Starting phenix.real_space_refine
on Thu Mar  5 12:20:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fjs_29246/03_2026/8fjs_29246.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fjs_29246/03_2026/8fjs_29246.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fjs_29246/03_2026/8fjs_29246.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fjs_29246/03_2026/8fjs_29246.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fjs_29246/03_2026/8fjs_29246.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fjs_29246/03_2026/8fjs_29246.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.100
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C   14300      2.51       5
     N    3600      2.21       5
     O    4625      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 22550
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 902
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 131}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W,
    X, Y
  Time building chain proxies: 1.72, per 1000 atoms: 0.08
  Number of scatterers: 22550
  At special positions: 0
  Unit cell: (90.72, 91.8, 219.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      25     16.00
     O    4625      8.00
     N    3600      7.00
     C   14300      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: 1.74
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5750

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 50 sheets defined
      29.6% alpha, 47.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 34
      removed outlier: 3.603A  pdb=" N   VAL A   5 " --> pdb=" O   LEU A   1 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLY A  34 " --> pdb=" O   GLY A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY A 106 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL A 108 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY B  34 " --> pdb=" O   GLY B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 108
      removed outlier: 3.964A  pdb=" N   GLY B 106 " --> pdb=" O   THR B 103 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   VAL B 108 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY C  34 " --> pdb=" O   GLY C  30 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY C 106 " --> pdb=" O   THR C 103 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL C 108 " --> pdb=" O   ARG C 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY D  34 " --> pdb=" O   GLY D  30 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY D 106 " --> pdb=" O   THR D 103 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   VAL D 108 " --> pdb=" O   ARG D 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY E  34 " --> pdb=" O   GLY E  30 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY E 106 " --> pdb=" O   THR E 103 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   VAL E 108 " --> pdb=" O   ARG E 105 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY F  34 " --> pdb=" O   GLY F  30 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY F 106 " --> pdb=" O   THR F 103 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL F 108 " --> pdb=" O   ARG F 105 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY G  34 " --> pdb=" O   GLY G  30 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY G 106 " --> pdb=" O   THR G 103 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   VAL G 108 " --> pdb=" O   ARG G 105 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY H  34 " --> pdb=" O   GLY H  30 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY H 106 " --> pdb=" O   THR H 103 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL H 108 " --> pdb=" O   ARG H 105 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY I  34 " --> pdb=" O   GLY I  30 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 103 through 108
      removed outlier: 3.964A  pdb=" N   GLY I 106 " --> pdb=" O   THR I 103 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   VAL I 108 " --> pdb=" O   ARG I 105 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY J  34 " --> pdb=" O   GLY J  30 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY J 106 " --> pdb=" O   THR J 103 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   VAL J 108 " --> pdb=" O   ARG J 105 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY K  34 " --> pdb=" O   GLY K  30 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY K 106 " --> pdb=" O   THR K 103 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   VAL K 108 " --> pdb=" O   ARG K 105 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY L  34 " --> pdb=" O   GLY L  30 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY L 106 " --> pdb=" O   THR L 103 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   VAL L 108 " --> pdb=" O   ARG L 105 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY M  34 " --> pdb=" O   GLY M  30 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY M 106 " --> pdb=" O   THR M 103 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   VAL M 108 " --> pdb=" O   ARG M 105 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY N  34 " --> pdb=" O   GLY N  30 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 103 through 108
      removed outlier: 3.964A  pdb=" N   GLY N 106 " --> pdb=" O   THR N 103 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL N 108 " --> pdb=" O   ARG N 105 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY O  34 " --> pdb=" O   GLY O  30 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY O 106 " --> pdb=" O   THR O 103 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   VAL O 108 " --> pdb=" O   ARG O 105 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY P  34 " --> pdb=" O   GLY P  30 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 103 through 108
      removed outlier: 3.964A  pdb=" N   GLY P 106 " --> pdb=" O   THR P 103 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL P 108 " --> pdb=" O   ARG P 105 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY Q  34 " --> pdb=" O   GLY Q  30 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY Q 106 " --> pdb=" O   THR Q 103 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   VAL Q 108 " --> pdb=" O   ARG Q 105 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY R  34 " --> pdb=" O   GLY R  30 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY R 106 " --> pdb=" O   THR R 103 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL R 108 " --> pdb=" O   ARG R 105 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY S  34 " --> pdb=" O   GLY S  30 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY S 106 " --> pdb=" O   THR S 103 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   VAL S 108 " --> pdb=" O   ARG S 105 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY T  34 " --> pdb=" O   GLY T  30 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY T 106 " --> pdb=" O   THR T 103 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL T 108 " --> pdb=" O   ARG T 105 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY U  34 " --> pdb=" O   GLY U  30 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY U 106 " --> pdb=" O   THR U 103 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   VAL U 108 " --> pdb=" O   ARG U 105 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY V  34 " --> pdb=" O   GLY V  30 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY V 106 " --> pdb=" O   THR V 103 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL V 108 " --> pdb=" O   ARG V 105 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY W  34 " --> pdb=" O   GLY W  30 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 103 through 108
      removed outlier: 3.964A  pdb=" N   GLY W 106 " --> pdb=" O   THR W 103 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   VAL W 108 " --> pdb=" O   ARG W 105 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY X  34 " --> pdb=" O   GLY X  30 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 103 through 108
      removed outlier: 3.963A  pdb=" N   GLY X 106 " --> pdb=" O   THR X 103 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   VAL X 108 " --> pdb=" O   ARG X 105 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 2 through 34
      removed outlier: 3.517A  pdb=" N   GLY Y  34 " --> pdb=" O   GLY Y  30 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 103 through 108
      removed outlier: 3.964A  pdb=" N   GLY Y 106 " --> pdb=" O   THR Y 103 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL Y 108 " --> pdb=" O   ARG Y 105 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40
      removed outlier: 3.777A  pdb=" N   THR A  52 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR A  64 " --> pdb=" O   ILE A  84 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER A  77 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   VAL A  78 " --> pdb=" O   THR A  67 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   THR A  67 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR A  64 " --> pdb=" O   ILE A  84 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR B  52 " --> pdb=" O   SER B  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR B  64 " --> pdb=" O   ILE B  84 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 38 through 40
      removed outlier: 3.701A  pdb=" N   SER B  77 " --> pdb=" O   SER B  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL B  78 " --> pdb=" O   THR B  67 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   THR B  67 " --> pdb=" O   VAL B  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR B  64 " --> pdb=" O   ILE B  84 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 38 through 40
      removed outlier: 3.777A  pdb=" N   THR C  52 " --> pdb=" O   SER C  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR C  64 " --> pdb=" O   ILE C  84 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER C  77 " --> pdb=" O   SER C  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL C  78 " --> pdb=" O   THR C  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR C  67 " --> pdb=" O   VAL C  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR C  64 " --> pdb=" O   ILE C  84 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR D  52 " --> pdb=" O   SER D  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR D  64 " --> pdb=" O   ILE D  84 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER D  77 " --> pdb=" O   SER D  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL D  78 " --> pdb=" O   THR D  67 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   THR D  67 " --> pdb=" O   VAL D  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR D  64 " --> pdb=" O   ILE D  84 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 38 through 40
      removed outlier: 3.777A  pdb=" N   THR E  52 " --> pdb=" O   SER E  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR E  64 " --> pdb=" O   ILE E  84 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER E  77 " --> pdb=" O   SER E  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL E  78 " --> pdb=" O   THR E  67 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   THR E  67 " --> pdb=" O   VAL E  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR E  64 " --> pdb=" O   ILE E  84 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR F  52 " --> pdb=" O   SER F  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR F  64 " --> pdb=" O   ILE F  84 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER F  77 " --> pdb=" O   SER F  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL F  78 " --> pdb=" O   THR F  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR F  67 " --> pdb=" O   VAL F  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR F  64 " --> pdb=" O   ILE F  84 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'G' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR G  52 " --> pdb=" O   SER G  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR G  64 " --> pdb=" O   ILE G  84 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'G' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER G  77 " --> pdb=" O   SER G  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL G  78 " --> pdb=" O   THR G  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR G  67 " --> pdb=" O   VAL G  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR G  64 " --> pdb=" O   ILE G  84 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR H  52 " --> pdb=" O   SER H  47 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   THR H  64 " --> pdb=" O   ILE H  84 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER H  77 " --> pdb=" O   SER H  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL H  78 " --> pdb=" O   THR H  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR H  67 " --> pdb=" O   VAL H  78 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   THR H  64 " --> pdb=" O   ILE H  84 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'I' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR I  52 " --> pdb=" O   SER I  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR I  64 " --> pdb=" O   ILE I  84 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'I' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER I  77 " --> pdb=" O   SER I  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL I  78 " --> pdb=" O   THR I  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR I  67 " --> pdb=" O   VAL I  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR I  64 " --> pdb=" O   ILE I  84 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'J' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR J  52 " --> pdb=" O   SER J  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR J  64 " --> pdb=" O   ILE J  84 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'J' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER J  77 " --> pdb=" O   SER J  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL J  78 " --> pdb=" O   THR J  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR J  67 " --> pdb=" O   VAL J  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR J  64 " --> pdb=" O   ILE J  84 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'K' and resid 38 through 40
      removed outlier: 3.777A  pdb=" N   THR K  52 " --> pdb=" O   SER K  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR K  64 " --> pdb=" O   ILE K  84 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'K' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER K  77 " --> pdb=" O   SER K  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL K  78 " --> pdb=" O   THR K  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR K  67 " --> pdb=" O   VAL K  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR K  64 " --> pdb=" O   ILE K  84 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'L' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR L  52 " --> pdb=" O   SER L  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR L  64 " --> pdb=" O   ILE L  84 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'L' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER L  77 " --> pdb=" O   SER L  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL L  78 " --> pdb=" O   THR L  67 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   THR L  67 " --> pdb=" O   VAL L  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR L  64 " --> pdb=" O   ILE L  84 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'M' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR M  52 " --> pdb=" O   SER M  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR M  64 " --> pdb=" O   ILE M  84 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'M' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER M  77 " --> pdb=" O   SER M  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL M  78 " --> pdb=" O   THR M  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR M  67 " --> pdb=" O   VAL M  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR M  64 " --> pdb=" O   ILE M  84 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'N' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR N  52 " --> pdb=" O   SER N  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR N  64 " --> pdb=" O   ILE N  84 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'N' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER N  77 " --> pdb=" O   SER N  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL N  78 " --> pdb=" O   THR N  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR N  67 " --> pdb=" O   VAL N  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR N  64 " --> pdb=" O   ILE N  84 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'O' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR O  52 " --> pdb=" O   SER O  47 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   THR O  64 " --> pdb=" O   ILE O  84 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'O' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER O  77 " --> pdb=" O   SER O  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL O  78 " --> pdb=" O   THR O  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR O  67 " --> pdb=" O   VAL O  78 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   THR O  64 " --> pdb=" O   ILE O  84 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'P' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR P  52 " --> pdb=" O   SER P  47 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   THR P  64 " --> pdb=" O   ILE P  84 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'P' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER P  77 " --> pdb=" O   SER P  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL P  78 " --> pdb=" O   THR P  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR P  67 " --> pdb=" O   VAL P  78 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   THR P  64 " --> pdb=" O   ILE P  84 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'Q' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR Q  52 " --> pdb=" O   SER Q  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR Q  64 " --> pdb=" O   ILE Q  84 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'Q' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER Q  77 " --> pdb=" O   SER Q  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL Q  78 " --> pdb=" O   THR Q  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR Q  67 " --> pdb=" O   VAL Q  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR Q  64 " --> pdb=" O   ILE Q  84 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'R' and resid 38 through 40
      removed outlier: 3.777A  pdb=" N   THR R  52 " --> pdb=" O   SER R  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR R  64 " --> pdb=" O   ILE R  84 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'R' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER R  77 " --> pdb=" O   SER R  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL R  78 " --> pdb=" O   THR R  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR R  67 " --> pdb=" O   VAL R  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR R  64 " --> pdb=" O   ILE R  84 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'S' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR S  52 " --> pdb=" O   SER S  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR S  64 " --> pdb=" O   ILE S  84 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'S' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER S  77 " --> pdb=" O   SER S  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL S  78 " --> pdb=" O   THR S  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR S  67 " --> pdb=" O   VAL S  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR S  64 " --> pdb=" O   ILE S  84 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'T' and resid 38 through 40
      removed outlier: 3.777A  pdb=" N   THR T  52 " --> pdb=" O   SER T  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR T  64 " --> pdb=" O   ILE T  84 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'T' and resid 38 through 40
      removed outlier: 3.701A  pdb=" N   SER T  77 " --> pdb=" O   SER T  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL T  78 " --> pdb=" O   THR T  67 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   THR T  67 " --> pdb=" O   VAL T  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR T  64 " --> pdb=" O   ILE T  84 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'U' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR U  52 " --> pdb=" O   SER U  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR U  64 " --> pdb=" O   ILE U  84 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'U' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER U  77 " --> pdb=" O   SER U  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL U  78 " --> pdb=" O   THR U  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR U  67 " --> pdb=" O   VAL U  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR U  64 " --> pdb=" O   ILE U  84 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'V' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR V  52 " --> pdb=" O   SER V  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR V  64 " --> pdb=" O   ILE V  84 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'V' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER V  77 " --> pdb=" O   SER V  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL V  78 " --> pdb=" O   THR V  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR V  67 " --> pdb=" O   VAL V  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR V  64 " --> pdb=" O   ILE V  84 " (cutoff:3.500A)
    Processing sheet with id=AE9, first strand: chain 'W' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR W  52 " --> pdb=" O   SER W  47 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   THR W  64 " --> pdb=" O   ILE W  84 " (cutoff:3.500A)
    Processing sheet with id=AF1, first strand: chain 'W' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER W  77 " --> pdb=" O   SER W  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL W  78 " --> pdb=" O   THR W  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR W  67 " --> pdb=" O   VAL W  78 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   THR W  64 " --> pdb=" O   ILE W  84 " (cutoff:3.500A)
    Processing sheet with id=AF2, first strand: chain 'X' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR X  52 " --> pdb=" O   SER X  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR X  64 " --> pdb=" O   ILE X  84 " (cutoff:3.500A)
    Processing sheet with id=AF3, first strand: chain 'X' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER X  77 " --> pdb=" O   SER X  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL X  78 " --> pdb=" O   THR X  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR X  67 " --> pdb=" O   VAL X  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR X  64 " --> pdb=" O   ILE X  84 " (cutoff:3.500A)
    Processing sheet with id=AF4, first strand: chain 'Y' and resid 38 through 40
      removed outlier: 3.776A  pdb=" N   THR Y  52 " --> pdb=" O   SER Y  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR Y  64 " --> pdb=" O   ILE Y  84 " (cutoff:3.500A)
    Processing sheet with id=AF5, first strand: chain 'Y' and resid 38 through 40
      removed outlier: 3.702A  pdb=" N   SER Y  77 " --> pdb=" O   SER Y  96 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL Y  78 " --> pdb=" O   THR Y  67 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   THR Y  67 " --> pdb=" O   VAL Y  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR Y  64 " --> pdb=" O   ILE Y  84 " (cutoff:3.500A)

    1575 hydrogen bonds defined for protein.
    4500 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: 5.28

  Time building geometry restraints manager: 2.39 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 7125
        1.34 -     1.46: 3774
        1.46 -     1.57: 11701
        1.57 -     1.69: 0
        1.69 -     1.80: 50
  Bond restraints: 22650
  Sorted by residual:
  bond pdb=" CB  ILE U  17 "
       pdb=" CG2 ILE U  17 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.021 3.30e-02 9.18e+02 4.23e-01
  bond pdb=" CB  ILE B  17 "
       pdb=" CG2 ILE B  17 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.021 3.30e-02 9.18e+02 4.18e-01
  bond pdb=" CB  ILE P  17 "
       pdb=" CG2 ILE P  17 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.021 3.30e-02 9.18e+02 4.14e-01
  bond pdb=" CB  ILE Q  17 "
       pdb=" CG2 ILE Q  17 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.021 3.30e-02 9.18e+02 4.14e-01
  bond pdb=" CB  ILE O  17 "
       pdb=" CG2 ILE O  17 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.021 3.30e-02 9.18e+02 4.04e-01
  ... (remaining 22645 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.71: 28714
        0.71 -     1.41: 1770
        1.41 -     2.12: 306
        2.12 -     2.82: 160
        2.82 -     3.53: 100
  Bond angle restraints: 31050
  Sorted by residual:
  angle pdb=" N   THR C  60 "
        pdb=" CA  THR C  60 "
        pdb=" C   THR C  60 "
      ideal   model   delta    sigma   weight residual
     112.59  110.24    2.35 1.22e+00 6.72e-01 3.72e+00
  angle pdb=" N   THR M  60 "
        pdb=" CA  THR M  60 "
        pdb=" C   THR M  60 "
      ideal   model   delta    sigma   weight residual
     112.59  110.24    2.35 1.22e+00 6.72e-01 3.70e+00
  angle pdb=" N   THR W  60 "
        pdb=" CA  THR W  60 "
        pdb=" C   THR W  60 "
      ideal   model   delta    sigma   weight residual
     112.59  110.25    2.34 1.22e+00 6.72e-01 3.69e+00
  angle pdb=" N   THR N  60 "
        pdb=" CA  THR N  60 "
        pdb=" C   THR N  60 "
      ideal   model   delta    sigma   weight residual
     112.59  110.25    2.34 1.22e+00 6.72e-01 3.69e+00
  angle pdb=" N   THR T  60 "
        pdb=" CA  THR T  60 "
        pdb=" C   THR T  60 "
      ideal   model   delta    sigma   weight residual
     112.59  110.25    2.34 1.22e+00 6.72e-01 3.67e+00
  ... (remaining 31045 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.37: 11400
        9.37 -    18.74: 1050
       18.74 -    28.12: 300
       28.12 -    37.49: 225
       37.49 -    46.86: 50
  Dihedral angle restraints: 13025
    sinusoidal: 3975
      harmonic: 9050
  Sorted by residual:
  dihedral pdb=" CA  GLN T  65 "
           pdb=" CB  GLN T  65 "
           pdb=" CG  GLN T  65 "
           pdb=" CD  GLN T  65 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -90.33   30.33     3      1.50e+01 4.44e-03 4.82e+00
  dihedral pdb=" CA  GLN J  65 "
           pdb=" CB  GLN J  65 "
           pdb=" CG  GLN J  65 "
           pdb=" CD  GLN J  65 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -90.32   30.32     3      1.50e+01 4.44e-03 4.82e+00
  dihedral pdb=" CA  GLN W  65 "
           pdb=" CB  GLN W  65 "
           pdb=" CG  GLN W  65 "
           pdb=" CD  GLN W  65 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -90.31   30.31     3      1.50e+01 4.44e-03 4.82e+00
  ... (remaining 13022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 2679
       0.026 -    0.052: 1039
       0.052 -    0.078: 332
       0.078 -    0.104: 366
       0.104 -    0.130: 184
  Chirality restraints: 4600
  Sorted by residual:
  chirality pdb=" CA  ILE C 129 "
            pdb=" N   ILE C 129 "
            pdb=" C   ILE C 129 "
            pdb=" CB  ILE C 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.25e-01
  chirality pdb=" CA  ILE K 129 "
            pdb=" N   ILE K 129 "
            pdb=" C   ILE K 129 "
            pdb=" CB  ILE K 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.19e-01
  chirality pdb=" CA  ILE L 129 "
            pdb=" N   ILE L 129 "
            pdb=" C   ILE L 129 "
            pdb=" CB  ILE L 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.17e-01
  ... (remaining 4597 not shown)

  Planarity restraints: 3675
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE S  29 "   -0.006 2.00e-02 2.50e+03   4.67e-03 3.82e-01
        pdb=" CG  PHE S  29 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 PHE S  29 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE S  29 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE S  29 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE S  29 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE S  29 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE W  29 "   -0.006 2.00e-02 2.50e+03   4.66e-03 3.81e-01
        pdb=" CG  PHE W  29 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 PHE W  29 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE W  29 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE W  29 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE W  29 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE W  29 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  29 "   -0.006 2.00e-02 2.50e+03   4.64e-03 3.77e-01
        pdb=" CG  PHE B  29 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  29 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  29 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  29 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  29 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  29 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 3672 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 8336
        2.87 -     3.38: 20122
        3.38 -     3.88: 39184
        3.88 -     4.39: 40997
        4.39 -     4.90: 75447
  Nonbonded interactions: 184086
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN T  74 "
            pdb=" OG  SER T  99 "
     model   vdw
     2.362 3.040
  nonbonded pdb=" OD1 ASN I  74 "
            pdb=" OG  SER I  99 "
     model   vdw
     2.362 3.040
  nonbonded pdb=" OD1 ASN F  74 "
            pdb=" OG  SER F  99 "
     model   vdw
     2.362 3.040
  nonbonded pdb=" OD1 ASN B  74 "
            pdb=" OG  SER B  99 "
     model   vdw
     2.362 3.040
  nonbonded pdb=" OD1 ASN P  74 "
            pdb=" OG  SER P  99 "
     model   vdw
     2.362 3.040
  ... (remaining 184081 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  selection = chain 'R'
  selection = chain 'S'
  selection = chain 'T'
  selection = chain 'U'
  selection = chain 'V'
  selection = chain 'W'
  selection = chain 'X'
  selection = chain 'Y'
}

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:             5.610
  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:             0.020
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     19.680
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
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      :  0.002   0.021  22650  Z= 0.108
  Angle     :  0.454   3.526  31050  Z= 0.259
  Chirality :  0.044   0.130   4600
  Planarity :  0.001   0.005   3675
  Dihedral  : 10.151  46.859   7275
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.15), residues: 3250
  helix:  2.67 (0.17), residues: 1025
  sheet: -0.62 (0.16), residues: 1125
  loop : -1.57 (0.17), residues: 1100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 105 
 TYR   0.002   0.001   TYR G  91 
 PHE   0.010   0.002   PHE W  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (22650)
  covalent geometry    : angle       0.45412 (31050)
  hydrogen bonds       : bond        0.15848 ( 1500)
  hydrogen bonds       : angle       5.71406 ( 4500)

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

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

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 0.819 
Fit side-chains
REVERT: B   89 ASN cc_start: 0.8648 (m110) cc_final: 0.8432 (m110)
REVERT: E   45 THR cc_start: 0.8707 (m) cc_final: 0.8414 (m)
REVERT: E   89 ASN cc_start: 0.8811 (m110) cc_final: 0.8423 (m110)
REVERT: F   89 ASN cc_start: 0.8933 (m110) cc_final: 0.8726 (m110)
REVERT: H   45 THR cc_start: 0.8755 (m) cc_final: 0.8494 (m)
REVERT: H   89 ASN cc_start: 0.8740 (m110) cc_final: 0.8229 (m-40)
REVERT: I   89 ASN cc_start: 0.8782 (m110) cc_final: 0.8497 (m110)
REVERT: J   89 ASN cc_start: 0.8878 (m110) cc_final: 0.8427 (m110)
REVERT: O   89 ASN cc_start: 0.8867 (m110) cc_final: 0.8555 (m-40)
REVERT: P   45 THR cc_start: 0.8693 (m) cc_final: 0.8433 (m)
REVERT: Q   45 THR cc_start: 0.8842 (m) cc_final: 0.8603 (m)
REVERT: S   89 ASN cc_start: 0.8842 (m110) cc_final: 0.8482 (m110)
REVERT: T   79 SER cc_start: 0.7676 (t) cc_final: 0.7462 (p)
REVERT: T   89 ASN cc_start: 0.8898 (m110) cc_final: 0.8696 (m-40)
REVERT: V   89 ASN cc_start: 0.8845 (m110) cc_final: 0.8481 (m110)
REVERT: X   45 THR cc_start: 0.8714 (m) cc_final: 0.8416 (m)
REVERT: Y   89 ASN cc_start: 0.8848 (m110) cc_final: 0.8298 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 269
  average time/residue: 0.2160
  time to fit residues: 81.1720
Evaluate side-chains
  187 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 325
   random chunks:
   chunk 197 optimal weight:    3.9990
   chunk 215 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 132 optimal weight:    2.9990
   chunk 261 optimal weight:    2.9990
   chunk 248 optimal weight:    0.9980
   chunk 207 optimal weight:    6.9990
   chunk 155 optimal weight:    0.3980
   chunk 244 optimal weight:    7.9990
   chunk 183 optimal weight:    0.9980
   chunk 298 optimal weight:    2.9990
   overall best weight:    1.6784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.114955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.095343 restraints weight = 25877.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 1.46
r_work: 0.2877 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.1443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  22650  Z= 0.173
  Angle     :  0.599   9.028  31050  Z= 0.317
  Chirality :  0.049   0.232   4600
  Planarity :  0.002   0.015   3675
  Dihedral  :  4.224  12.809   3350
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  5.51 %
    Favored  : 93.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.15), residues: 3250
  helix:  2.21 (0.16), residues: 1025
  sheet: -0.31 (0.15), residues: 1200
  loop : -1.61 (0.17), residues: 1025

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG M 105 
 TYR   0.007   0.002   TYR K  91 
 PHE   0.014   0.002   PHE M  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 (22650)
  covalent geometry    : angle       0.59884 (31050)
  hydrogen bonds       : bond        0.04836 ( 1500)
  hydrogen bonds       : angle       4.22580 ( 4500)

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

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

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 194
  time to evaluate  : 0.713 
Fit side-chains
REVERT: C   41 VAL cc_start: 0.8611 (m) cc_final: 0.8344 (t)
REVERT: E   45 THR cc_start: 0.8867 (m) cc_final: 0.8568 (m)
REVERT: F   89 ASN cc_start: 0.8947 (m110) cc_final: 0.8704 (m110)
REVERT: H   89 ASN cc_start: 0.8880 (m110) cc_final: 0.8508 (m-40)
REVERT: J  120 ASN cc_start: 0.8773 (p0) cc_final: 0.8565 (p0)
REVERT: K   79 SER cc_start: 0.8174 (t) cc_final: 0.7962 (t)
REVERT: M  120 ASN cc_start: 0.8753 (p0) cc_final: 0.8547 (p0)
REVERT: O   41 VAL cc_start: 0.8728 (m) cc_final: 0.8499 (t)
REVERT: O   89 ASN cc_start: 0.8960 (m110) cc_final: 0.8659 (m-40)
REVERT: T   79 SER cc_start: 0.7882 (t) cc_final: 0.7639 (t)
REVERT: U   41 VAL cc_start: 0.8608 (m) cc_final: 0.8266 (t)
REVERT: U   81 MET cc_start: 0.7598 (mtp) cc_final: 0.7391 (mtt)
REVERT: U  120 ASN cc_start: 0.8756 (p0) cc_final: 0.8532 (p0)
REVERT: X   45 THR cc_start: 0.9055 (m) cc_final: 0.8785 (m)
  outliers start: 21
  outliers final: 16
  residues processed: 212
  average time/residue: 0.2293
  time to fit residues: 67.0516
Evaluate side-chains
  186 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 170
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain E residue  123 THR
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain H residue  123 THR
Chi-restraints excluded: chain J residue   45 THR
Chi-restraints excluded: chain N residue  123 THR
Chi-restraints excluded: chain P residue    8 LEU
Chi-restraints excluded: chain P residue  123 THR
Chi-restraints excluded: chain U residue    8 LEU
Chi-restraints excluded: chain U residue  123 THR
Chi-restraints excluded: chain W residue   79 SER
Chi-restraints excluded: chain X residue  123 THR
Chi-restraints excluded: chain Y residue   79 SER
Chi-restraints excluded: chain Y residue  123 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 325
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 264 optimal weight:    3.9990
   chunk 249 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   chunk 228 optimal weight:    0.3980
   chunk 8 optimal weight:    4.9990
   chunk 315 optimal weight:    3.9990
   chunk 244 optimal weight:    4.9990
   chunk 295 optimal weight:    0.7980
   chunk 189 optimal weight:    8.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    1.3382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.115284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.095723 restraints weight = 25970.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 1.46
r_work: 0.2885 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2779 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  22650  Z= 0.146
  Angle     :  0.539   7.805  31050  Z= 0.288
  Chirality :  0.047   0.181   4600
  Planarity :  0.002   0.019   3675
  Dihedral  :  4.247  14.349   3350
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  7.34 %
    Favored  : 90.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.15), residues: 3250
  helix:  2.17 (0.17), residues: 1025
  sheet: -0.31 (0.15), residues: 1200
  loop : -1.48 (0.17), residues: 1025

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I 105 
 TYR   0.006   0.002   TYR K  91 
 PHE   0.017   0.002   PHE M  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (22650)
  covalent geometry    : angle       0.53853 (31050)
  hydrogen bonds       : bond        0.04250 ( 1500)
  hydrogen bonds       : angle       4.05137 ( 4500)

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

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

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 158
  time to evaluate  : 0.701 
Fit side-chains
REVERT: C   41 VAL cc_start: 0.8548 (m) cc_final: 0.8318 (t)
REVERT: E   45 THR cc_start: 0.8872 (m) cc_final: 0.8564 (m)
REVERT: F   89 ASN cc_start: 0.8950 (m110) cc_final: 0.8729 (m110)
REVERT: H   45 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8632 (m)
REVERT: H   89 ASN cc_start: 0.8862 (m110) cc_final: 0.8500 (m-40)
REVERT: J  120 ASN cc_start: 0.8787 (p0) cc_final: 0.8525 (p0)
REVERT: L   81 MET cc_start: 0.7480 (mtp) cc_final: 0.7277 (mtt)
REVERT: M  120 ASN cc_start: 0.8754 (p0) cc_final: 0.8526 (p0)
REVERT: N   79 SER cc_start: 0.8145 (t) cc_final: 0.7869 (p)
REVERT: O   41 VAL cc_start: 0.8724 (m) cc_final: 0.8512 (t)
REVERT: O   89 ASN cc_start: 0.8904 (m110) cc_final: 0.8650 (m-40)
REVERT: T   79 SER cc_start: 0.7918 (t) cc_final: 0.7694 (t)
REVERT: U   41 VAL cc_start: 0.8480 (m) cc_final: 0.8116 (t)
REVERT: U  120 ASN cc_start: 0.8853 (p0) cc_final: 0.8587 (p0)
REVERT: W   45 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8810 (t)
REVERT: X   45 THR cc_start: 0.9065 (m) cc_final: 0.8775 (m)
  outliers start: 50
  outliers final: 39
  residues processed: 194
  average time/residue: 0.2420
  time to fit residues: 64.1482
Evaluate side-chains
  183 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 142
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue   79 SER
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain E residue  123 THR
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain G residue   45 THR
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   43 THR
Chi-restraints excluded: chain H residue   45 THR
Chi-restraints excluded: chain H residue   79 SER
Chi-restraints excluded: chain H residue  123 THR
Chi-restraints excluded: chain I residue   37 THR
Chi-restraints excluded: chain I residue   45 THR
Chi-restraints excluded: chain J residue   45 THR
Chi-restraints excluded: chain K residue   37 THR
Chi-restraints excluded: chain K residue   45 THR
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   45 THR
Chi-restraints excluded: chain L residue   79 SER
Chi-restraints excluded: chain M residue   37 THR
Chi-restraints excluded: chain O residue   37 THR
Chi-restraints excluded: chain P residue    8 LEU
Chi-restraints excluded: chain P residue  123 THR
Chi-restraints excluded: chain Q residue   37 THR
Chi-restraints excluded: chain Q residue   43 THR
Chi-restraints excluded: chain R residue   37 THR
Chi-restraints excluded: chain R residue   79 SER
Chi-restraints excluded: chain S residue   37 THR
Chi-restraints excluded: chain S residue   43 THR
Chi-restraints excluded: chain U residue    8 LEU
Chi-restraints excluded: chain U residue  123 THR
Chi-restraints excluded: chain V residue   37 THR
Chi-restraints excluded: chain W residue   37 THR
Chi-restraints excluded: chain W residue   45 THR
Chi-restraints excluded: chain W residue   79 SER
Chi-restraints excluded: chain X residue  123 THR
Chi-restraints excluded: chain Y residue   37 THR
Chi-restraints excluded: chain Y residue   79 SER
Chi-restraints excluded: chain Y residue  123 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 325
   random chunks:
   chunk 250 optimal weight:    0.9990
   chunk 176 optimal weight:   10.0000
   chunk 115 optimal weight:    3.9990
   chunk 123 optimal weight:    0.7980
   chunk 102 optimal weight:    1.9990
   chunk 227 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 140 optimal weight:    6.9990
   chunk 189 optimal weight:    0.9980
   chunk 117 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   overall best weight:    1.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.115414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.095885 restraints weight = 25872.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 1.45
r_work: 0.2893 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2786 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  22650  Z= 0.132
  Angle     :  0.513   7.599  31050  Z= 0.273
  Chirality :  0.047   0.167   4600
  Planarity :  0.002   0.017   3675
  Dihedral  :  4.164  15.058   3350
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  :  9.63 %
    Favored  : 87.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.15), residues: 3250
  helix:  2.20 (0.17), residues: 1025
  sheet:  0.12 (0.15), residues: 1100
  loop : -1.37 (0.16), residues: 1125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 105 
 TYR   0.005   0.001   TYR K  91 
 PHE   0.017   0.002   PHE M  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (22650)
  covalent geometry    : angle       0.51262 (31050)
  hydrogen bonds       : bond        0.04005 ( 1500)
  hydrogen bonds       : angle       3.93489 ( 4500)

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

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

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 144
  time to evaluate  : 0.796 
Fit side-chains
REVERT: C   41 VAL cc_start: 0.8526 (m) cc_final: 0.8310 (t)
REVERT: E   45 THR cc_start: 0.8840 (m) cc_final: 0.8529 (m)
REVERT: F   89 ASN cc_start: 0.8961 (m110) cc_final: 0.8721 (m110)
REVERT: H   89 ASN cc_start: 0.8871 (m110) cc_final: 0.8509 (m-40)
REVERT: H  122 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8911 (tt0)
REVERT: J  120 ASN cc_start: 0.8771 (p0) cc_final: 0.8509 (p0)
REVERT: L   79 SER cc_start: 0.8389 (OUTLIER) cc_final: 0.7841 (t)
REVERT: L   81 MET cc_start: 0.7534 (mtp) cc_final: 0.7223 (mtt)
REVERT: M  120 ASN cc_start: 0.8733 (p0) cc_final: 0.8508 (p0)
REVERT: N   79 SER cc_start: 0.8094 (t) cc_final: 0.7827 (p)
REVERT: O   89 ASN cc_start: 0.8897 (m110) cc_final: 0.8591 (m110)
REVERT: T   79 SER cc_start: 0.7897 (t) cc_final: 0.7656 (t)
REVERT: U   41 VAL cc_start: 0.8497 (m) cc_final: 0.8144 (t)
REVERT: U  120 ASN cc_start: 0.8830 (p0) cc_final: 0.8582 (p0)
REVERT: W   45 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8712 (t)
REVERT: X   45 THR cc_start: 0.9083 (m) cc_final: 0.8803 (m)
  outliers start: 70
  outliers final: 40
  residues processed: 203
  average time/residue: 0.2462
  time to fit residues: 68.1888
Evaluate side-chains
  172 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 129
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue   79 SER
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain D residue   45 THR
Chi-restraints excluded: chain D residue   79 SER
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain E residue  123 THR
Chi-restraints excluded: chain F residue   45 THR
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   43 THR
Chi-restraints excluded: chain H residue   79 SER
Chi-restraints excluded: chain H residue  122 GLU
Chi-restraints excluded: chain H residue  123 THR
Chi-restraints excluded: chain I residue   37 THR
Chi-restraints excluded: chain J residue   45 THR
Chi-restraints excluded: chain K residue   37 THR
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   45 THR
Chi-restraints excluded: chain L residue   79 SER
Chi-restraints excluded: chain M residue   37 THR
Chi-restraints excluded: chain N residue  123 THR
Chi-restraints excluded: chain O residue   37 THR
Chi-restraints excluded: chain P residue    8 LEU
Chi-restraints excluded: chain P residue  123 THR
Chi-restraints excluded: chain Q residue   37 THR
Chi-restraints excluded: chain R residue   37 THR
Chi-restraints excluded: chain R residue   79 SER
Chi-restraints excluded: chain S residue   37 THR
Chi-restraints excluded: chain S residue   43 THR
Chi-restraints excluded: chain U residue    8 LEU
Chi-restraints excluded: chain U residue   37 THR
Chi-restraints excluded: chain U residue  123 THR
Chi-restraints excluded: chain V residue   37 THR
Chi-restraints excluded: chain W residue   37 THR
Chi-restraints excluded: chain W residue   45 THR
Chi-restraints excluded: chain W residue   79 SER
Chi-restraints excluded: chain X residue  123 THR
Chi-restraints excluded: chain Y residue   37 THR
Chi-restraints excluded: chain Y residue   79 SER
Chi-restraints excluded: chain Y residue  123 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 325
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 249 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 256 optimal weight:    0.9980
   chunk 262 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0770
   chunk 173 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 215 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   overall best weight:    0.7540

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

Flipped N/Q/H residues before XYZ refinement:
T  89 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.118302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.098818 restraints weight = 25498.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 1.45
r_work: 0.2936 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2831 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  22650  Z= 0.107
  Angle     :  0.505   7.013  31050  Z= 0.269
  Chirality :  0.047   0.180   4600
  Planarity :  0.002   0.014   3675
  Dihedral  :  3.879  13.421   3350
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 12.00 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.15), residues: 3250
  helix:  2.40 (0.17), residues: 1025
  sheet:  0.17 (0.15), residues: 1100
  loop : -1.16 (0.17), residues: 1125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG M 105 
 TYR   0.003   0.001   TYR K  91 
 PHE   0.016   0.001   PHE M  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (22650)
  covalent geometry    : angle       0.50520 (31050)
  hydrogen bonds       : bond        0.03547 ( 1500)
  hydrogen bonds       : angle       3.77767 ( 4500)

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

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

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 153
  time to evaluate  : 0.650 
Fit side-chains
REVERT: C   41 VAL cc_start: 0.8452 (m) cc_final: 0.8235 (t)
REVERT: E   45 THR cc_start: 0.8775 (m) cc_final: 0.8466 (m)
REVERT: F   89 ASN cc_start: 0.8942 (m110) cc_final: 0.8711 (m110)
REVERT: H   89 ASN cc_start: 0.8838 (m110) cc_final: 0.8446 (m-40)
REVERT: J  120 ASN cc_start: 0.8616 (p0) cc_final: 0.8392 (p0)
REVERT: L   81 MET cc_start: 0.7465 (mtp) cc_final: 0.7153 (mtt)
REVERT: N   79 SER cc_start: 0.8020 (t) cc_final: 0.7768 (p)
REVERT: O   89 ASN cc_start: 0.8891 (m110) cc_final: 0.8566 (m110)
REVERT: T   79 SER cc_start: 0.7812 (t) cc_final: 0.7545 (t)
REVERT: U  120 ASN cc_start: 0.8666 (p0) cc_final: 0.8465 (p0)
REVERT: X   45 THR cc_start: 0.9043 (m) cc_final: 0.8746 (m)
REVERT: Y   65 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7710 (mp10)
  outliers start: 31
  outliers final: 23
  residues processed: 179
  average time/residue: 0.2994
  time to fit residues: 69.6565
Evaluate side-chains
  156 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain C residue   79 SER
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   79 SER
Chi-restraints excluded: chain I residue   37 THR
Chi-restraints excluded: chain K residue   37 THR
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   79 SER
Chi-restraints excluded: chain N residue  123 THR
Chi-restraints excluded: chain O residue   37 THR
Chi-restraints excluded: chain P residue    8 LEU
Chi-restraints excluded: chain Q residue   37 THR
Chi-restraints excluded: chain Q residue   43 THR
Chi-restraints excluded: chain R residue   37 THR
Chi-restraints excluded: chain R residue   79 SER
Chi-restraints excluded: chain S residue   37 THR
Chi-restraints excluded: chain U residue    8 LEU
Chi-restraints excluded: chain U residue   37 THR
Chi-restraints excluded: chain V residue   37 THR
Chi-restraints excluded: chain W residue   37 THR
Chi-restraints excluded: chain X residue   37 THR
Chi-restraints excluded: chain Y residue   65 GLN
Chi-restraints excluded: chain Y residue   79 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 325
   random chunks:
   chunk 259 optimal weight:    0.7980
   chunk 160 optimal weight:    5.9990
   chunk 286 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 220 optimal weight:    7.9990
   chunk 34 optimal weight:    0.6980
   chunk 267 optimal weight:    2.9990
   chunk 123 optimal weight:    4.9990
   chunk 206 optimal weight:    0.9980
   chunk 103 optimal weight:    7.9990
   chunk 150 optimal weight:    7.9990
   overall best weight:    2.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.112045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.092854 restraints weight = 26043.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 1.42
r_work: 0.2829 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2725 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  22650  Z= 0.198
  Angle     :  0.620   8.689  31050  Z= 0.320
  Chirality :  0.051   0.214   4600
  Planarity :  0.002   0.016   3675
  Dihedral  :  4.531  18.442   3350
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 12.31 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.14), residues: 3250
  helix:  1.93 (0.16), residues: 1025
  sheet:  0.14 (0.15), residues: 1100
  loop : -1.43 (0.16), residues: 1125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG E 105 
 TYR   0.007   0.002   TYR K  91 
 PHE   0.021   0.002   PHE M  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 (22650)
  covalent geometry    : angle       0.62030 (31050)
  hydrogen bonds       : bond        0.04959 ( 1500)
  hydrogen bonds       : angle       4.11595 ( 4500)

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

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

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 127
  time to evaluate  : 0.796 
Fit side-chains
REVERT: D   79 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.7990 (t)
REVERT: E   45 THR cc_start: 0.8994 (m) cc_final: 0.8672 (m)
REVERT: F   89 ASN cc_start: 0.9001 (m110) cc_final: 0.8771 (m110)
REVERT: H   89 ASN cc_start: 0.8864 (m110) cc_final: 0.8516 (m-40)
REVERT: J   65 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8318 (mt0)
REVERT: K   45 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8900 (t)
REVERT: L   79 SER cc_start: 0.8185 (OUTLIER) cc_final: 0.7726 (t)
REVERT: M   79 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.7787 (t)
REVERT: O   89 ASN cc_start: 0.8951 (m110) cc_final: 0.8739 (m-40)
REVERT: Q   65 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8114 (mp10)
REVERT: R   65 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7738 (mt0)
REVERT: T   79 SER cc_start: 0.7921 (t) cc_final: 0.7591 (t)
REVERT: U   41 VAL cc_start: 0.8640 (m) cc_final: 0.8367 (t)
REVERT: W   45 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8837 (t)
REVERT: W   65 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8481 (mm-40)
REVERT: X   41 VAL cc_start: 0.8589 (m) cc_final: 0.8310 (t)
REVERT: X   45 THR cc_start: 0.9105 (m) cc_final: 0.8831 (m)
REVERT: Y   65 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.7812 (mp10)
  outliers start: 70
  outliers final: 49
  residues processed: 185
  average time/residue: 0.2857
  time to fit residues: 69.9236
Evaluate side-chains
  174 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 115
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue   79 SER
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain D residue   45 THR
Chi-restraints excluded: chain D residue   79 SER
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain E residue  123 THR
Chi-restraints excluded: chain F residue   45 THR
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain G residue   45 THR
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   43 THR
Chi-restraints excluded: chain H residue   79 SER
Chi-restraints excluded: chain H residue  123 THR
Chi-restraints excluded: chain I residue   37 THR
Chi-restraints excluded: chain I residue   43 THR
Chi-restraints excluded: chain J residue   45 THR
Chi-restraints excluded: chain J residue   65 GLN
Chi-restraints excluded: chain K residue   37 THR
Chi-restraints excluded: chain K residue   45 THR
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   45 THR
Chi-restraints excluded: chain L residue   79 SER
Chi-restraints excluded: chain M residue   37 THR
Chi-restraints excluded: chain M residue   79 SER
Chi-restraints excluded: chain N residue   81 MET
Chi-restraints excluded: chain N residue  123 THR
Chi-restraints excluded: chain O residue   37 THR
Chi-restraints excluded: chain P residue    8 LEU
Chi-restraints excluded: chain P residue   43 THR
Chi-restraints excluded: chain P residue  123 THR
Chi-restraints excluded: chain Q residue   37 THR
Chi-restraints excluded: chain Q residue   43 THR
Chi-restraints excluded: chain Q residue   65 GLN
Chi-restraints excluded: chain R residue   37 THR
Chi-restraints excluded: chain R residue   65 GLN
Chi-restraints excluded: chain R residue   79 SER
Chi-restraints excluded: chain S residue   37 THR
Chi-restraints excluded: chain S residue   43 THR
Chi-restraints excluded: chain S residue  123 THR
Chi-restraints excluded: chain T residue   43 THR
Chi-restraints excluded: chain U residue    8 LEU
Chi-restraints excluded: chain U residue   37 THR
Chi-restraints excluded: chain U residue   45 THR
Chi-restraints excluded: chain U residue  123 THR
Chi-restraints excluded: chain V residue   37 THR
Chi-restraints excluded: chain V residue   43 THR
Chi-restraints excluded: chain W residue   37 THR
Chi-restraints excluded: chain W residue   45 THR
Chi-restraints excluded: chain W residue   65 GLN
Chi-restraints excluded: chain W residue   79 SER
Chi-restraints excluded: chain X residue   37 THR
Chi-restraints excluded: chain X residue  123 THR
Chi-restraints excluded: chain Y residue   37 THR
Chi-restraints excluded: chain Y residue   65 GLN
Chi-restraints excluded: chain Y residue   79 SER
Chi-restraints excluded: chain Y residue  123 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 325
   random chunks:
   chunk 196 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 317 optimal weight:    2.9990
   chunk 267 optimal weight:    4.9990
   chunk 174 optimal weight:    0.9980
   chunk 265 optimal weight:    4.9990
   chunk 297 optimal weight:    1.9990
   chunk 119 optimal weight:    0.5980
   chunk 136 optimal weight:    3.9990
   chunk 170 optimal weight:    0.9990
   chunk 254 optimal weight:    2.9990
   overall best weight:    1.1186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.115276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.095951 restraints weight = 25890.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 1.43
r_work: 0.2892 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2789 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  22650  Z= 0.131
  Angle     :  0.536   7.298  31050  Z= 0.286
  Chirality :  0.048   0.190   4600
  Planarity :  0.002   0.018   3675
  Dihedral  :  4.235  17.638   3350
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.86 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.15), residues: 3250
  helix:  2.13 (0.17), residues: 1025
  sheet:  0.19 (0.15), residues: 1100
  loop : -1.26 (0.16), residues: 1125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG U 105 
 TYR   0.005   0.001   TYR K  91 
 PHE   0.019   0.002   PHE M  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (22650)
  covalent geometry    : angle       0.53636 (31050)
  hydrogen bonds       : bond        0.04009 ( 1500)
  hydrogen bonds       : angle       3.90878 ( 4500)

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

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

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 137
  time to evaluate  : 0.817 
Fit side-chains
REVERT: E   45 THR cc_start: 0.8860 (m) cc_final: 0.8526 (m)
REVERT: F   89 ASN cc_start: 0.8983 (m110) cc_final: 0.8764 (m110)
REVERT: H   89 ASN cc_start: 0.8836 (m110) cc_final: 0.8460 (m-40)
REVERT: J  120 ASN cc_start: 0.8765 (p0) cc_final: 0.8499 (p0)
REVERT: L   79 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.7770 (t)
REVERT: M   79 SER cc_start: 0.8173 (p) cc_final: 0.7649 (t)
REVERT: N   79 SER cc_start: 0.8148 (t) cc_final: 0.7872 (p)
REVERT: O   89 ASN cc_start: 0.8972 (m110) cc_final: 0.8723 (m-40)
REVERT: R   65 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7658 (mt0)
REVERT: T   79 SER cc_start: 0.7900 (t) cc_final: 0.7577 (t)
REVERT: U   41 VAL cc_start: 0.8502 (m) cc_final: 0.8202 (t)
REVERT: U  120 ASN cc_start: 0.8789 (p0) cc_final: 0.8529 (p0)
REVERT: V  122 GLU cc_start: 0.8812 (tt0) cc_final: 0.8512 (pt0)
REVERT: X   45 THR cc_start: 0.9077 (m) cc_final: 0.8787 (m)
REVERT: Y   65 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7728 (mp10)
  outliers start: 52
  outliers final: 41
  residues processed: 178
  average time/residue: 0.2966
  time to fit residues: 68.5764
Evaluate side-chains
  176 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 132
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain C residue   79 SER
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain D residue   79 SER
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain E residue  123 THR
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   43 THR
Chi-restraints excluded: chain H residue   79 SER
Chi-restraints excluded: chain I residue   37 THR
Chi-restraints excluded: chain K residue   37 THR
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   45 THR
Chi-restraints excluded: chain L residue   79 SER
Chi-restraints excluded: chain L residue  123 THR
Chi-restraints excluded: chain M residue   37 THR
Chi-restraints excluded: chain N residue  123 THR
Chi-restraints excluded: chain O residue   37 THR
Chi-restraints excluded: chain P residue    8 LEU
Chi-restraints excluded: chain P residue   43 THR
Chi-restraints excluded: chain P residue  123 THR
Chi-restraints excluded: chain Q residue   37 THR
Chi-restraints excluded: chain Q residue   43 THR
Chi-restraints excluded: chain R residue   37 THR
Chi-restraints excluded: chain R residue   43 THR
Chi-restraints excluded: chain R residue   65 GLN
Chi-restraints excluded: chain R residue   79 SER
Chi-restraints excluded: chain S residue   37 THR
Chi-restraints excluded: chain S residue   43 THR
Chi-restraints excluded: chain U residue    8 LEU
Chi-restraints excluded: chain U residue   37 THR
Chi-restraints excluded: chain U residue  123 THR
Chi-restraints excluded: chain V residue   37 THR
Chi-restraints excluded: chain W residue   37 THR
Chi-restraints excluded: chain W residue   79 SER
Chi-restraints excluded: chain X residue   37 THR
Chi-restraints excluded: chain X residue  123 THR
Chi-restraints excluded: chain Y residue   37 THR
Chi-restraints excluded: chain Y residue   65 GLN
Chi-restraints excluded: chain Y residue   79 SER
Chi-restraints excluded: chain Y residue  123 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 325
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 261 optimal weight:    1.9990
   chunk 216 optimal weight:    8.9990
   chunk 88 optimal weight:    1.9990
   chunk 168 optimal weight:    4.9990
   chunk 160 optimal weight:    4.9990
   chunk 185 optimal weight:    4.9990
   chunk 289 optimal weight:    0.6980
   chunk 224 optimal weight:    4.9990
   chunk 167 optimal weight:    3.9990
   overall best weight:    2.3388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.109936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.090374 restraints weight = 26323.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.2906 rms_B_bonded: 1.46
r_work: 0.2829 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2724 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  22650  Z= 0.215
  Angle     :  0.639   8.425  31050  Z= 0.331
  Chirality :  0.052   0.197   4600
  Planarity :  0.002   0.023   3675
  Dihedral  :  4.770  21.694   3350
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 13.48 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.14), residues: 3250
  helix:  1.80 (0.16), residues: 1025
  sheet:  0.11 (0.15), residues: 1100
  loop : -1.54 (0.16), residues: 1125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG S 105 
 TYR   0.008   0.002   TYR K  91 
 PHE   0.023   0.002   PHE M  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 (22650)
  covalent geometry    : angle       0.63902 (31050)
  hydrogen bonds       : bond        0.05172 ( 1500)
  hydrogen bonds       : angle       4.14855 ( 4500)

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

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

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 113
  time to evaluate  : 0.784 
Fit side-chains
REVERT: D   79 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8016 (t)
REVERT: E   45 THR cc_start: 0.9035 (m) cc_final: 0.8718 (m)
REVERT: F   89 ASN cc_start: 0.9017 (m110) cc_final: 0.8783 (m110)
REVERT: H   45 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8713 (m)
REVERT: H   89 ASN cc_start: 0.8890 (m110) cc_final: 0.8556 (m-40)
REVERT: J   65 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8341 (mt0)
REVERT: L   79 SER cc_start: 0.8190 (OUTLIER) cc_final: 0.7729 (t)
REVERT: M   79 SER cc_start: 0.8310 (OUTLIER) cc_final: 0.7799 (t)
REVERT: O   89 ASN cc_start: 0.8978 (m110) cc_final: 0.8752 (m-40)
REVERT: Q   65 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8144 (mp10)
REVERT: R   65 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7771 (mt0)
REVERT: T   79 SER cc_start: 0.7945 (t) cc_final: 0.7655 (t)
REVERT: U   41 VAL cc_start: 0.8682 (m) cc_final: 0.8430 (t)
REVERT: V  122 GLU cc_start: 0.8855 (tt0) cc_final: 0.8554 (pt0)
REVERT: W   45 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8869 (t)
REVERT: X   45 THR cc_start: 0.9119 (m) cc_final: 0.8837 (m)
REVERT: Y   65 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7886 (mp10)
REVERT: Y   79 SER cc_start: 0.8094 (OUTLIER) cc_final: 0.7654 (t)
  outliers start: 75
  outliers final: 58
  residues processed: 176
  average time/residue: 0.2853
  time to fit residues: 65.7992
Evaluate side-chains
  177 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 109
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue   79 SER
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain D residue   45 THR
Chi-restraints excluded: chain D residue   79 SER
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain E residue  123 THR
Chi-restraints excluded: chain F residue   45 THR
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain G residue   45 THR
Chi-restraints excluded: chain G residue  103 THR
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   43 THR
Chi-restraints excluded: chain H residue   45 THR
Chi-restraints excluded: chain H residue   79 SER
Chi-restraints excluded: chain H residue  123 THR
Chi-restraints excluded: chain I residue   37 THR
Chi-restraints excluded: chain I residue   43 THR
Chi-restraints excluded: chain I residue   45 THR
Chi-restraints excluded: chain J residue   65 GLN
Chi-restraints excluded: chain K residue   37 THR
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   45 THR
Chi-restraints excluded: chain L residue   79 SER
Chi-restraints excluded: chain L residue  123 THR
Chi-restraints excluded: chain M residue   37 THR
Chi-restraints excluded: chain M residue   79 SER
Chi-restraints excluded: chain M residue  103 THR
Chi-restraints excluded: chain N residue  123 THR
Chi-restraints excluded: chain O residue   37 THR
Chi-restraints excluded: chain P residue    8 LEU
Chi-restraints excluded: chain P residue   43 THR
Chi-restraints excluded: chain P residue   45 THR
Chi-restraints excluded: chain P residue  103 THR
Chi-restraints excluded: chain P residue  123 THR
Chi-restraints excluded: chain Q residue   37 THR
Chi-restraints excluded: chain Q residue   43 THR
Chi-restraints excluded: chain Q residue   65 GLN
Chi-restraints excluded: chain Q residue  123 THR
Chi-restraints excluded: chain R residue   37 THR
Chi-restraints excluded: chain R residue   43 THR
Chi-restraints excluded: chain R residue   45 THR
Chi-restraints excluded: chain R residue   65 GLN
Chi-restraints excluded: chain R residue   79 SER
Chi-restraints excluded: chain S residue   37 THR
Chi-restraints excluded: chain S residue   43 THR
Chi-restraints excluded: chain S residue   45 THR
Chi-restraints excluded: chain S residue  123 THR
Chi-restraints excluded: chain T residue   43 THR
Chi-restraints excluded: chain T residue  103 THR
Chi-restraints excluded: chain U residue    8 LEU
Chi-restraints excluded: chain U residue   37 THR
Chi-restraints excluded: chain U residue  123 THR
Chi-restraints excluded: chain V residue   37 THR
Chi-restraints excluded: chain V residue   43 THR
Chi-restraints excluded: chain W residue   37 THR
Chi-restraints excluded: chain W residue   45 THR
Chi-restraints excluded: chain W residue   79 SER
Chi-restraints excluded: chain X residue   37 THR
Chi-restraints excluded: chain X residue  123 THR
Chi-restraints excluded: chain Y residue   37 THR
Chi-restraints excluded: chain Y residue   65 GLN
Chi-restraints excluded: chain Y residue   79 SER
Chi-restraints excluded: chain Y residue  123 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 325
   random chunks:
   chunk 314 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 317 optimal weight:    0.8980
   chunk 290 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 159 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 199 optimal weight:    7.9990
   chunk 150 optimal weight:    0.6980
   chunk 281 optimal weight:    0.8980
   chunk 126 optimal weight:    0.5980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.117276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.097655 restraints weight = 25745.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 1.47
r_work: 0.2920 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  22650  Z= 0.110
  Angle     :  0.505   6.632  31050  Z= 0.272
  Chirality :  0.047   0.192   4600
  Planarity :  0.002   0.015   3675
  Dihedral  :  4.100  18.190   3350
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 15.18 %
    Favored  : 83.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.15), residues: 3250
  helix:  2.22 (0.17), residues: 1025
  sheet:  0.18 (0.15), residues: 1100
  loop : -1.15 (0.17), residues: 1125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG M 105 
 TYR   0.003   0.001   TYR K  91 
 PHE   0.017   0.001   PHE M  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (22650)
  covalent geometry    : angle       0.50509 (31050)
  hydrogen bonds       : bond        0.03578 ( 1500)
  hydrogen bonds       : angle       3.81535 ( 4500)

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

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

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 145
  time to evaluate  : 0.808 
Fit side-chains
REVERT: E   45 THR cc_start: 0.8896 (m) cc_final: 0.8571 (m)
REVERT: F   89 ASN cc_start: 0.9022 (m110) cc_final: 0.8796 (m110)
REVERT: H   79 SER cc_start: 0.8003 (OUTLIER) cc_final: 0.7424 (t)
REVERT: H   89 ASN cc_start: 0.8871 (m110) cc_final: 0.8505 (m-40)
REVERT: L   79 SER cc_start: 0.8027 (OUTLIER) cc_final: 0.7585 (t)
REVERT: M   79 SER cc_start: 0.8206 (OUTLIER) cc_final: 0.7655 (t)
REVERT: O   89 ASN cc_start: 0.9012 (m110) cc_final: 0.8758 (m-40)
REVERT: R   65 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7797 (mt0)
REVERT: T   79 SER cc_start: 0.7890 (t) cc_final: 0.7570 (t)
REVERT: U   41 VAL cc_start: 0.8490 (m) cc_final: 0.8176 (t)
REVERT: W   65 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7819 (mp10)
REVERT: X   45 THR cc_start: 0.9078 (m) cc_final: 0.8777 (m)
REVERT: Y   65 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7739 (mp10)
REVERT: Y   79 SER cc_start: 0.8116 (OUTLIER) cc_final: 0.7660 (t)
  outliers start: 38
  outliers final: 26
  residues processed: 178
  average time/residue: 0.3415
  time to fit residues: 76.9170
Evaluate side-chains
  167 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 134
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain C residue   79 SER
Chi-restraints excluded: chain D residue   79 SER
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain E residue  123 THR
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   79 SER
Chi-restraints excluded: chain I residue   37 THR
Chi-restraints excluded: chain K residue   37 THR
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   79 SER
Chi-restraints excluded: chain M residue   37 THR
Chi-restraints excluded: chain M residue   79 SER
Chi-restraints excluded: chain N residue  123 THR
Chi-restraints excluded: chain O residue   37 THR
Chi-restraints excluded: chain P residue    8 LEU
Chi-restraints excluded: chain Q residue   37 THR
Chi-restraints excluded: chain Q residue   43 THR
Chi-restraints excluded: chain R residue   37 THR
Chi-restraints excluded: chain R residue   65 GLN
Chi-restraints excluded: chain R residue   79 SER
Chi-restraints excluded: chain S residue   37 THR
Chi-restraints excluded: chain S residue   43 THR
Chi-restraints excluded: chain U residue    8 LEU
Chi-restraints excluded: chain U residue   37 THR
Chi-restraints excluded: chain V residue   37 THR
Chi-restraints excluded: chain W residue   37 THR
Chi-restraints excluded: chain W residue   65 GLN
Chi-restraints excluded: chain W residue   79 SER
Chi-restraints excluded: chain X residue   37 THR
Chi-restraints excluded: chain Y residue   37 THR
Chi-restraints excluded: chain Y residue   65 GLN
Chi-restraints excluded: chain Y residue   79 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 325
   random chunks:
   chunk 89 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 287 optimal weight:    1.9990
   chunk 163 optimal weight:    0.1980
   chunk 79 optimal weight:    0.8980
   chunk 191 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 57 optimal weight:    7.9990
   chunk 128 optimal weight:    3.9990
   chunk 257 optimal weight:    0.0020
   chunk 32 optimal weight:    7.9990
   overall best weight:    0.7790

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.116557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.097145 restraints weight = 25874.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 1.44
r_work: 0.2936 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  22650  Z= 0.109
  Angle     :  0.512   7.331  31050  Z= 0.272
  Chirality :  0.047   0.186   4600
  Planarity :  0.002   0.019   3675
  Dihedral  :  3.932  14.803   3350
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 15.73 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.15), residues: 3250
  helix:  2.34 (0.17), residues: 1025
  sheet:  0.18 (0.15), residues: 1100
  loop : -1.00 (0.17), residues: 1125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 105 
 TYR   0.003   0.001   TYR K  91 
 PHE   0.017   0.001   PHE M  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (22650)
  covalent geometry    : angle       0.51169 (31050)
  hydrogen bonds       : bond        0.03623 ( 1500)
  hydrogen bonds       : angle       3.74575 ( 4500)

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

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

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6500 Ramachandran restraints generated.
    3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 139
  time to evaluate  : 0.780 
Fit side-chains
REVERT: E   45 THR cc_start: 0.8865 (m) cc_final: 0.8530 (m)
REVERT: F   89 ASN cc_start: 0.8977 (m110) cc_final: 0.8755 (m110)
REVERT: H   89 ASN cc_start: 0.8818 (m110) cc_final: 0.8433 (m-40)
REVERT: O   89 ASN cc_start: 0.8904 (m110) cc_final: 0.8607 (m110)
REVERT: R   65 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7770 (mt0)
REVERT: T   79 SER cc_start: 0.7837 (t) cc_final: 0.7502 (t)
REVERT: U   41 VAL cc_start: 0.8541 (m) cc_final: 0.8226 (t)
REVERT: W   65 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7782 (mp10)
REVERT: X   45 THR cc_start: 0.9072 (m) cc_final: 0.8773 (m)
REVERT: Y   65 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.7654 (mp10)
  outliers start: 29
  outliers final: 25
  residues processed: 164
  average time/residue: 0.3303
  time to fit residues: 68.9554
Evaluate side-chains
  163 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain C residue   79 SER
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain E residue  123 THR
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   79 SER
Chi-restraints excluded: chain I residue   37 THR
Chi-restraints excluded: chain K residue   37 THR
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   79 SER
Chi-restraints excluded: chain M residue   37 THR
Chi-restraints excluded: chain N residue  123 THR
Chi-restraints excluded: chain O residue   37 THR
Chi-restraints excluded: chain P residue    8 LEU
Chi-restraints excluded: chain Q residue   37 THR
Chi-restraints excluded: chain Q residue   43 THR
Chi-restraints excluded: chain R residue   37 THR
Chi-restraints excluded: chain R residue   65 GLN
Chi-restraints excluded: chain S residue   37 THR
Chi-restraints excluded: chain U residue    8 LEU
Chi-restraints excluded: chain U residue   37 THR
Chi-restraints excluded: chain V residue   37 THR
Chi-restraints excluded: chain W residue   37 THR
Chi-restraints excluded: chain W residue   65 GLN
Chi-restraints excluded: chain W residue   79 SER
Chi-restraints excluded: chain X residue   37 THR
Chi-restraints excluded: chain Y residue   37 THR
Chi-restraints excluded: chain Y residue   65 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 325
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 262 optimal weight:    1.9990
   chunk 164 optimal weight:   10.0000
   chunk 73 optimal weight:    4.9990
   chunk 254 optimal weight:    8.9990
   chunk 59 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 165 optimal weight:    0.9990
   chunk 115 optimal weight:    2.9990
   chunk 156 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.5988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.113054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.093746 restraints weight = 26118.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 1.43
r_work: 0.2846 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2742 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  22650  Z= 0.162
  Angle     :  0.577   7.645  31050  Z= 0.302
  Chirality :  0.049   0.186   4600
  Planarity :  0.002   0.023   3675
  Dihedral  :  4.367  16.731   3350
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 15.65 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.15), residues: 3250
  helix:  2.05 (0.17), residues: 1025
  sheet:  0.17 (0.15), residues: 1100
  loop : -1.21 (0.17), residues: 1125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG B 105 
 TYR   0.006   0.002   TYR K  91 
 PHE   0.022   0.002   PHE M  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (22650)
  covalent geometry    : angle       0.57718 (31050)
  hydrogen bonds       : bond        0.04544 ( 1500)
  hydrogen bonds       : angle       3.97071 ( 4500)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4650.47 seconds
wall clock time: 80 minutes 46.18 seconds (4846.18 seconds total)