7952 (ttmt)
REVERT: R   77 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8421 (tm-30)
  outliers start: 11
  outliers final: 9
  residues processed: 305
  average time/residue: 0.2410
  time to fit residues: 103.3755
Evaluate side-chains
  301 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 290
  time to evaluate  : 1.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain D residue   32 ASP
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain H residue   21 ASP
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain I residue   21 ASP
Chi-restraints excluded: chain M residue   53 GLU
Chi-restraints excluded: chain N residue   15 LYS
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 106 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    1.7786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.090251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.080452 restraints weight = 19224.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 1.74
r_work: 0.2840 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2730 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.4168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  11214  Z= 0.272
  Angle     :  0.474   4.640  15264  Z= 0.253
  Chirality :  0.037   0.110   1746
  Planarity :  0.003   0.027   1998
  Dihedral  :  3.699  18.648   1512
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 14.39 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.45 (0.21), residues: 1368
  helix:  2.80 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -2.17 (0.47), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP G   5 
 PHE   0.009   0.001   PHE O  68 
 TYR   0.012   0.001   TYR J  57 
 ARG   0.002   0.000   ARG A  80 

*********************** 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
  326 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 311
  time to evaluate  : 1.262 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ASP cc_start: 0.8658 (m-30) cc_final: 0.8386 (m-30)
REVERT: B   37 LYS cc_start: 0.9048 (ttmt) cc_final: 0.7677 (tptt)
REVERT: B   47 TYR cc_start: 0.9371 (t80) cc_final: 0.9164 (t80)
REVERT: B   56 LEU cc_start: 0.9420 (mt) cc_final: 0.9073 (mt)
REVERT: B   66 LYS cc_start: 0.8854 (tptp) cc_final: 0.7740 (ttmt)
REVERT: B   69 LYS cc_start: 0.8985 (tmtt) cc_final: 0.8740 (tttm)
REVERT: C   10 ASP cc_start: 0.8773 (m-30) cc_final: 0.8261 (m-30)
REVERT: C   37 LYS cc_start: 0.9027 (ttmt) cc_final: 0.7539 (tptt)
REVERT: C   69 LYS cc_start: 0.9137 (tmtt) cc_final: 0.8849 (tttm)
REVERT: C   72 ASP cc_start: 0.9261 (m-30) cc_final: 0.8892 (m-30)
REVERT: D   10 ASP cc_start: 0.8698 (m-30) cc_final: 0.7930 (m-30)
REVERT: D   66 LYS cc_start: 0.8856 (tptp) cc_final: 0.7274 (mttm)
REVERT: D   72 ASP cc_start: 0.9089 (m-30) cc_final: 0.8883 (m-30)
REVERT: E   37 LYS cc_start: 0.9150 (ttmt) cc_final: 0.7842 (tptt)
REVERT: E   66 LYS cc_start: 0.8580 (tptp) cc_final: 0.7784 (tppt)
REVERT: F   10 ASP cc_start: 0.8628 (m-30) cc_final: 0.8237 (m-30)
REVERT: F   37 LYS cc_start: 0.9113 (ttmt) cc_final: 0.7511 (tptt)
REVERT: G   10 ASP cc_start: 0.8692 (m-30) cc_final: 0.8444 (m-30)
REVERT: G   32 ASP cc_start: 0.8423 (m-30) cc_final: 0.7932 (m-30)
REVERT: G   33 LYS cc_start: 0.8892 (mttt) cc_final: 0.8672 (mtpp)
REVERT: H   72 ASP cc_start: 0.9321 (m-30) cc_final: 0.8986 (m-30)
REVERT: I    8 TYR cc_start: 0.8779 (t80) cc_final: 0.8482 (t80)
REVERT: I   53 GLU cc_start: 0.8493 (mt-10) cc_final: 0.7948 (mt-10)
REVERT: I   69 LYS cc_start: 0.9012 (tmtt) cc_final: 0.8569 (tttp)
REVERT: M   59 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8720 (m110)
REVERT: M   69 LYS cc_start: 0.9225 (tmtt) cc_final: 0.7920 (ttmt)
REVERT: N   15 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7532 (ttpt)
REVERT: N   69 LYS cc_start: 0.9132 (tmtt) cc_final: 0.7990 (ttmt)
REVERT: O   32 ASP cc_start: 0.8267 (m-30) cc_final: 0.7909 (m-30)
REVERT: O   69 LYS cc_start: 0.9190 (tmtt) cc_final: 0.8069 (ttmt)
REVERT: O   72 ASP cc_start: 0.9066 (m-30) cc_final: 0.8808 (m-30)
REVERT: P   54 TYR cc_start: 0.9309 (t80) cc_final: 0.9058 (t80)
REVERT: P   69 LYS cc_start: 0.9160 (tmtt) cc_final: 0.8124 (ttmt)
REVERT: Q   25 THR cc_start: 0.9147 (m) cc_final: 0.8803 (p)
REVERT: Q   32 ASP cc_start: 0.8435 (m-30) cc_final: 0.7949 (m-30)
REVERT: Q   69 LYS cc_start: 0.9085 (tmtt) cc_final: 0.7683 (tttt)
REVERT: R   69 LYS cc_start: 0.9224 (tmtt) cc_final: 0.8071 (ttmt)
  outliers start: 15
  outliers final: 9
  residues processed: 319
  average time/residue: 0.2263
  time to fit residues: 101.8577
Evaluate side-chains
  305 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 294
  time to evaluate  : 1.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   32 ASP
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain E residue   39 SER
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain M residue   53 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 120 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9980
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
D  55 ASN
R  26 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.091660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.081867 restraints weight = 19002.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 1.74
r_work: 0.2870 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2761 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.4322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11214  Z= 0.173
  Angle     :  0.434   6.150  15264  Z= 0.231
  Chirality :  0.034   0.115   1746
  Planarity :  0.003   0.025   1998
  Dihedral  :  3.596  15.670   1512
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 15.57 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.70 (0.21), residues: 1368
  helix:  3.00 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -2.40 (0.46), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G   5 
 PHE   0.006   0.001   PHE O  68 
 TYR   0.008   0.001   TYR J  57 
 ARG   0.001   0.000   ARG P  80 

*********************** 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
  317 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 306
  time to evaluate  : 1.208 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ASP cc_start: 0.8585 (m-30) cc_final: 0.8312 (m-30)
REVERT: B   37 LYS cc_start: 0.9026 (ttmt) cc_final: 0.7680 (tptt)
REVERT: B   56 LEU cc_start: 0.9393 (mt) cc_final: 0.9027 (mt)
REVERT: B   66 LYS cc_start: 0.8866 (tptp) cc_final: 0.7762 (ttmt)
REVERT: B   69 LYS cc_start: 0.8955 (tmtt) cc_final: 0.8711 (tttm)
REVERT: C   10 ASP cc_start: 0.8696 (m-30) cc_final: 0.8129 (m-30)
REVERT: C   37 LYS cc_start: 0.9004 (ttmt) cc_final: 0.7553 (tptt)
REVERT: C   69 LYS cc_start: 0.9111 (tmtt) cc_final: 0.8837 (tttm)
REVERT: C   72 ASP cc_start: 0.9196 (m-30) cc_final: 0.8798 (m-30)
REVERT: D   10 ASP cc_start: 0.8653 (m-30) cc_final: 0.7963 (m-30)
REVERT: D   11 ASP cc_start: 0.8237 (m-30) cc_final: 0.8024 (m-30)
REVERT: D   66 LYS cc_start: 0.8833 (tptp) cc_final: 0.7244 (mttm)
REVERT: D   72 ASP cc_start: 0.9088 (m-30) cc_final: 0.8872 (m-30)
REVERT: E   37 LYS cc_start: 0.9160 (ttmt) cc_final: 0.7888 (tptt)
REVERT: E   66 LYS cc_start: 0.8641 (tptp) cc_final: 0.7719 (tppt)
REVERT: F   10 ASP cc_start: 0.8612 (m-30) cc_final: 0.8218 (m-30)
REVERT: F   37 LYS cc_start: 0.9071 (ttmt) cc_final: 0.7501 (tptt)
REVERT: G   10 ASP cc_start: 0.8738 (m-30) cc_final: 0.8527 (m-30)
REVERT: G   32 ASP cc_start: 0.8369 (m-30) cc_final: 0.7914 (m-30)
REVERT: G   33 LYS cc_start: 0.8807 (mttt) cc_final: 0.8589 (mtpp)
REVERT: H   72 ASP cc_start: 0.9289 (m-30) cc_final: 0.8956 (m-30)
REVERT: I    8 TYR cc_start: 0.8745 (t80) cc_final: 0.8481 (t80)
REVERT: I   53 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7842 (mt-10)
REVERT: I   69 LYS cc_start: 0.8970 (tmtt) cc_final: 0.8530 (tttp)
REVERT: J   10 ASP cc_start: 0.8966 (m-30) cc_final: 0.8477 (m-30)
REVERT: M   69 LYS cc_start: 0.9237 (tmtt) cc_final: 0.8230 (ttmt)
REVERT: N   15 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.7535 (ttpt)
REVERT: N   69 LYS cc_start: 0.9114 (tmtt) cc_final: 0.7964 (ttmt)
REVERT: O   32 ASP cc_start: 0.8293 (m-30) cc_final: 0.7950 (m-30)
REVERT: O   69 LYS cc_start: 0.9205 (tmtt) cc_final: 0.8043 (ttmt)
REVERT: O   72 ASP cc_start: 0.8911 (m-30) cc_final: 0.8644 (m-30)
REVERT: P   54 TYR cc_start: 0.9303 (t80) cc_final: 0.9020 (t80)
REVERT: P   69 LYS cc_start: 0.9181 (tmtt) cc_final: 0.8093 (ttmt)
REVERT: P   77 GLN cc_start: 0.8622 (tp-100) cc_final: 0.8341 (tm-30)
REVERT: Q   25 THR cc_start: 0.9126 (m) cc_final: 0.8825 (p)
REVERT: Q   32 ASP cc_start: 0.8409 (m-30) cc_final: 0.7977 (m-30)
REVERT: Q   69 LYS cc_start: 0.9070 (tmtt) cc_final: 0.7552 (tttt)
REVERT: R   69 LYS cc_start: 0.9191 (tmtt) cc_final: 0.7999 (ttmt)
REVERT: R   77 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8264 (tm-30)
  outliers start: 11
  outliers final: 8
  residues processed: 310
  average time/residue: 0.2268
  time to fit residues: 99.5585
Evaluate side-chains
  304 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 295
  time to evaluate  : 1.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain D residue   32 ASP
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain H residue   21 ASP
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain M residue   53 GLU
Chi-restraints excluded: chain N residue   15 LYS
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 107 optimal weight:    0.9980
   chunk 93 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 105 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 108 optimal weight:    4.9990
   chunk 2 optimal weight:    0.4980
   chunk 97 optimal weight:    0.9990
   chunk 121 optimal weight:    2.9990
   overall best weight:    0.8782

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.092146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.082368 restraints weight = 19014.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 1.74
r_work: 0.2879 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2770 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.4371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11214  Z= 0.163
  Angle     :  0.428   4.769  15264  Z= 0.227
  Chirality :  0.034   0.109   1746
  Planarity :  0.003   0.026   1998
  Dihedral  :  3.574  15.311   1512
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 15.49 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.86 (0.21), residues: 1368
  helix:  3.12 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -2.48 (0.46), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP L   5 
 PHE   0.006   0.001   PHE N  68 
 TYR   0.011   0.001   TYR K  47 
 ARG   0.001   0.000   ARG P  80 

*********************** 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
  314 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 301
  time to evaluate  : 1.239 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ASP cc_start: 0.8506 (m-30) cc_final: 0.8132 (m-30)
REVERT: B   37 LYS cc_start: 0.9016 (ttmt) cc_final: 0.7651 (tptt)
REVERT: B   56 LEU cc_start: 0.9397 (mt) cc_final: 0.9027 (mt)
REVERT: B   66 LYS cc_start: 0.8862 (tptp) cc_final: 0.7762 (ttmt)
REVERT: B   69 LYS cc_start: 0.8950 (tmtt) cc_final: 0.8705 (tttm)
REVERT: C   10 ASP cc_start: 0.8686 (m-30) cc_final: 0.8128 (m-30)
REVERT: C   37 LYS cc_start: 0.8986 (ttmt) cc_final: 0.7547 (tptt)
REVERT: C   69 LYS cc_start: 0.9117 (tmtt) cc_final: 0.8855 (tttm)
REVERT: C   72 ASP cc_start: 0.9196 (m-30) cc_final: 0.8803 (m-30)
REVERT: D   10 ASP cc_start: 0.8643 (m-30) cc_final: 0.7940 (m-30)
REVERT: D   66 LYS cc_start: 0.8865 (tptp) cc_final: 0.7345 (mttt)
REVERT: E   37 LYS cc_start: 0.9171 (ttmt) cc_final: 0.7885 (tptt)
REVERT: E   66 LYS cc_start: 0.8668 (tptp) cc_final: 0.7733 (tppt)
REVERT: F   10 ASP cc_start: 0.8566 (m-30) cc_final: 0.8172 (m-30)
REVERT: F   37 LYS cc_start: 0.9053 (ttmt) cc_final: 0.7536 (tptt)
REVERT: G   10 ASP cc_start: 0.8733 (m-30) cc_final: 0.8518 (m-30)
REVERT: G   33 LYS cc_start: 0.8816 (mttt) cc_final: 0.8588 (mtpp)
REVERT: H   72 ASP cc_start: 0.9278 (m-30) cc_final: 0.8941 (m-30)
REVERT: I    8 TYR cc_start: 0.8750 (t80) cc_final: 0.8487 (t80)
REVERT: I   53 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7915 (mt-10)
REVERT: I   69 LYS cc_start: 0.8966 (tmtt) cc_final: 0.8520 (tttp)
REVERT: M   69 LYS cc_start: 0.9228 (tmtt) cc_final: 0.8218 (ttmt)
REVERT: N   15 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.7538 (ttpt)
REVERT: N   69 LYS cc_start: 0.9118 (tmtt) cc_final: 0.7957 (ttmt)
REVERT: O   32 ASP cc_start: 0.8298 (m-30) cc_final: 0.7773 (m-30)
REVERT: O   69 LYS cc_start: 0.9222 (tmtt) cc_final: 0.8081 (ttmt)
REVERT: O   72 ASP cc_start: 0.8965 (m-30) cc_final: 0.8694 (m-30)
REVERT: P   21 ASP cc_start: 0.8226 (t0) cc_final: 0.7977 (t0)
REVERT: P   54 TYR cc_start: 0.9280 (t80) cc_final: 0.9065 (t80)
REVERT: P   69 LYS cc_start: 0.9177 (tmtt) cc_final: 0.8051 (ttmt)
REVERT: P   77 GLN cc_start: 0.8645 (tp-100) cc_final: 0.8412 (tm-30)
REVERT: Q   25 THR cc_start: 0.9070 (m) cc_final: 0.8784 (p)
REVERT: Q   32 ASP cc_start: 0.8427 (m-30) cc_final: 0.8066 (m-30)
REVERT: Q   69 LYS cc_start: 0.9070 (tmtt) cc_final: 0.7546 (tttt)
REVERT: R   15 LYS cc_start: 0.8511 (mttp) cc_final: 0.7456 (ttpt)
REVERT: R   69 LYS cc_start: 0.9198 (tmtt) cc_final: 0.8019 (ttmt)
REVERT: R   77 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8290 (tm-30)
  outliers start: 13
  outliers final: 8
  residues processed: 309
  average time/residue: 0.2256
  time to fit residues: 99.0108
Evaluate side-chains
  305 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 296
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain D residue   32 ASP
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain E residue   39 SER
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain M residue   53 GLU
Chi-restraints excluded: chain N residue   15 LYS
Chi-restraints excluded: chain O residue   57 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   chunk 91 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 70 optimal weight:    6.9990
   chunk 81 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   overall best weight:    1.0784

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.091627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.081905 restraints weight = 19000.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 1.73
r_work: 0.2873 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2764 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.4382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11214  Z= 0.188
  Angle     :  0.447   5.473  15264  Z= 0.238
  Chirality :  0.035   0.109   1746
  Planarity :  0.003   0.025   1998
  Dihedral  :  3.600  15.325   1512
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 15.91 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.82 (0.21), residues: 1368
  helix:  3.10 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -2.56 (0.45), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G   5 
 PHE   0.006   0.001   PHE O  68 
 TYR   0.017   0.001   TYR K  47 
 ARG   0.001   0.000   ARG N  58 

********************** 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
  312 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 302
  time to evaluate  : 1.244 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ASP cc_start: 0.8579 (m-30) cc_final: 0.8219 (m-30)
REVERT: B   37 LYS cc_start: 0.8999 (ttmt) cc_final: 0.7609 (tptt)
REVERT: B   56 LEU cc_start: 0.9409 (mt) cc_final: 0.9040 (mt)
REVERT: B   66 LYS cc_start: 0.8859 (tptp) cc_final: 0.7771 (ttmt)
REVERT: B   69 LYS cc_start: 0.8966 (tmtt) cc_final: 0.8726 (tttm)
REVERT: C   10 ASP cc_start: 0.8737 (m-30) cc_final: 0.8153 (m-30)
REVERT: C   37 LYS cc_start: 0.8990 (ttmt) cc_final: 0.7548 (tptt)
REVERT: C   69 LYS cc_start: 0.9126 (tmtt) cc_final: 0.8860 (tttm)
REVERT: C   72 ASP cc_start: 0.9221 (m-30) cc_final: 0.8824 (m-30)
REVERT: D   10 ASP cc_start: 0.8620 (m-30) cc_final: 0.7950 (m-30)
REVERT: D   66 LYS cc_start: 0.8875 (tptp) cc_final: 0.7356 (mttt)
REVERT: E   37 LYS cc_start: 0.9157 (ttmt) cc_final: 0.7867 (tptt)
REVERT: E   66 LYS cc_start: 0.8663 (tptp) cc_final: 0.7729 (tppt)
REVERT: F   10 ASP cc_start: 0.8561 (m-30) cc_final: 0.8158 (m-30)
REVERT: F   37 LYS cc_start: 0.9065 (ttmt) cc_final: 0.7541 (tptt)
REVERT: G   10 ASP cc_start: 0.8737 (m-30) cc_final: 0.8519 (m-30)
REVERT: G   33 LYS cc_start: 0.8823 (mttt) cc_final: 0.8597 (mtpp)
REVERT: H   72 ASP cc_start: 0.9296 (m-30) cc_final: 0.8968 (m-30)
REVERT: I    8 TYR cc_start: 0.8764 (t80) cc_final: 0.8448 (t80)
REVERT: I   53 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7907 (mt-10)
REVERT: I   69 LYS cc_start: 0.8972 (tmtt) cc_final: 0.8524 (tttp)
REVERT: M   69 LYS cc_start: 0.9238 (tmtt) cc_final: 0.8229 (ttmt)
REVERT: N   15 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.7534 (ttpt)
REVERT: N   69 LYS cc_start: 0.9122 (tmtt) cc_final: 0.7957 (ttmt)
REVERT: O   32 ASP cc_start: 0.8308 (m-30) cc_final: 0.7777 (m-30)
REVERT: O   69 LYS cc_start: 0.9226 (tmtt) cc_final: 0.8077 (ttmt)
REVERT: O   72 ASP cc_start: 0.8917 (m-30) cc_final: 0.8642 (m-30)
REVERT: P   21 ASP cc_start: 0.8183 (t0) cc_final: 0.7947 (t0)
REVERT: P   69 LYS cc_start: 0.9181 (tmtt) cc_final: 0.8047 (ttmt)
REVERT: P   77 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8411 (tm-30)
REVERT: Q   23 LEU cc_start: 0.9094 (tp) cc_final: 0.8832 (tp)
REVERT: Q   25 THR cc_start: 0.9124 (m) cc_final: 0.8803 (p)
REVERT: Q   32 ASP cc_start: 0.8415 (m-30) cc_final: 0.7996 (m-30)
REVERT: Q   69 LYS cc_start: 0.9075 (tmtt) cc_final: 0.7551 (tttt)
REVERT: R   69 LYS cc_start: 0.9204 (tmtt) cc_final: 0.8033 (ttmt)
REVERT: R   77 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8280 (tm-30)
  outliers start: 10
  outliers final: 7
  residues processed: 306
  average time/residue: 0.2180
  time to fit residues: 94.7436
Evaluate side-chains
  305 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 297
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain D residue   32 ASP
Chi-restraints excluded: chain E residue   32 ASP
Chi-restraints excluded: chain E residue   39 SER
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain M residue   53 GLU
Chi-restraints excluded: chain N residue   15 LYS
Chi-restraints excluded: chain O residue   57 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 91 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 114 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 38 optimal weight:    0.4980
   chunk 63 optimal weight:    5.9990
   overall best weight:    1.0384

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.091742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.082031 restraints weight = 18841.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 1.72
r_work: 0.2876 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2766 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.4421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11214  Z= 0.183
  Angle     :  0.441   4.880  15264  Z= 0.235
  Chirality :  0.035   0.109   1746
  Planarity :  0.003   0.021   1998
  Dihedral  :  3.608  15.546   1512
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 16.67 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.85 (0.21), residues: 1368
  helix:  3.12 (0.13), residues: 1206
  sheet:  None (None), residues: 0
  loop : -2.57 (0.45), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G   5 
 PHE   0.006   0.001   PHE O  68 
 TYR   0.019   0.001   TYR K  47 
 ARG   0.001   0.000   ARG A  80 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4681.73 seconds
wall clock time: 84 minutes 39.91 seconds (5079.91 seconds total)