Starting phenix.real_space_refine
on Thu Feb  5 10:10:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m4p_63626/02_2026/9m4p_63626.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m4p_63626/02_2026/9m4p_63626.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m4p_63626/02_2026/9m4p_63626.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m4p_63626/02_2026/9m4p_63626.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m4p_63626/02_2026/9m4p_63626.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m4p_63626/02_2026/9m4p_63626.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.024
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      49      5.16       5
     C   10304      2.51       5
     N    2807      2.21       5
     O    3255      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16415
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "G"
      Number of atoms: 2345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2345
          Classifications: {'peptide': 293}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 283}
    Chain: "A"
      Number of atoms: 2345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2345
          Classifications: {'peptide': 293}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 283}
    Chain: "B"
      Number of atoms: 2345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2345
          Classifications: {'peptide': 293}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 283}
    Chain: "C"
      Number of atoms: 2345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2345
          Classifications: {'peptide': 293}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 283}
    Chain: "D"
      Number of atoms: 2345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2345
          Classifications: {'peptide': 293}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 283}
    Chain: "E"
      Number of atoms: 2345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2345
          Classifications: {'peptide': 293}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 283}
    Chain: "F"
      Number of atoms: 2345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2345
          Classifications: {'peptide': 293}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 283}
  Time building chain proxies: 3.86, per 1000 atoms: 0.24
  Number of scatterers: 16415
  At special positions: 0
  Unit cell: (111.32, 109.48, 114.08, 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      49     16.00
     O    3255      8.00
     N    2807      7.00
     C   10304      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: 1.47
  Conformation dependent library (CDL) restraints added in 765.0 milliseconds
  

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3794

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 36 sheets defined
      4.1% alpha, 47.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'G' and resid 1 through 6
    Processing helix  chain 'G' and resid 217 through 222
      removed outlier: 4.105A  pdb=" N   SER G 221 " --> pdb=" O   SER G 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1 through 6
      removed outlier: 3.529A  pdb=" N   ILE A   5 " --> pdb=" O   ASP A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 222
      removed outlier: 4.125A  pdb=" N   SER A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1 through 6
    Processing helix  chain 'B' and resid 217 through 223
      removed outlier: 4.102A  pdb=" N   SER B 221 " --> pdb=" O   SER B 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1 through 6
      removed outlier: 3.523A  pdb=" N   ILE C   5 " --> pdb=" O   ASP C   2 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 217 through 222
      removed outlier: 4.132A  pdb=" N   SER C 221 " --> pdb=" O   SER C 217 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1 through 6
      removed outlier: 3.508A  pdb=" N   ILE D   5 " --> pdb=" O   ASP D   2 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 217 through 222
      removed outlier: 4.095A  pdb=" N   SER D 221 " --> pdb=" O   SER D 217 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1 through 6
    Processing helix  chain 'E' and resid 217 through 222
      removed outlier: 4.123A  pdb=" N   SER E 221 " --> pdb=" O   SER E 217 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1 through 6
    Processing helix  chain 'F' and resid 217 through 222
      removed outlier: 4.133A  pdb=" N   SER F 221 " --> pdb=" O   SER F 217 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'G' and resid 21 through 22
    Processing sheet with id=AA2, first strand: chain 'G' and resid 21 through 22
      removed outlier: 6.837A  pdb=" N   ALA G 229 " --> pdb=" O   TYR G 101 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   TYR G 101 " --> pdb=" O   ALA G 229 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   VAL G 231 " --> pdb=" O   SER G  99 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'G' and resid 70 through 71
      removed outlier: 3.712A  pdb=" N   LYS G  75 " --> pdb=" O   GLU G  71 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   SER G  76 " --> pdb=" O   LEU G 258 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ASP G 254 " --> pdb=" O   PRO G  81 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   TYR G 256 " --> pdb=" O   ALA G  79 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   ALA G  79 " --> pdb=" O   TYR G 256 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 153 through 158
      removed outlier: 4.551A  pdb=" N   GLY G 166 " --> pdb=" O   GLU G 158 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL G  86 " --> pdb=" O   TRP G 167 " (cutoff:3.500A)
      removed outlier: 8.296A  pdb=" N   SER G  82 " --> pdb=" O   PHE G 171 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   ALA G  79 " --> pdb=" O   TYR G 256 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   TYR G 256 " --> pdb=" O   ALA G  79 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ASP G 254 " --> pdb=" O   PRO G  81 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'G' and resid 251 through 260
    current: chain 'G' and resid 279 through 285
      removed outlier: 3.727A  pdb=" N   LYS G 283 " --> pdb=" O   THR G 292 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'G' and resid 109 through 127
      removed outlier: 7.380A  pdb=" N   THR G 109 " --> pdb=" O   VAL G 149 " (cutoff:3.500A)
      removed outlier: 5.518A  pdb=" N   VAL G 149 " --> pdb=" O   THR G 109 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LYS G 147 " --> pdb=" O   GLU G 111 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   THR A 109 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   VAL A 149 " --> pdb=" O   THR A 109 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LYS A 147 " --> pdb=" O   GLU A 111 " (cutoff:3.500A)
      removed outlier: 7.382A  pdb=" N   THR B 109 " --> pdb=" O   VAL B 149 " (cutoff:3.500A)
      removed outlier: 5.524A  pdb=" N   VAL B 149 " --> pdb=" O   THR B 109 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LYS B 147 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   THR C 109 " --> pdb=" O   VAL C 149 " (cutoff:3.500A)
      removed outlier: 5.571A  pdb=" N   VAL C 149 " --> pdb=" O   THR C 109 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS C 147 " --> pdb=" O   GLU C 111 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   THR D 109 " --> pdb=" O   VAL D 149 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   VAL D 149 " --> pdb=" O   THR D 109 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LYS D 147 " --> pdb=" O   GLU D 111 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   THR E 109 " --> pdb=" O   VAL E 149 " (cutoff:3.500A)
      removed outlier: 5.532A  pdb=" N   VAL E 149 " --> pdb=" O   THR E 109 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LYS E 147 " --> pdb=" O   GLU E 111 " (cutoff:3.500A)
      removed outlier: 7.381A  pdb=" N   THR F 109 " --> pdb=" O   VAL F 149 " (cutoff:3.500A)
      removed outlier: 5.528A  pdb=" N   VAL F 149 " --> pdb=" O   THR F 109 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LYS F 147 " --> pdb=" O   GLU F 111 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 174 through 175
    Processing sheet with id=AA7, first strand: chain 'A' and resid 21 through 22
    Processing sheet with id=AA8, first strand: chain 'A' and resid 21 through 22
      removed outlier: 6.849A  pdb=" N   ALA A 229 " --> pdb=" O   TYR A 101 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   TYR A 101 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   VAL A 231 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 70 through 71
      removed outlier: 3.706A  pdb=" N   LYS A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER A  76 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   ASP A 254 " --> pdb=" O   PRO A  81 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   TYR A 256 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   ALA A  79 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 153 through 158
      removed outlier: 4.546A  pdb=" N   GLY A 166 " --> pdb=" O   GLU A 158 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL A  86 " --> pdb=" O   TRP A 167 " (cutoff:3.500A)
      removed outlier: 8.284A  pdb=" N   SER A  82 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   ALA A  79 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   TYR A 256 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   ASP A 254 " --> pdb=" O   PRO A  81 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 251 through 260
    current: chain 'A' and resid 279 through 285
      removed outlier: 3.743A  pdb=" N   LYS A 283 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 174 through 175
    Processing sheet with id=AB3, first strand: chain 'B' and resid 21 through 22
    Processing sheet with id=AB4, first strand: chain 'B' and resid 21 through 22
      removed outlier: 6.862A  pdb=" N   ALA B 229 " --> pdb=" O   TYR B 101 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   TYR B 101 " --> pdb=" O   ALA B 229 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   VAL B 231 " --> pdb=" O   SER B  99 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 70 through 71
      removed outlier: 3.708A  pdb=" N   LYS B  75 " --> pdb=" O   GLU B  71 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER B  76 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   ASP B 254 " --> pdb=" O   PRO B  81 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   TYR B 256 " --> pdb=" O   ALA B  79 " (cutoff:3.500A)
      removed outlier: 5.227A  pdb=" N   ALA B  79 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 153 through 158
      removed outlier: 4.543A  pdb=" N   GLY B 166 " --> pdb=" O   GLU B 158 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   VAL B  86 " --> pdb=" O   TRP B 167 " (cutoff:3.500A)
      removed outlier: 8.327A  pdb=" N   SER B  82 " --> pdb=" O   PHE B 171 " (cutoff:3.500A)
      removed outlier: 5.227A  pdb=" N   ALA B  79 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   TYR B 256 " --> pdb=" O   ALA B  79 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   ASP B 254 " --> pdb=" O   PRO B  81 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 251 through 260
    current: chain 'B' and resid 279 through 285
      removed outlier: 3.744A  pdb=" N   LYS B 283 " --> pdb=" O   THR B 292 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 174 through 175
    Processing sheet with id=AB8, first strand: chain 'C' and resid 21 through 22
    Processing sheet with id=AB9, first strand: chain 'C' and resid 21 through 22
      removed outlier: 6.830A  pdb=" N   ALA C 229 " --> pdb=" O   TYR C 101 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   TYR C 101 " --> pdb=" O   ALA C 229 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   VAL C 231 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 70 through 71
      removed outlier: 3.696A  pdb=" N   LYS C  75 " --> pdb=" O   GLU C  71 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER C  76 " --> pdb=" O   LEU C 258 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   ASP C 254 " --> pdb=" O   PRO C  81 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   TYR C 256 " --> pdb=" O   ALA C  79 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   ALA C  79 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 153 through 158
      removed outlier: 4.555A  pdb=" N   GLY C 166 " --> pdb=" O   GLU C 158 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL C  86 " --> pdb=" O   TRP C 167 " (cutoff:3.500A)
      removed outlier: 8.291A  pdb=" N   SER C  82 " --> pdb=" O   PHE C 171 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   ALA C  79 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   TYR C 256 " --> pdb=" O   ALA C  79 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   ASP C 254 " --> pdb=" O   PRO C  81 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 251 through 260
    current: chain 'C' and resid 279 through 285
      removed outlier: 3.693A  pdb=" N   LYS C 283 " --> pdb=" O   THR C 292 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 174 through 175
    Processing sheet with id=AC4, first strand: chain 'D' and resid 21 through 22
    Processing sheet with id=AC5, first strand: chain 'D' and resid 21 through 22
      removed outlier: 6.842A  pdb=" N   ALA D 229 " --> pdb=" O   TYR D 101 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   TYR D 101 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL D 231 " --> pdb=" O   SER D  99 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 70 through 71
      removed outlier: 3.691A  pdb=" N   LYS D  75 " --> pdb=" O   GLU D  71 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   SER D  76 " --> pdb=" O   LEU D 258 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   ASP D 254 " --> pdb=" O   PRO D  81 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   TYR D 256 " --> pdb=" O   ALA D  79 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   ALA D  79 " --> pdb=" O   TYR D 256 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'D' and resid 153 through 158
      removed outlier: 4.522A  pdb=" N   GLY D 166 " --> pdb=" O   GLU D 158 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   VAL D  86 " --> pdb=" O   TRP D 167 " (cutoff:3.500A)
      removed outlier: 8.323A  pdb=" N   SER D  82 " --> pdb=" O   PHE D 171 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   ALA D  79 " --> pdb=" O   TYR D 256 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   TYR D 256 " --> pdb=" O   ALA D  79 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   ASP D 254 " --> pdb=" O   PRO D  81 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 251 through 260
    current: chain 'D' and resid 279 through 285
      removed outlier: 3.702A  pdb=" N   LYS D 283 " --> pdb=" O   THR D 292 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'D' and resid 174 through 175
    Processing sheet with id=AC9, first strand: chain 'E' and resid 21 through 22
    Processing sheet with id=AD1, first strand: chain 'E' and resid 21 through 22
      removed outlier: 6.821A  pdb=" N   ALA E 229 " --> pdb=" O   TYR E 101 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   TYR E 101 " --> pdb=" O   ALA E 229 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   VAL E 231 " --> pdb=" O   SER E  99 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'E' and resid 70 through 71
      removed outlier: 3.705A  pdb=" N   LYS E  75 " --> pdb=" O   GLU E  71 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   SER E  76 " --> pdb=" O   LEU E 258 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   ASP E 254 " --> pdb=" O   PRO E  81 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   TYR E 256 " --> pdb=" O   ALA E  79 " (cutoff:3.500A)
      removed outlier: 5.214A  pdb=" N   ALA E  79 " --> pdb=" O   TYR E 256 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'E' and resid 153 through 158
      removed outlier: 4.553A  pdb=" N   GLY E 166 " --> pdb=" O   GLU E 158 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL E  86 " --> pdb=" O   TRP E 167 " (cutoff:3.500A)
      removed outlier: 8.363A  pdb=" N   SER E  82 " --> pdb=" O   PHE E 171 " (cutoff:3.500A)
      removed outlier: 5.214A  pdb=" N   ALA E  79 " --> pdb=" O   TYR E 256 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   TYR E 256 " --> pdb=" O   ALA E  79 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   ASP E 254 " --> pdb=" O   PRO E  81 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 251 through 260
    current: chain 'E' and resid 279 through 285
      removed outlier: 3.675A  pdb=" N   LYS E 283 " --> pdb=" O   THR E 292 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'E' and resid 174 through 175
    Processing sheet with id=AD5, first strand: chain 'F' and resid 21 through 22
    Processing sheet with id=AD6, first strand: chain 'F' and resid 21 through 22
      removed outlier: 6.846A  pdb=" N   ALA F 229 " --> pdb=" O   TYR F 101 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   TYR F 101 " --> pdb=" O   ALA F 229 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   VAL F 231 " --> pdb=" O   SER F  99 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'F' and resid 70 through 71
      removed outlier: 3.718A  pdb=" N   LYS F  75 " --> pdb=" O   GLU F  71 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   SER F  76 " --> pdb=" O   LEU F 258 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   ASP F 254 " --> pdb=" O   PRO F  81 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   TYR F 256 " --> pdb=" O   ALA F  79 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   ALA F  79 " --> pdb=" O   TYR F 256 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'F' and resid 153 through 158
      removed outlier: 4.533A  pdb=" N   GLY F 166 " --> pdb=" O   GLU F 158 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL F  86 " --> pdb=" O   TRP F 167 " (cutoff:3.500A)
      removed outlier: 8.300A  pdb=" N   SER F  82 " --> pdb=" O   PHE F 171 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   ALA F  79 " --> pdb=" O   TYR F 256 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   TYR F 256 " --> pdb=" O   ALA F  79 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   ASP F 254 " --> pdb=" O   PRO F  81 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 251 through 260
    current: chain 'F' and resid 279 through 285
      removed outlier: 3.718A  pdb=" N   LYS F 283 " --> pdb=" O   THR F 292 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'F' and resid 174 through 175

    586 hydrogen bonds defined for protein.
    1518 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.71

  Time building geometry restraints manager: 1.88 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: 5362
        1.34 -     1.46: 3262
        1.46 -     1.57: 8057
        1.57 -     1.69: 0
        1.69 -     1.80: 98
  Bond restraints: 16779
  Sorted by residual:
  bond pdb=" N   ASP C 108 "
       pdb=" CA  ASP C 108 "
    ideal  model  delta    sigma   weight residual
    1.454  1.478 -0.024 1.17e-02 7.31e+03 4.27e+00
  bond pdb=" N   LYS E  46 "
       pdb=" CA  LYS E  46 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.025 1.21e-02 6.83e+03 4.12e+00
  bond pdb=" N   LYS C  46 "
       pdb=" CA  LYS C  46 "
    ideal  model  delta    sigma   weight residual
    1.459  1.483 -0.024 1.21e-02 6.83e+03 4.05e+00
  bond pdb=" N   LYS G  46 "
       pdb=" CA  LYS G  46 "
    ideal  model  delta    sigma   weight residual
    1.459  1.483 -0.024 1.21e-02 6.83e+03 4.05e+00
  bond pdb=" N   LYS A  46 "
       pdb=" CA  LYS A  46 "
    ideal  model  delta    sigma   weight residual
    1.459  1.483 -0.024 1.21e-02 6.83e+03 3.96e+00
  ... (remaining 16774 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 22222
        1.39 -     2.78: 414
        2.78 -     4.17: 58
        4.17 -     5.56: 14
        5.56 -     6.94: 7
  Bond angle restraints: 22715
  Sorted by residual:
  angle pdb=" CA  ILE C 107 "
        pdb=" C   ILE C 107 "
        pdb=" N   ASP C 108 "
      ideal   model   delta    sigma   weight residual
     116.10  112.21    3.89 1.20e+00 6.94e-01 1.05e+01
  angle pdb=" CA  ASP C 108 "
        pdb=" CB  ASP C 108 "
        pdb=" CG  ASP C 108 "
      ideal   model   delta    sigma   weight residual
     112.60  115.40   -2.80 1.00e+00 1.00e+00 7.85e+00
  angle pdb=" C   TYR E 102 "
        pdb=" CA  TYR E 102 "
        pdb=" CB  TYR E 102 "
      ideal   model   delta    sigma   weight residual
     113.57  109.91    3.66 1.57e+00 4.06e-01 5.44e+00
  angle pdb=" CA  LYS C  46 "
        pdb=" C   LYS C  46 "
        pdb=" O   LYS C  46 "
      ideal   model   delta    sigma   weight residual
     120.55  118.08    2.47 1.06e+00 8.90e-01 5.42e+00
  angle pdb=" CA  LYS G  46 "
        pdb=" C   LYS G  46 "
        pdb=" O   LYS G  46 "
      ideal   model   delta    sigma   weight residual
     120.55  118.08    2.47 1.06e+00 8.90e-01 5.42e+00
  ... (remaining 22710 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.66: 9355
       16.66 -    33.32: 485
       33.32 -    49.98: 95
       49.98 -    66.64: 26
       66.64 -    83.30: 7
  Dihedral angle restraints: 9968
    sinusoidal: 4032
      harmonic: 5936
  Sorted by residual:
  dihedral pdb=" CA  LEU A 146 "
           pdb=" CB  LEU A 146 "
           pdb=" CG  LEU A 146 "
           pdb=" CD1 LEU A 146 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.89  -59.89     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  ARG G 251 "
           pdb=" CB  ARG G 251 "
           pdb=" CG  ARG G 251 "
           pdb=" CD  ARG G 251 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.42  -59.58     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   LYS A  46 "
           pdb=" CA  LYS A  46 "
           pdb=" CB  LYS A  46 "
           pdb=" CG  LYS A  46 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   -0.84  -59.16     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 9965 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1333
       0.026 -    0.052: 660
       0.052 -    0.078: 202
       0.078 -    0.104: 100
       0.104 -    0.131: 134
  Chirality restraints: 2429
  Sorted by residual:
  chirality pdb=" CA  ILE B 136 "
            pdb=" N   ILE B 136 "
            pdb=" C   ILE B 136 "
            pdb=" CB  ILE B 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.26e-01
  chirality pdb=" CA  ILE E 136 "
            pdb=" N   ILE E 136 "
            pdb=" C   ILE E 136 "
            pdb=" CB  ILE E 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.26e-01
  chirality pdb=" CA  ILE G 136 "
            pdb=" N   ILE G 136 "
            pdb=" C   ILE G 136 "
            pdb=" CB  ILE G 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.20e-01
  ... (remaining 2426 not shown)

  Planarity restraints: 2933
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E  54 "    0.005 2.00e-02 2.50e+03   9.81e-03 9.62e-01
        pdb=" C   VAL E  54 "   -0.017 2.00e-02 2.50e+03
        pdb=" O   VAL E  54 "    0.006 2.00e-02 2.50e+03
        pdb=" N   ILE E  55 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  54 "   -0.005 2.00e-02 2.50e+03   9.60e-03 9.21e-01
        pdb=" C   VAL A  54 "    0.017 2.00e-02 2.50e+03
        pdb=" O   VAL A  54 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   ILE A  55 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C  90 "    0.016 5.00e-02 4.00e+02   2.38e-02 9.08e-01
        pdb=" N   PRO C  91 "   -0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO C  91 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO C  91 "    0.013 5.00e-02 4.00e+02
  ... (remaining 2930 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 5196
        2.83 -     3.35: 14084
        3.35 -     3.86: 25943
        3.86 -     4.38: 30472
        4.38 -     4.90: 56919
  Nonbonded interactions: 132614
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN D  87 "
            pdb=" OE2 GLU D 250 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" NE2 GLN A  87 "
            pdb=" OE2 GLU A 250 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" NE2 GLN B  87 "
            pdb=" OE2 GLU B 250 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" OH  TYR G 148 "
            pdb=" OD1 ASN F 178 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   ALA G  62 "
            pdb=" NH1 ARG G 251 "
     model   vdw
     2.332 3.120
  ... (remaining 132609 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'G'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.350
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
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   0.027  16779  Z= 0.115
  Angle     :  0.503   6.945  22715  Z= 0.273
  Chirality :  0.044   0.131   2429
  Planarity :  0.003   0.024   2933
  Dihedral  : 10.977  83.301   6174
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  :  6.29 %
    Favored  : 90.62 %
  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: -0.81 (0.19), residues: 2037
  helix: -1.93 (0.61), residues: 42
  sheet:  0.16 (0.17), residues: 1057
  loop : -1.26 (0.19), residues: 938

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 104 
 TYR   0.009   0.001   TYR F 249 
 PHE   0.009   0.001   PHE E 224 
 TRP   0.007   0.001   TRP G  80 
 HIS   0.001   0.000   HIS E  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (16779)
  covalent geometry    : angle       0.50331 (22715)
  hydrogen bonds       : bond        0.25303 (  558)
  hydrogen bonds       : angle      10.59004 ( 1518)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  514 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 458
  time to evaluate  : 0.696 
Fit side-chains
REVERT: G   21 LYS cc_start: 0.8478 (mttp) cc_final: 0.8254 (mtmt)
REVERT: G   87 GLN cc_start: 0.8847 (pt0) cc_final: 0.8385 (pt0)
REVERT: G  146 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8720 (tp)
REVERT: G  237 LYS cc_start: 0.8397 (mtmm) cc_final: 0.8070 (mttm)
REVERT: G  281 ARG cc_start: 0.8727 (ttm-80) cc_final: 0.8439 (ttm110)
REVERT: G  288 LYS cc_start: 0.8304 (mttm) cc_final: 0.7790 (mtpt)
REVERT: A    3 SER cc_start: 0.8706 (t) cc_final: 0.8479 (p)
REVERT: A   21 LYS cc_start: 0.8621 (mttp) cc_final: 0.8387 (mtmt)
REVERT: A   87 GLN cc_start: 0.8812 (pt0) cc_final: 0.8339 (pt0)
REVERT: A   89 GLN cc_start: 0.8715 (tt0) cc_final: 0.8451 (tt0)
REVERT: A  113 MET cc_start: 0.8578 (ttp) cc_final: 0.8347 (ttp)
REVERT: A  118 TYR cc_start: 0.7821 (m-80) cc_final: 0.7581 (m-80)
REVERT: A  281 ARG cc_start: 0.8621 (ttm-80) cc_final: 0.8379 (ttm110)
REVERT: A  288 LYS cc_start: 0.8387 (mttm) cc_final: 0.8169 (mttp)
REVERT: B   21 LYS cc_start: 0.8580 (mttp) cc_final: 0.8339 (mtmt)
REVERT: B   87 GLN cc_start: 0.8730 (pt0) cc_final: 0.8346 (pt0)
REVERT: B  237 LYS cc_start: 0.8488 (mtmm) cc_final: 0.8050 (mttm)
REVERT: B  281 ARG cc_start: 0.8680 (ttm-80) cc_final: 0.8422 (ttm110)
REVERT: C   21 LYS cc_start: 0.8605 (mttp) cc_final: 0.8363 (mtmt)
REVERT: C   87 GLN cc_start: 0.8691 (pt0) cc_final: 0.8237 (pt0)
REVERT: C   89 GLN cc_start: 0.8822 (tt0) cc_final: 0.8562 (tt0)
REVERT: C  113 MET cc_start: 0.8614 (ttp) cc_final: 0.8406 (ttp)
REVERT: C  237 LYS cc_start: 0.8431 (mtmm) cc_final: 0.8000 (mttm)
REVERT: C  257 GLN cc_start: 0.8509 (mt0) cc_final: 0.8301 (mt0)
REVERT: C  281 ARG cc_start: 0.8710 (ttm-80) cc_final: 0.8303 (ttm170)
REVERT: D   21 LYS cc_start: 0.8606 (mttp) cc_final: 0.8355 (mtmt)
REVERT: D   87 GLN cc_start: 0.8803 (pt0) cc_final: 0.8358 (pt0)
REVERT: D  113 MET cc_start: 0.8693 (ttp) cc_final: 0.8422 (ttp)
REVERT: D  201 ASN cc_start: 0.8606 (p0) cc_final: 0.8078 (p0)
REVERT: D  237 LYS cc_start: 0.8488 (mtmm) cc_final: 0.8090 (mttm)
REVERT: D  281 ARG cc_start: 0.8720 (ttm-80) cc_final: 0.8479 (ttm110)
REVERT: E   21 LYS cc_start: 0.8634 (mttp) cc_final: 0.8378 (mtmt)
REVERT: E   87 GLN cc_start: 0.8788 (pt0) cc_final: 0.8380 (pt0)
REVERT: E  113 MET cc_start: 0.8573 (ttp) cc_final: 0.8321 (ttp)
REVERT: E  149 VAL cc_start: 0.9151 (p) cc_final: 0.8925 (t)
REVERT: E  190 VAL cc_start: 0.8384 (t) cc_final: 0.8162 (p)
REVERT: E  200 ARG cc_start: 0.8257 (mtt180) cc_final: 0.7946 (mtp85)
REVERT: E  237 LYS cc_start: 0.8420 (mtmm) cc_final: 0.8038 (mttm)
REVERT: E  245 ILE cc_start: 0.8358 (mm) cc_final: 0.8151 (tt)
REVERT: E  276 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7712 (m-30)
REVERT: E  281 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.8189 (ttm170)
REVERT: F   49 ASN cc_start: 0.7876 (t0) cc_final: 0.7547 (t0)
REVERT: F   87 GLN cc_start: 0.8723 (pt0) cc_final: 0.8320 (pt0)
REVERT: F   89 GLN cc_start: 0.8737 (tt0) cc_final: 0.8534 (tt0)
REVERT: F  146 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8772 (tp)
REVERT: F  237 LYS cc_start: 0.8341 (mtmm) cc_final: 0.8109 (mttm)
REVERT: F  281 ARG cc_start: 0.8772 (ttm-80) cc_final: 0.8096 (ttm170)
  outliers start: 56
  outliers final: 20
  residues processed: 493
  average time/residue: 0.1658
  time to fit residues: 115.5213
Evaluate side-chains
  375 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 352
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain G residue  146 LEU
Chi-restraints excluded: chain G residue  276 ASP
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  276 ASP
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  276 ASP
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain E residue   46 LYS
Chi-restraints excluded: chain E residue   54 VAL
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain E residue  276 ASP
Chi-restraints excluded: chain F residue   46 LYS
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue  146 LEU
Chi-restraints excluded: chain F residue  276 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 194 optimal weight:    8.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    5.9990
   chunk 200 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    6.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
G  49 ASN
A  49 ASN
C 194 GLN
C 257 GLN
D 257 GLN
E  49 ASN
E 178 ASN
F 257 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.117378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.100071 restraints weight = 19094.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 1.64
r_work: 0.2923 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  16779  Z= 0.151
  Angle     :  0.571   8.979  22715  Z= 0.307
  Chirality :  0.048   0.173   2429
  Planarity :  0.004   0.029   2933
  Dihedral  :  5.946  53.297   2266
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 10.31 %
    Favored  : 86.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.18), residues: 2037
  helix: -3.21 (0.35), residues: 42
  sheet:  0.29 (0.16), residues: 1092
  loop : -1.27 (0.19), residues: 903

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 104 
 TYR   0.015   0.002   TYR F  68 
 PHE   0.011   0.001   PHE E 224 
 TRP   0.006   0.001   TRP C 260 
 HIS   0.002   0.000   HIS B 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (16779)
  covalent geometry    : angle       0.57095 (22715)
  hydrogen bonds       : bond        0.04056 (  558)
  hydrogen bonds       : angle       6.53566 ( 1518)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  404 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 354
  time to evaluate  : 0.643 
Fit side-chains
REVERT: G   75 LYS cc_start: 0.8267 (ptpt) cc_final: 0.7806 (pttt)
REVERT: G   87 GLN cc_start: 0.8817 (pt0) cc_final: 0.8540 (pt0)
REVERT: G  231 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8442 (t)
REVERT: G  237 LYS cc_start: 0.8396 (mtmm) cc_final: 0.8144 (mttm)
REVERT: G  281 ARG cc_start: 0.8765 (ttm-80) cc_final: 0.8476 (ttm110)
REVERT: G  288 LYS cc_start: 0.8534 (mttm) cc_final: 0.8119 (mmtm)
REVERT: A   87 GLN cc_start: 0.8727 (pt0) cc_final: 0.8440 (pt0)
REVERT: A   89 GLN cc_start: 0.8789 (tt0) cc_final: 0.8562 (tt0)
REVERT: A  227 ASP cc_start: 0.8106 (p0) cc_final: 0.7752 (p0)
REVERT: A  288 LYS cc_start: 0.8641 (mttm) cc_final: 0.8436 (mttp)
REVERT: B   30 LYS cc_start: 0.8351 (tptt) cc_final: 0.8013 (ttmm)
REVERT: B   87 GLN cc_start: 0.8688 (pt0) cc_final: 0.8417 (pt0)
REVERT: B  164 LYS cc_start: 0.8608 (pttp) cc_final: 0.8142 (ptmm)
REVERT: B  237 LYS cc_start: 0.8467 (mtmm) cc_final: 0.8114 (mttm)
REVERT: B  279 SER cc_start: 0.8950 (p) cc_final: 0.8692 (t)
REVERT: B  281 ARG cc_start: 0.8684 (ttm-80) cc_final: 0.8463 (ttm110)
REVERT: C   75 LYS cc_start: 0.8288 (ptpt) cc_final: 0.7853 (pttt)
REVERT: C   87 GLN cc_start: 0.8674 (pt0) cc_final: 0.8364 (pt0)
REVERT: C   89 GLN cc_start: 0.8796 (tt0) cc_final: 0.8553 (tt0)
REVERT: C  227 ASP cc_start: 0.8282 (p0) cc_final: 0.7948 (p0)
REVERT: C  237 LYS cc_start: 0.8445 (mtmm) cc_final: 0.8019 (mttm)
REVERT: C  281 ARG cc_start: 0.8743 (ttm-80) cc_final: 0.8237 (ttm170)
REVERT: C  283 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7914 (tptm)
REVERT: C  288 LYS cc_start: 0.8625 (mttp) cc_final: 0.8304 (mmtm)
REVERT: D   75 LYS cc_start: 0.8330 (ptpt) cc_final: 0.7876 (pttt)
REVERT: D   87 GLN cc_start: 0.8775 (pt0) cc_final: 0.8563 (pt0)
REVERT: D  164 LYS cc_start: 0.8618 (pttp) cc_final: 0.8118 (ptmm)
REVERT: D  201 ASN cc_start: 0.8599 (p0) cc_final: 0.8094 (p0)
REVERT: D  231 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8484 (t)
REVERT: D  237 LYS cc_start: 0.8451 (mtmm) cc_final: 0.8116 (mttm)
REVERT: D  281 ARG cc_start: 0.8741 (ttm-80) cc_final: 0.8491 (ttm110)
REVERT: E   87 GLN cc_start: 0.8761 (pt0) cc_final: 0.8508 (pt0)
REVERT: E  149 VAL cc_start: 0.9188 (OUTLIER) cc_final: 0.8939 (t)
REVERT: E  237 LYS cc_start: 0.8431 (mtmm) cc_final: 0.8051 (mttm)
REVERT: E  281 ARG cc_start: 0.8669 (ttm-80) cc_final: 0.8080 (ttm-80)
REVERT: F   49 ASN cc_start: 0.7833 (t0) cc_final: 0.7586 (t0)
REVERT: F   75 LYS cc_start: 0.8206 (ptpt) cc_final: 0.7711 (pttt)
REVERT: F   87 GLN cc_start: 0.8700 (pt0) cc_final: 0.8445 (pt0)
REVERT: F  164 LYS cc_start: 0.8610 (pttp) cc_final: 0.8120 (ptmm)
REVERT: F  231 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8366 (t)
REVERT: F  237 LYS cc_start: 0.8318 (mtmm) cc_final: 0.8117 (mttm)
REVERT: F  281 ARG cc_start: 0.8767 (ttm-80) cc_final: 0.8517 (ttm110)
  outliers start: 50
  outliers final: 17
  residues processed: 395
  average time/residue: 0.1645
  time to fit residues: 91.3313
Evaluate side-chains
  348 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 326
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue  161 THR
Chi-restraints excluded: chain G residue  231 VAL
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain C residue    9 THR
Chi-restraints excluded: chain C residue   70 GLU
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  283 LYS
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  161 THR
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain F residue   70 GLU
Chi-restraints excluded: chain F residue  161 THR
Chi-restraints excluded: chain F residue  231 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 111 optimal weight:    6.9990
   chunk 8 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 95 optimal weight:    0.7980
   chunk 137 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 129 optimal weight:    6.9990
   chunk 54 optimal weight:    6.9990
   chunk 119 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
G  49 ASN
B 259 HIS
D  49 ASN
D 194 GLN
E 178 ASN
F 178 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.114677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.097273 restraints weight = 19437.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 1.67
r_work: 0.2906 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2767 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  16779  Z= 0.187
  Angle     :  0.578   9.083  22715  Z= 0.309
  Chirality :  0.048   0.150   2429
  Planarity :  0.004   0.031   2933
  Dihedral  :  4.964  51.809   2231
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 12.74 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.89 (0.18), residues: 2037
  helix: -3.88 (0.23), residues: 42
  sheet:  0.15 (0.15), residues: 1099
  loop : -1.33 (0.19), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 104 
 TYR   0.012   0.002   TYR B  40 
 PHE   0.013   0.002   PHE G 224 
 TRP   0.009   0.001   TRP A 260 
 HIS   0.005   0.001   HIS F 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 (16779)
  covalent geometry    : angle       0.57839 (22715)
  hydrogen bonds       : bond        0.03720 (  558)
  hydrogen bonds       : angle       6.07554 ( 1518)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  385 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 332
  time to evaluate  : 0.483 
Fit side-chains
REVERT: G  164 LYS cc_start: 0.8619 (pttp) cc_final: 0.8055 (ptmm)
REVERT: G  231 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8428 (t)
REVERT: G  237 LYS cc_start: 0.8397 (mtmm) cc_final: 0.8136 (mttm)
REVERT: G  281 ARG cc_start: 0.8815 (ttm-80) cc_final: 0.8543 (ttm110)
REVERT: G  288 LYS cc_start: 0.8621 (mttm) cc_final: 0.8191 (mmtm)
REVERT: A   87 GLN cc_start: 0.8734 (pt0) cc_final: 0.8432 (pt0)
REVERT: A   89 GLN cc_start: 0.8773 (tt0) cc_final: 0.8550 (tt0)
REVERT: A  227 ASP cc_start: 0.8204 (p0) cc_final: 0.7946 (p0)
REVERT: B   36 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8353 (mtmm)
REVERT: B   46 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7491 (ptmm)
REVERT: B   87 GLN cc_start: 0.8646 (pt0) cc_final: 0.8441 (pt0)
REVERT: B  164 LYS cc_start: 0.8623 (pttp) cc_final: 0.8174 (ptmm)
REVERT: B  227 ASP cc_start: 0.8331 (p0) cc_final: 0.8115 (p0)
REVERT: B  237 LYS cc_start: 0.8407 (mtmm) cc_final: 0.8088 (mttm)
REVERT: B  281 ARG cc_start: 0.8775 (ttm-80) cc_final: 0.8522 (ttm110)
REVERT: C   87 GLN cc_start: 0.8689 (pt0) cc_final: 0.8450 (pt0)
REVERT: C   89 GLN cc_start: 0.8777 (tt0) cc_final: 0.8574 (tt0)
REVERT: C  164 LYS cc_start: 0.8684 (pttp) cc_final: 0.8153 (ptmm)
REVERT: C  227 ASP cc_start: 0.8310 (p0) cc_final: 0.8068 (p0)
REVERT: C  237 LYS cc_start: 0.8416 (mtmm) cc_final: 0.8035 (mttm)
REVERT: C  277 ARG cc_start: 0.8461 (mtp-110) cc_final: 0.8154 (mtp-110)
REVERT: C  281 ARG cc_start: 0.8806 (ttm-80) cc_final: 0.8279 (ttm170)
REVERT: C  288 LYS cc_start: 0.8677 (mttp) cc_final: 0.8351 (mmtm)
REVERT: D   34 MET cc_start: 0.9104 (mtt) cc_final: 0.8766 (mtt)
REVERT: D   87 GLN cc_start: 0.8751 (pt0) cc_final: 0.8550 (pt0)
REVERT: D  101 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8724 (p90)
REVERT: D  164 LYS cc_start: 0.8604 (pttp) cc_final: 0.8157 (ptmm)
REVERT: D  201 ASN cc_start: 0.8578 (p0) cc_final: 0.8062 (p0)
REVERT: D  237 LYS cc_start: 0.8402 (mtmm) cc_final: 0.8116 (mttm)
REVERT: D  240 LYS cc_start: 0.7513 (ttpp) cc_final: 0.7222 (tttt)
REVERT: D  281 ARG cc_start: 0.8783 (ttm-80) cc_final: 0.8527 (ttm110)
REVERT: E   87 GLN cc_start: 0.8790 (pt0) cc_final: 0.8567 (pt0)
REVERT: E  149 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8893 (t)
REVERT: E  164 LYS cc_start: 0.8794 (pttp) cc_final: 0.8232 (ptmm)
REVERT: E  201 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.7932 (p0)
REVERT: E  203 SER cc_start: 0.8903 (p) cc_final: 0.8645 (t)
REVERT: E  237 LYS cc_start: 0.8414 (mtmm) cc_final: 0.8086 (mttm)
REVERT: E  277 ARG cc_start: 0.8552 (mtp-110) cc_final: 0.8200 (mtp-110)
REVERT: E  281 ARG cc_start: 0.8721 (ttm-80) cc_final: 0.8168 (ttm-80)
REVERT: F   49 ASN cc_start: 0.7872 (t0) cc_final: 0.7560 (t0)
REVERT: F   75 LYS cc_start: 0.8320 (ptpt) cc_final: 0.7794 (pttt)
REVERT: F   87 GLN cc_start: 0.8701 (pt0) cc_final: 0.8414 (pt0)
REVERT: F  101 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.8533 (p90)
REVERT: F  164 LYS cc_start: 0.8666 (pttp) cc_final: 0.8174 (ptmm)
REVERT: F  231 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8363 (t)
REVERT: F  237 LYS cc_start: 0.8310 (mtmm) cc_final: 0.7948 (mmtt)
REVERT: F  277 ARG cc_start: 0.8513 (mtp-110) cc_final: 0.8282 (mtp180)
REVERT: F  281 ARG cc_start: 0.8826 (ttm-80) cc_final: 0.8582 (ttm110)
  outliers start: 53
  outliers final: 30
  residues processed: 371
  average time/residue: 0.1557
  time to fit residues: 80.1954
Evaluate side-chains
  349 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 312
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   86 VAL
Chi-restraints excluded: chain G residue  106 SER
Chi-restraints excluded: chain G residue  161 THR
Chi-restraints excluded: chain G residue  231 VAL
Chi-restraints excluded: chain G residue  257 GLN
Chi-restraints excluded: chain A residue   36 LYS
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  237 LYS
Chi-restraints excluded: chain B residue   36 LYS
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain C residue    9 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   70 GLU
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   36 LYS
Chi-restraints excluded: chain D residue  101 TYR
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain E residue   14 ILE
Chi-restraints excluded: chain E residue   36 LYS
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  161 THR
Chi-restraints excluded: chain E residue  201 ASN
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain F residue   36 LYS
Chi-restraints excluded: chain F residue   38 VAL
Chi-restraints excluded: chain F residue  101 TYR
Chi-restraints excluded: chain F residue  161 THR
Chi-restraints excluded: chain F residue  231 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 142 optimal weight:    0.8980
   chunk 112 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 50 optimal weight:    0.5980
   chunk 106 optimal weight:    4.9990
   chunk 121 optimal weight:    0.8980
   chunk 118 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   chunk 120 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    2.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 178 ASN
C 178 ASN
E 178 ASN
F 259 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.113353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.095561 restraints weight = 19295.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 1.72
r_work: 0.2927 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2782 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  16779  Z= 0.197
  Angle     :  0.581   9.323  22715  Z= 0.310
  Chirality :  0.048   0.145   2429
  Planarity :  0.004   0.030   2933
  Dihedral  :  4.654  53.057   2223
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 12.80 %
    Favored  : 82.96 %
  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: -0.98 (0.18), residues: 2037
  helix: -4.17 (0.23), residues: 42
  sheet:  0.10 (0.15), residues: 1099
  loop : -1.39 (0.19), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 104 
 TYR   0.013   0.002   TYR D  65 
 PHE   0.013   0.002   PHE E 224 
 TRP   0.010   0.001   TRP C 260 
 HIS   0.007   0.001   HIS C 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (16779)
  covalent geometry    : angle       0.58090 (22715)
  hydrogen bonds       : bond        0.03535 (  558)
  hydrogen bonds       : angle       5.82296 ( 1518)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  408 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 331
  time to evaluate  : 0.649 
Fit side-chains
REVERT: G   36 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8452 (mtmm)
REVERT: G  164 LYS cc_start: 0.8605 (pttp) cc_final: 0.8076 (ptmm)
REVERT: G  227 ASP cc_start: 0.8339 (p0) cc_final: 0.8081 (p0)
REVERT: G  231 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8507 (t)
REVERT: G  237 LYS cc_start: 0.8444 (mtmm) cc_final: 0.8190 (mttm)
REVERT: G  260 TRP cc_start: 0.8746 (t-100) cc_final: 0.8541 (t-100)
REVERT: G  281 ARG cc_start: 0.8858 (ttm-80) cc_final: 0.8578 (ttm110)
REVERT: G  288 LYS cc_start: 0.8626 (mttm) cc_final: 0.8213 (mmtm)
REVERT: A   87 GLN cc_start: 0.8749 (pt0) cc_final: 0.8427 (pt0)
REVERT: A   89 GLN cc_start: 0.8801 (tt0) cc_final: 0.8567 (tt0)
REVERT: A  227 ASP cc_start: 0.8281 (p0) cc_final: 0.7980 (p0)
REVERT: B   36 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8374 (mtmm)
REVERT: B   46 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7510 (ptmm)
REVERT: B   87 GLN cc_start: 0.8686 (pt0) cc_final: 0.8439 (pt0)
REVERT: B  164 LYS cc_start: 0.8600 (pttp) cc_final: 0.8165 (ptmm)
REVERT: B  198 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8376 (ttpt)
REVERT: B  227 ASP cc_start: 0.8444 (p0) cc_final: 0.8139 (p0)
REVERT: B  237 LYS cc_start: 0.8438 (mtmm) cc_final: 0.8080 (mttm)
REVERT: B  240 LYS cc_start: 0.7260 (ttpp) cc_final: 0.7021 (tttt)
REVERT: B  281 ARG cc_start: 0.8795 (ttm-80) cc_final: 0.8544 (ttm110)
REVERT: C   30 LYS cc_start: 0.8299 (tttp) cc_final: 0.7992 (tttm)
REVERT: C   87 GLN cc_start: 0.8756 (pt0) cc_final: 0.8517 (pt0)
REVERT: C  164 LYS cc_start: 0.8701 (pttp) cc_final: 0.8210 (ptmm)
REVERT: C  198 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8285 (ttpt)
REVERT: C  237 LYS cc_start: 0.8440 (mtmm) cc_final: 0.8079 (mttm)
REVERT: C  281 ARG cc_start: 0.8830 (ttm-80) cc_final: 0.8306 (ttm170)
REVERT: C  288 LYS cc_start: 0.8722 (mttp) cc_final: 0.8403 (mmtm)
REVERT: D   34 MET cc_start: 0.9145 (mtt) cc_final: 0.8723 (mtt)
REVERT: D   87 GLN cc_start: 0.8849 (pt0) cc_final: 0.8645 (pt0)
REVERT: D  101 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.8697 (p90)
REVERT: D  164 LYS cc_start: 0.8611 (pttp) cc_final: 0.8171 (ptmm)
REVERT: D  175 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8893 (t)
REVERT: D  198 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8311 (ttpt)
REVERT: D  201 ASN cc_start: 0.8621 (p0) cc_final: 0.8037 (p0)
REVERT: D  237 LYS cc_start: 0.8468 (mtmm) cc_final: 0.8158 (mttm)
REVERT: D  240 LYS cc_start: 0.7581 (ttpp) cc_final: 0.7326 (tttp)
REVERT: D  281 ARG cc_start: 0.8825 (ttm-80) cc_final: 0.8576 (ttm110)
REVERT: E   29 ASP cc_start: 0.8243 (t0) cc_final: 0.7892 (t70)
REVERT: E   87 GLN cc_start: 0.8844 (pt0) cc_final: 0.8629 (pt0)
REVERT: E  149 VAL cc_start: 0.9218 (OUTLIER) cc_final: 0.8872 (t)
REVERT: E  164 LYS cc_start: 0.8804 (pttp) cc_final: 0.8260 (ptmm)
REVERT: E  198 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8387 (ttpt)
REVERT: E  201 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.7938 (p0)
REVERT: E  203 SER cc_start: 0.8943 (p) cc_final: 0.8671 (t)
REVERT: E  237 LYS cc_start: 0.8448 (mtmm) cc_final: 0.8116 (mttm)
REVERT: E  277 ARG cc_start: 0.8632 (mtp-110) cc_final: 0.8274 (mtp-110)
REVERT: E  281 ARG cc_start: 0.8749 (ttm-80) cc_final: 0.8203 (ttm-80)
REVERT: F   49 ASN cc_start: 0.7888 (t0) cc_final: 0.7545 (t0)
REVERT: F   87 GLN cc_start: 0.8788 (pt0) cc_final: 0.8500 (pt0)
REVERT: F  101 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.8624 (p90)
REVERT: F  164 LYS cc_start: 0.8680 (pttp) cc_final: 0.8189 (ptmm)
REVERT: F  198 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8063 (ttpt)
REVERT: F  227 ASP cc_start: 0.8289 (p0) cc_final: 0.8030 (p0)
REVERT: F  231 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8434 (t)
REVERT: F  237 LYS cc_start: 0.8304 (mtmm) cc_final: 0.7942 (mmtt)
REVERT: F  277 ARG cc_start: 0.8435 (mtp-110) cc_final: 0.8234 (mtp180)
REVERT: F  281 ARG cc_start: 0.8854 (ttm-80) cc_final: 0.8592 (ttm110)
  outliers start: 77
  outliers final: 40
  residues processed: 394
  average time/residue: 0.1616
  time to fit residues: 89.1542
Evaluate side-chains
  366 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 312
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue    9 THR
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   38 VAL
Chi-restraints excluded: chain G residue   87 GLN
Chi-restraints excluded: chain G residue  106 SER
Chi-restraints excluded: chain G residue  161 THR
Chi-restraints excluded: chain G residue  231 VAL
Chi-restraints excluded: chain G residue  257 GLN
Chi-restraints excluded: chain A residue   36 LYS
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue   36 LYS
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain C residue   70 GLU
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  198 LYS
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   36 LYS
Chi-restraints excluded: chain D residue   75 LYS
Chi-restraints excluded: chain D residue  101 TYR
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  198 LYS
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain E residue   14 ILE
Chi-restraints excluded: chain E residue   38 VAL
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  161 THR
Chi-restraints excluded: chain E residue  175 VAL
Chi-restraints excluded: chain E residue  198 LYS
Chi-restraints excluded: chain E residue  201 ASN
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain F residue   36 LYS
Chi-restraints excluded: chain F residue   38 VAL
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue  101 TYR
Chi-restraints excluded: chain F residue  161 THR
Chi-restraints excluded: chain F residue  175 VAL
Chi-restraints excluded: chain F residue  198 LYS
Chi-restraints excluded: chain F residue  231 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 121 optimal weight:    3.9990
   chunk 92 optimal weight:    0.7980
   chunk 190 optimal weight:    0.9980
   chunk 113 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 202 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
A 178 ASN
D 259 HIS
E 178 ASN
F 178 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.115094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.097392 restraints weight = 19315.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 1.74
r_work: 0.2929 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2788 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  16779  Z= 0.125
  Angle     :  0.515   9.633  22715  Z= 0.276
  Chirality :  0.046   0.139   2429
  Planarity :  0.003   0.028   2933
  Dihedral  :  4.358  55.193   2223
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 14.18 %
    Favored  : 81.91 %
  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: -0.92 (0.18), residues: 2037
  helix: -4.22 (0.26), residues: 42
  sheet:  0.17 (0.15), residues: 1085
  loop : -1.37 (0.19), residues: 910

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 236 
 TYR   0.013   0.001   TYR B  68 
 PHE   0.011   0.001   PHE E 224 
 TRP   0.015   0.001   TRP D 260 
 HIS   0.009   0.001   HIS E 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (16779)
  covalent geometry    : angle       0.51473 (22715)
  hydrogen bonds       : bond        0.02959 (  558)
  hydrogen bonds       : angle       5.52230 ( 1518)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  403 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 332
  time to evaluate  : 0.508 
Fit side-chains
REVERT: G   29 ASP cc_start: 0.8317 (t0) cc_final: 0.7950 (t70)
REVERT: G  164 LYS cc_start: 0.8546 (pttp) cc_final: 0.8039 (ptmm)
REVERT: G  227 ASP cc_start: 0.8325 (p0) cc_final: 0.8031 (p0)
REVERT: G  231 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8519 (t)
REVERT: G  237 LYS cc_start: 0.8346 (mtmm) cc_final: 0.8106 (mttm)
REVERT: G  281 ARG cc_start: 0.8827 (ttm-80) cc_final: 0.8546 (ttm110)
REVERT: G  288 LYS cc_start: 0.8584 (mttm) cc_final: 0.8175 (mmtm)
REVERT: A    5 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8134 (pt)
REVERT: A   87 GLN cc_start: 0.8729 (pt0) cc_final: 0.8436 (pt0)
REVERT: A   89 GLN cc_start: 0.8783 (tt0) cc_final: 0.8537 (tt0)
REVERT: A  227 ASP cc_start: 0.8207 (p0) cc_final: 0.7907 (p0)
REVERT: B   36 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8407 (mtmm)
REVERT: B   46 LYS cc_start: 0.8116 (mmtm) cc_final: 0.7451 (ptmm)
REVERT: B   87 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8421 (pt0)
REVERT: B  101 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.8485 (p90)
REVERT: B  164 LYS cc_start: 0.8559 (pttp) cc_final: 0.8129 (ptmm)
REVERT: B  198 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8340 (ttpt)
REVERT: B  227 ASP cc_start: 0.8410 (p0) cc_final: 0.8077 (p0)
REVERT: B  237 LYS cc_start: 0.8415 (mtmm) cc_final: 0.8072 (mttm)
REVERT: B  240 LYS cc_start: 0.7246 (ttpp) cc_final: 0.7020 (tttt)
REVERT: B  281 ARG cc_start: 0.8758 (ttm-80) cc_final: 0.8526 (ttm110)
REVERT: B  288 LYS cc_start: 0.8606 (mttp) cc_final: 0.8314 (mmtm)
REVERT: C   30 LYS cc_start: 0.8284 (tttp) cc_final: 0.7977 (tttm)
REVERT: C   87 GLN cc_start: 0.8681 (pt0) cc_final: 0.8463 (pt0)
REVERT: C  164 LYS cc_start: 0.8573 (pttp) cc_final: 0.8077 (ptmm)
REVERT: C  198 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8328 (ttpt)
REVERT: C  203 SER cc_start: 0.8806 (p) cc_final: 0.8554 (t)
REVERT: C  237 LYS cc_start: 0.8455 (mtmm) cc_final: 0.8106 (mttm)
REVERT: C  281 ARG cc_start: 0.8776 (ttm-80) cc_final: 0.8235 (ttm170)
REVERT: C  288 LYS cc_start: 0.8710 (mttp) cc_final: 0.8390 (mmtm)
REVERT: D   34 MET cc_start: 0.9125 (mtt) cc_final: 0.8706 (mtt)
REVERT: D   87 GLN cc_start: 0.8777 (pt0) cc_final: 0.8537 (pt0)
REVERT: D  101 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.8583 (p90)
REVERT: D  164 LYS cc_start: 0.8552 (pttp) cc_final: 0.8193 (ptmm)
REVERT: D  198 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8322 (ttpt)
REVERT: D  201 ASN cc_start: 0.8605 (p0) cc_final: 0.8036 (p0)
REVERT: D  231 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8519 (t)
REVERT: D  237 LYS cc_start: 0.8433 (mtmm) cc_final: 0.8118 (mttm)
REVERT: D  240 LYS cc_start: 0.7524 (ttpp) cc_final: 0.7269 (tttp)
REVERT: D  281 ARG cc_start: 0.8815 (ttm-80) cc_final: 0.8568 (ttm110)
REVERT: D  288 LYS cc_start: 0.8581 (mttp) cc_final: 0.8191 (mmtm)
REVERT: E   87 GLN cc_start: 0.8839 (pt0) cc_final: 0.8633 (pt0)
REVERT: E  113 MET cc_start: 0.8822 (ttp) cc_final: 0.8580 (ttp)
REVERT: E  149 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8867 (t)
REVERT: E  164 LYS cc_start: 0.8780 (pttp) cc_final: 0.8227 (ptmm)
REVERT: E  198 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8385 (ttpt)
REVERT: E  201 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.7910 (p0)
REVERT: E  237 LYS cc_start: 0.8423 (mtmm) cc_final: 0.8107 (mttm)
REVERT: E  277 ARG cc_start: 0.8624 (mtp-110) cc_final: 0.8292 (mtp-110)
REVERT: E  281 ARG cc_start: 0.8707 (ttm-80) cc_final: 0.8157 (ttm-80)
REVERT: E  288 LYS cc_start: 0.8674 (mttm) cc_final: 0.8385 (mmtm)
REVERT: F   49 ASN cc_start: 0.7704 (t0) cc_final: 0.7446 (t0)
REVERT: F   87 GLN cc_start: 0.8718 (pt0) cc_final: 0.8450 (pt0)
REVERT: F  101 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8531 (p90)
REVERT: F  164 LYS cc_start: 0.8649 (pttp) cc_final: 0.8166 (ptmm)
REVERT: F  198 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8027 (ttpt)
REVERT: F  203 SER cc_start: 0.8926 (p) cc_final: 0.8653 (t)
REVERT: F  227 ASP cc_start: 0.8246 (p0) cc_final: 0.7920 (p0)
REVERT: F  237 LYS cc_start: 0.8339 (mtmm) cc_final: 0.7919 (mmtt)
REVERT: F  281 ARG cc_start: 0.8828 (ttm-80) cc_final: 0.8575 (ttm110)
  outliers start: 71
  outliers final: 34
  residues processed: 384
  average time/residue: 0.1486
  time to fit residues: 79.8493
Evaluate side-chains
  364 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 315
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   60 THR
Chi-restraints excluded: chain G residue   86 VAL
Chi-restraints excluded: chain G residue   87 GLN
Chi-restraints excluded: chain G residue  161 THR
Chi-restraints excluded: chain G residue  231 VAL
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue   36 LYS
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue   87 GLN
Chi-restraints excluded: chain B residue  101 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain C residue    9 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   70 GLU
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  198 LYS
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   36 LYS
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   75 LYS
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  101 TYR
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  198 LYS
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain E residue   14 ILE
Chi-restraints excluded: chain E residue   36 LYS
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  161 THR
Chi-restraints excluded: chain E residue  198 LYS
Chi-restraints excluded: chain E residue  201 ASN
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain F residue   60 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue  101 TYR
Chi-restraints excluded: chain F residue  161 THR
Chi-restraints excluded: chain F residue  198 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 101 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 199 optimal weight:    6.9990
   chunk 161 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 84 optimal weight:    2.9990
   chunk 170 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   chunk 147 optimal weight:    7.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
G 178 ASN
A 178 ASN
E 178 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.112976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.095815 restraints weight = 19312.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.65
r_work: 0.2898 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2759 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.3024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  16779  Z= 0.220
  Angle     :  0.594  10.749  22715  Z= 0.315
  Chirality :  0.049   0.148   2429
  Planarity :  0.004   0.031   2933
  Dihedral  :  4.709  55.331   2223
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 15.17 %
    Favored  : 80.75 %
  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: -1.03 (0.18), residues: 2037
  helix: -4.29 (0.27), residues: 42
  sheet:  0.04 (0.15), residues: 1099
  loop : -1.37 (0.20), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 104 
 TYR   0.014   0.002   TYR D  65 
 PHE   0.013   0.002   PHE E 224 
 TRP   0.015   0.001   TRP D 260 
 HIS   0.009   0.001   HIS E 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 (16779)
  covalent geometry    : angle       0.59439 (22715)
  hydrogen bonds       : bond        0.03521 (  558)
  hydrogen bonds       : angle       5.67149 ( 1518)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  390 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 316
  time to evaluate  : 0.563 
Fit side-chains
REVERT: G  164 LYS cc_start: 0.8579 (pttp) cc_final: 0.8051 (ptmm)
REVERT: G  227 ASP cc_start: 0.8353 (p0) cc_final: 0.8029 (p0)
REVERT: G  231 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8485 (t)
REVERT: G  237 LYS cc_start: 0.8303 (mtmm) cc_final: 0.8070 (mttm)
REVERT: G  240 LYS cc_start: 0.7523 (ttpp) cc_final: 0.7267 (tttp)
REVERT: G  281 ARG cc_start: 0.8870 (ttm-80) cc_final: 0.8573 (ttm110)
REVERT: G  288 LYS cc_start: 0.8622 (mttm) cc_final: 0.8104 (mtpt)
REVERT: A    5 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8189 (pt)
REVERT: A   87 GLN cc_start: 0.8752 (pt0) cc_final: 0.8432 (pt0)
REVERT: A  198 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8227 (ttpt)
REVERT: A  227 ASP cc_start: 0.8223 (p0) cc_final: 0.7895 (p0)
REVERT: B   30 LYS cc_start: 0.8443 (tttp) cc_final: 0.8125 (ttmt)
REVERT: B   36 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8380 (mtmm)
REVERT: B   46 LYS cc_start: 0.8064 (mmtm) cc_final: 0.7464 (ptmm)
REVERT: B   87 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8440 (pt0)
REVERT: B  101 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.8651 (p90)
REVERT: B  164 LYS cc_start: 0.8563 (pttp) cc_final: 0.8118 (ptmm)
REVERT: B  198 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8385 (ttpt)
REVERT: B  237 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8105 (mttm)
REVERT: B  240 LYS cc_start: 0.7303 (ttpp) cc_final: 0.7072 (tttt)
REVERT: B  281 ARG cc_start: 0.8795 (ttm-80) cc_final: 0.8538 (ttm110)
REVERT: C   30 LYS cc_start: 0.8264 (tttp) cc_final: 0.7971 (tttm)
REVERT: C   87 GLN cc_start: 0.8696 (pt0) cc_final: 0.8472 (pt0)
REVERT: C  164 LYS cc_start: 0.8612 (pttp) cc_final: 0.8093 (ptmm)
REVERT: C  198 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8296 (ttpt)
REVERT: C  203 SER cc_start: 0.8848 (p) cc_final: 0.8601 (t)
REVERT: C  237 LYS cc_start: 0.8439 (mtmm) cc_final: 0.8099 (mttm)
REVERT: C  277 ARG cc_start: 0.8418 (mtp-110) cc_final: 0.8133 (mtp-110)
REVERT: C  281 ARG cc_start: 0.8835 (ttm-80) cc_final: 0.8286 (ttm170)
REVERT: C  288 LYS cc_start: 0.8734 (mttp) cc_final: 0.8428 (mmtm)
REVERT: D   34 MET cc_start: 0.9155 (mtt) cc_final: 0.8678 (mtt)
REVERT: D   87 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8603 (pt0)
REVERT: D  101 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.8721 (p90)
REVERT: D  164 LYS cc_start: 0.8597 (pttp) cc_final: 0.8246 (ptmm)
REVERT: D  198 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8260 (ttpt)
REVERT: D  237 LYS cc_start: 0.8435 (mtmm) cc_final: 0.8136 (mttm)
REVERT: D  281 ARG cc_start: 0.8829 (ttm-80) cc_final: 0.8572 (ttm110)
REVERT: D  288 LYS cc_start: 0.8570 (mttp) cc_final: 0.8183 (mmtm)
REVERT: E   87 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8596 (pt0)
REVERT: E  113 MET cc_start: 0.8767 (ttp) cc_final: 0.8509 (ttp)
REVERT: E  149 VAL cc_start: 0.9213 (OUTLIER) cc_final: 0.8856 (t)
REVERT: E  164 LYS cc_start: 0.8792 (pttp) cc_final: 0.8250 (ptmm)
REVERT: E  198 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8350 (ttpt)
REVERT: E  201 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.7846 (p0)
REVERT: E  237 LYS cc_start: 0.8439 (mtmm) cc_final: 0.8123 (mttm)
REVERT: E  277 ARG cc_start: 0.8650 (mtp-110) cc_final: 0.8279 (mtp-110)
REVERT: E  281 ARG cc_start: 0.8763 (ttm-80) cc_final: 0.8232 (ttm-80)
REVERT: F   49 ASN cc_start: 0.7903 (t0) cc_final: 0.7543 (t0)
REVERT: F   87 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8463 (pt0)
REVERT: F  101 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.8628 (p90)
REVERT: F  164 LYS cc_start: 0.8665 (pttp) cc_final: 0.8180 (ptmm)
REVERT: F  198 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8015 (ttpt)
REVERT: F  203 SER cc_start: 0.8962 (p) cc_final: 0.8691 (t)
REVERT: F  227 ASP cc_start: 0.8237 (p0) cc_final: 0.7897 (p0)
REVERT: F  237 LYS cc_start: 0.8360 (mtmm) cc_final: 0.7947 (mmtt)
REVERT: F  277 ARG cc_start: 0.8428 (mtp-110) cc_final: 0.8153 (mtp-110)
REVERT: F  281 ARG cc_start: 0.8866 (ttm-80) cc_final: 0.8597 (ttm110)
  outliers start: 74
  outliers final: 43
  residues processed: 372
  average time/residue: 0.1750
  time to fit residues: 90.3404
Evaluate side-chains
  371 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 310
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   38 VAL
Chi-restraints excluded: chain G residue   60 THR
Chi-restraints excluded: chain G residue   86 VAL
Chi-restraints excluded: chain G residue   87 GLN
Chi-restraints excluded: chain G residue  106 SER
Chi-restraints excluded: chain G residue  161 THR
Chi-restraints excluded: chain G residue  231 VAL
Chi-restraints excluded: chain G residue  257 GLN
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   36 LYS
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue   36 LYS
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue   87 GLN
Chi-restraints excluded: chain B residue  101 TYR
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain C residue    9 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   70 GLU
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  198 LYS
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   36 LYS
Chi-restraints excluded: chain D residue   75 LYS
Chi-restraints excluded: chain D residue   87 GLN
Chi-restraints excluded: chain D residue  101 TYR
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  198 LYS
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain E residue   14 ILE
Chi-restraints excluded: chain E residue   36 LYS
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   87 GLN
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  161 THR
Chi-restraints excluded: chain E residue  190 VAL
Chi-restraints excluded: chain E residue  198 LYS
Chi-restraints excluded: chain E residue  201 ASN
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain F residue   36 LYS
Chi-restraints excluded: chain F residue   60 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue   87 GLN
Chi-restraints excluded: chain F residue  101 TYR
Chi-restraints excluded: chain F residue  106 SER
Chi-restraints excluded: chain F residue  161 THR
Chi-restraints excluded: chain F residue  198 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 154 optimal weight:    2.9990
   chunk 175 optimal weight:    0.3980
   chunk 126 optimal weight:    1.9990
   chunk 183 optimal weight:    3.9990
   chunk 137 optimal weight:    0.1980
   chunk 31 optimal weight:    5.9990
   chunk 182 optimal weight:    0.4980
   chunk 12 optimal weight:    9.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
C 178 ASN
E 178 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.116636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.098842 restraints weight = 18988.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 1.75
r_work: 0.2974 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.3084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  16779  Z= 0.099
  Angle     :  0.489   8.597  22715  Z= 0.264
  Chirality :  0.045   0.135   2429
  Planarity :  0.003   0.028   2933
  Dihedral  :  4.223  56.729   2223
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.21 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.90 (0.18), residues: 2037
  helix: -4.28 (0.28), residues: 42
  sheet:  0.17 (0.15), residues: 1085
  loop : -1.34 (0.20), residues: 910

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 104 
 TYR   0.014   0.001   TYR B  68 
 PHE   0.010   0.001   PHE E 224 
 TRP   0.019   0.001   TRP D 260 
 HIS   0.007   0.001   HIS E 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (16779)
  covalent geometry    : angle       0.48893 (22715)
  hydrogen bonds       : bond        0.02728 (  558)
  hydrogen bonds       : angle       5.33151 ( 1518)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  397 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 344
  time to evaluate  : 0.607 
Fit side-chains
REVERT: G   29 ASP cc_start: 0.8294 (t0) cc_final: 0.7946 (t70)
REVERT: G  164 LYS cc_start: 0.8528 (pttp) cc_final: 0.7976 (ptmm)
REVERT: G  198 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8199 (ttpt)
REVERT: G  203 SER cc_start: 0.8886 (p) cc_final: 0.8623 (t)
REVERT: G  227 ASP cc_start: 0.8274 (p0) cc_final: 0.7972 (p0)
REVERT: G  237 LYS cc_start: 0.8291 (mtmm) cc_final: 0.8043 (mttm)
REVERT: G  240 LYS cc_start: 0.7472 (ttpp) cc_final: 0.7216 (tttp)
REVERT: G  281 ARG cc_start: 0.8813 (ttm-80) cc_final: 0.8517 (ttm110)
REVERT: G  288 LYS cc_start: 0.8563 (mttm) cc_final: 0.8166 (mmtm)
REVERT: A    5 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8068 (pt)
REVERT: A   87 GLN cc_start: 0.8693 (pt0) cc_final: 0.8440 (pt0)
REVERT: A  164 LYS cc_start: 0.8465 (pttp) cc_final: 0.8059 (ptmm)
REVERT: A  198 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8170 (ttpt)
REVERT: A  227 ASP cc_start: 0.8171 (p0) cc_final: 0.7879 (p0)
REVERT: A  231 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8457 (t)
REVERT: B   30 LYS cc_start: 0.8545 (tttp) cc_final: 0.8204 (ttmt)
REVERT: B   46 LYS cc_start: 0.8083 (mmtm) cc_final: 0.7401 (ptmm)
REVERT: B   87 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8380 (pt0)
REVERT: B  164 LYS cc_start: 0.8510 (pttp) cc_final: 0.8034 (ptmm)
REVERT: B  227 ASP cc_start: 0.8345 (p0) cc_final: 0.8083 (p0)
REVERT: B  237 LYS cc_start: 0.8449 (mtmm) cc_final: 0.8094 (mttm)
REVERT: B  240 LYS cc_start: 0.7206 (ttpp) cc_final: 0.6979 (tttt)
REVERT: B  281 ARG cc_start: 0.8728 (ttm-80) cc_final: 0.8466 (ttm110)
REVERT: B  288 LYS cc_start: 0.8535 (mttp) cc_final: 0.8249 (mmtm)
REVERT: C   30 LYS cc_start: 0.8242 (tttp) cc_final: 0.7925 (tttm)
REVERT: C  164 LYS cc_start: 0.8538 (pttp) cc_final: 0.7983 (ptmm)
REVERT: C  203 SER cc_start: 0.8802 (p) cc_final: 0.8567 (t)
REVERT: C  227 ASP cc_start: 0.8283 (p0) cc_final: 0.8072 (p0)
REVERT: C  237 LYS cc_start: 0.8433 (mtmm) cc_final: 0.8087 (mttm)
REVERT: C  277 ARG cc_start: 0.8416 (mtp-110) cc_final: 0.8144 (mtp-110)
REVERT: C  281 ARG cc_start: 0.8757 (ttm-80) cc_final: 0.8181 (ttm170)
REVERT: D   29 ASP cc_start: 0.8380 (t0) cc_final: 0.8041 (t70)
REVERT: D   87 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8564 (pt0)
REVERT: D  101 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8531 (p90)
REVERT: D  164 LYS cc_start: 0.8518 (pttp) cc_final: 0.8038 (ptmm)
REVERT: D  201 ASN cc_start: 0.8576 (p0) cc_final: 0.7979 (p0)
REVERT: D  237 LYS cc_start: 0.8397 (mtmm) cc_final: 0.8057 (mttm)
REVERT: D  281 ARG cc_start: 0.8781 (ttm-80) cc_final: 0.8526 (ttm110)
REVERT: D  288 LYS cc_start: 0.8491 (mttp) cc_final: 0.8102 (mmtm)
REVERT: E  113 MET cc_start: 0.8790 (ttp) cc_final: 0.8530 (ttp)
REVERT: E  149 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8812 (t)
REVERT: E  164 LYS cc_start: 0.8742 (pttp) cc_final: 0.8154 (ptmm)
REVERT: E  201 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.7739 (p0)
REVERT: E  237 LYS cc_start: 0.8416 (mtmm) cc_final: 0.8084 (mttm)
REVERT: E  277 ARG cc_start: 0.8612 (mtp-110) cc_final: 0.8263 (mtp-110)
REVERT: E  281 ARG cc_start: 0.8692 (ttm-80) cc_final: 0.8184 (ttm-80)
REVERT: F   34 MET cc_start: 0.9100 (mtt) cc_final: 0.8839 (mtt)
REVERT: F   87 GLN cc_start: 0.8702 (pt0) cc_final: 0.8437 (pt0)
REVERT: F  101 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.8507 (p90)
REVERT: F  164 LYS cc_start: 0.8586 (pttp) cc_final: 0.8070 (ptmm)
REVERT: F  203 SER cc_start: 0.8971 (p) cc_final: 0.8725 (t)
REVERT: F  227 ASP cc_start: 0.8242 (p0) cc_final: 0.7920 (p0)
REVERT: F  237 LYS cc_start: 0.8335 (mtmm) cc_final: 0.7884 (mmtt)
REVERT: F  277 ARG cc_start: 0.8413 (mtp-110) cc_final: 0.8163 (mtp-110)
REVERT: F  281 ARG cc_start: 0.8815 (ttm-80) cc_final: 0.8549 (ttm110)
  outliers start: 53
  outliers final: 27
  residues processed: 382
  average time/residue: 0.1662
  time to fit residues: 88.1892
Evaluate side-chains
  356 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 319
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue   86 VAL
Chi-restraints excluded: chain G residue   87 GLN
Chi-restraints excluded: chain G residue  198 LYS
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   36 LYS
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue   87 GLN
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain C residue    9 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   70 GLU
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   36 LYS
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   75 LYS
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   87 GLN
Chi-restraints excluded: chain D residue  101 TYR
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain E residue   36 LYS
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  201 ASN
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain F residue   36 LYS
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue  101 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 10 optimal weight:    0.4980
   chunk 151 optimal weight:    2.9990
   chunk 121 optimal weight:    4.9990
   chunk 114 optimal weight:    9.9990
   chunk 160 optimal weight:    3.9990
   chunk 142 optimal weight:    0.0770
   chunk 1 optimal weight:    7.9990
   chunk 29 optimal weight:    0.0270
   chunk 12 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0870
   overall best weight:    0.7376

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

Flipped N/Q/H residues before XYZ refinement:
G 178 ASN
A 178 ASN
E 178 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.117389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.099670 restraints weight = 19081.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 1.76
r_work: 0.3051 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.3170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  16779  Z= 0.095
  Angle     :  0.484   9.130  22715  Z= 0.261
  Chirality :  0.045   0.136   2429
  Planarity :  0.003   0.029   2933
  Dihedral  :  4.021  55.422   2221
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.48 %
    Favored  : 79.59 %
  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: -0.80 (0.18), residues: 2037
  helix: -4.26 (0.30), residues: 42
  sheet:  0.25 (0.15), residues: 1085
  loop : -1.29 (0.19), residues: 910

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 277 
 TYR   0.013   0.001   TYR B  68 
 PHE   0.009   0.001   PHE E 224 
 TRP   0.019   0.001   TRP G 260 
 HIS   0.004   0.001   HIS C 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (16779)
  covalent geometry    : angle       0.48411 (22715)
  hydrogen bonds       : bond        0.02586 (  558)
  hydrogen bonds       : angle       5.16120 ( 1518)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  382 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 329
  time to evaluate  : 0.683 
Fit side-chains
REVERT: G   29 ASP cc_start: 0.8244 (t0) cc_final: 0.7895 (t70)
REVERT: G  164 LYS cc_start: 0.8555 (pttp) cc_final: 0.8031 (ptmm)
REVERT: G  198 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8286 (ttpt)
REVERT: G  203 SER cc_start: 0.8867 (p) cc_final: 0.8614 (t)
REVERT: G  237 LYS cc_start: 0.8307 (mtmm) cc_final: 0.8077 (mttm)
REVERT: G  240 LYS cc_start: 0.7517 (ttpp) cc_final: 0.7282 (tttp)
REVERT: G  281 ARG cc_start: 0.8822 (ttm-80) cc_final: 0.8530 (ttm110)
REVERT: G  288 LYS cc_start: 0.8592 (mttm) cc_final: 0.8076 (mtpt)
REVERT: A    5 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8062 (pt)
REVERT: A   29 ASP cc_start: 0.8149 (t0) cc_final: 0.7808 (t70)
REVERT: A   87 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8431 (pt0)
REVERT: A  164 LYS cc_start: 0.8499 (pttp) cc_final: 0.8133 (ptmm)
REVERT: A  203 SER cc_start: 0.8981 (p) cc_final: 0.8701 (t)
REVERT: A  227 ASP cc_start: 0.8154 (p0) cc_final: 0.7871 (p0)
REVERT: A  231 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8481 (t)
REVERT: A  277 ARG cc_start: 0.8459 (mtp-110) cc_final: 0.8233 (mtp85)
REVERT: B   30 LYS cc_start: 0.8516 (tttp) cc_final: 0.8207 (ttmt)
REVERT: B   46 LYS cc_start: 0.8134 (mmtm) cc_final: 0.7449 (ptmm)
REVERT: B   87 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8407 (pt0)
REVERT: B  164 LYS cc_start: 0.8525 (pttp) cc_final: 0.8090 (ptmm)
REVERT: B  203 SER cc_start: 0.8868 (p) cc_final: 0.8648 (t)
REVERT: B  231 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8522 (t)
REVERT: B  237 LYS cc_start: 0.8453 (mtmm) cc_final: 0.8113 (mttm)
REVERT: B  240 LYS cc_start: 0.7229 (ttpp) cc_final: 0.7013 (tttt)
REVERT: B  281 ARG cc_start: 0.8720 (ttm-80) cc_final: 0.8450 (ttm110)
REVERT: B  288 LYS cc_start: 0.8583 (mttp) cc_final: 0.8308 (mmtm)
REVERT: C   29 ASP cc_start: 0.8376 (t0) cc_final: 0.8032 (t70)
REVERT: C   30 LYS cc_start: 0.8255 (tttp) cc_final: 0.7932 (tttm)
REVERT: C  106 SER cc_start: 0.9264 (OUTLIER) cc_final: 0.9013 (m)
REVERT: C  164 LYS cc_start: 0.8569 (pttp) cc_final: 0.8023 (ptmm)
REVERT: C  203 SER cc_start: 0.8787 (p) cc_final: 0.8565 (t)
REVERT: C  227 ASP cc_start: 0.8276 (p0) cc_final: 0.8057 (p0)
REVERT: C  237 LYS cc_start: 0.8425 (mtmm) cc_final: 0.7985 (mmtt)
REVERT: C  277 ARG cc_start: 0.8451 (mtp-110) cc_final: 0.8186 (mtp-110)
REVERT: C  281 ARG cc_start: 0.8772 (ttm-80) cc_final: 0.8208 (ttm170)
REVERT: D   29 ASP cc_start: 0.8363 (t0) cc_final: 0.8027 (t70)
REVERT: D  164 LYS cc_start: 0.8546 (pttp) cc_final: 0.8075 (ptmm)
REVERT: D  198 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8350 (ttpt)
REVERT: D  201 ASN cc_start: 0.8570 (p0) cc_final: 0.7980 (p0)
REVERT: D  237 LYS cc_start: 0.8362 (mtmm) cc_final: 0.8059 (mttm)
REVERT: D  281 ARG cc_start: 0.8782 (ttm-80) cc_final: 0.8523 (ttm110)
REVERT: D  288 LYS cc_start: 0.8521 (mttp) cc_final: 0.8159 (mmtm)
REVERT: E  113 MET cc_start: 0.8793 (ttp) cc_final: 0.8547 (ttp)
REVERT: E  149 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8804 (t)
REVERT: E  164 LYS cc_start: 0.8738 (pttp) cc_final: 0.8197 (ptmm)
REVERT: E  201 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.7779 (p0)
REVERT: E  237 LYS cc_start: 0.8406 (mtmm) cc_final: 0.8105 (mttm)
REVERT: E  277 ARG cc_start: 0.8594 (mtp-110) cc_final: 0.8262 (mtp-110)
REVERT: E  281 ARG cc_start: 0.8703 (ttm-80) cc_final: 0.8106 (ttm-80)
REVERT: E  293 ASN cc_start: 0.7503 (t0) cc_final: 0.7273 (t0)
REVERT: F   87 GLN cc_start: 0.8718 (pt0) cc_final: 0.8494 (pt0)
REVERT: F  101 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.8447 (p90)
REVERT: F  164 LYS cc_start: 0.8599 (pttp) cc_final: 0.8121 (ptmm)
REVERT: F  198 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8054 (ttpt)
REVERT: F  227 ASP cc_start: 0.8217 (p0) cc_final: 0.7892 (p0)
REVERT: F  237 LYS cc_start: 0.8332 (mtmm) cc_final: 0.7918 (mmtt)
REVERT: F  281 ARG cc_start: 0.8822 (ttm-80) cc_final: 0.8563 (ttm110)
  outliers start: 53
  outliers final: 29
  residues processed: 367
  average time/residue: 0.1627
  time to fit residues: 83.2012
Evaluate side-chains
  359 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 318
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   60 THR
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue   86 VAL
Chi-restraints excluded: chain G residue   87 GLN
Chi-restraints excluded: chain G residue  198 LYS
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   36 LYS
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue   87 GLN
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue   87 GLN
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain C residue    9 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   70 GLU
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   36 LYS
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   75 LYS
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  198 LYS
Chi-restraints excluded: chain E residue   14 ILE
Chi-restraints excluded: chain E residue   36 LYS
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   87 GLN
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  201 ASN
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain F residue   36 LYS
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue  101 TYR
Chi-restraints excluded: chain F residue  198 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 136 optimal weight:    8.9990
   chunk 75 optimal weight:    6.9990
   chunk 77 optimal weight:    0.3980
   chunk 97 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 199 optimal weight:    4.9990
   chunk 165 optimal weight:    9.9990
   chunk 45 optimal weight:    1.9990
   chunk 190 optimal weight:    4.9990
   chunk 134 optimal weight:    0.0050
   overall best weight:    1.2800

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

Flipped N/Q/H residues before XYZ refinement:
G 178 ASN
B 178 ASN
F 178 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.115948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.098180 restraints weight = 19069.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 1.76
r_work: 0.2983 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  16779  Z= 0.127
  Angle     :  0.517   9.492  22715  Z= 0.277
  Chirality :  0.046   0.149   2429
  Planarity :  0.003   0.029   2933
  Dihedral  :  4.158  55.406   2221
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.60 %
    Favored  : 79.98 %
  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: -0.82 (0.18), residues: 2037
  helix: -4.28 (0.28), residues: 42
  sheet:  0.24 (0.15), residues: 1085
  loop : -1.31 (0.19), residues: 910

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 104 
 TYR   0.012   0.001   TYR B 101 
 PHE   0.010   0.001   PHE E 224 
 TRP   0.018   0.001   TRP G 260 
 HIS   0.004   0.001   HIS C 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (16779)
  covalent geometry    : angle       0.51686 (22715)
  hydrogen bonds       : bond        0.02847 (  558)
  hydrogen bonds       : angle       5.26156 ( 1518)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 317
  time to evaluate  : 0.664 
Fit side-chains
REVERT: G   29 ASP cc_start: 0.8340 (t0) cc_final: 0.7989 (t70)
REVERT: G  164 LYS cc_start: 0.8528 (pttp) cc_final: 0.7979 (ptmm)
REVERT: G  198 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8199 (ttpt)
REVERT: G  203 SER cc_start: 0.8908 (p) cc_final: 0.8666 (t)
REVERT: G  237 LYS cc_start: 0.8290 (mtmm) cc_final: 0.8049 (mttm)
REVERT: G  240 LYS cc_start: 0.7424 (ttpp) cc_final: 0.7191 (tttp)
REVERT: G  281 ARG cc_start: 0.8813 (ttm-80) cc_final: 0.8504 (ttm110)
REVERT: G  288 LYS cc_start: 0.8556 (mttm) cc_final: 0.8026 (mtpt)
REVERT: A    5 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.7974 (pt)
REVERT: A   87 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8396 (pt0)
REVERT: A  164 LYS cc_start: 0.8485 (pttp) cc_final: 0.8091 (ptmm)
REVERT: A  203 SER cc_start: 0.9002 (p) cc_final: 0.8730 (t)
REVERT: A  227 ASP cc_start: 0.8180 (p0) cc_final: 0.7888 (p0)
REVERT: B   30 LYS cc_start: 0.8560 (tttp) cc_final: 0.8234 (ttmt)
REVERT: B   36 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8376 (mtmm)
REVERT: B   46 LYS cc_start: 0.8116 (mmtm) cc_final: 0.7422 (ptmm)
REVERT: B   87 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8398 (pt0)
REVERT: B  164 LYS cc_start: 0.8527 (pttp) cc_final: 0.8063 (ptmm)
REVERT: B  203 SER cc_start: 0.8918 (p) cc_final: 0.8713 (t)
REVERT: B  231 VAL cc_start: 0.8772 (OUTLIER) cc_final: 0.8523 (t)
REVERT: B  237 LYS cc_start: 0.8467 (mtmm) cc_final: 0.8113 (mttm)
REVERT: B  240 LYS cc_start: 0.7187 (ttpp) cc_final: 0.6940 (tttt)
REVERT: B  281 ARG cc_start: 0.8724 (ttm-80) cc_final: 0.8434 (ttm110)
REVERT: B  288 LYS cc_start: 0.8555 (mttp) cc_final: 0.8272 (mmtm)
REVERT: C   30 LYS cc_start: 0.8255 (tttp) cc_final: 0.7942 (tttm)
REVERT: C  106 SER cc_start: 0.9231 (OUTLIER) cc_final: 0.9015 (m)
REVERT: C  164 LYS cc_start: 0.8549 (pttp) cc_final: 0.7978 (ptmm)
REVERT: C  203 SER cc_start: 0.8823 (p) cc_final: 0.8605 (t)
REVERT: C  227 ASP cc_start: 0.8291 (p0) cc_final: 0.8082 (p0)
REVERT: C  237 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8084 (mttm)
REVERT: C  277 ARG cc_start: 0.8456 (mtp-110) cc_final: 0.8193 (mtp-110)
REVERT: C  281 ARG cc_start: 0.8797 (ttm-80) cc_final: 0.8221 (ttm170)
REVERT: C  288 LYS cc_start: 0.8706 (mttp) cc_final: 0.8402 (mmtm)
REVERT: D  164 LYS cc_start: 0.8519 (pttp) cc_final: 0.8047 (ptmm)
REVERT: D  198 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8305 (ttpt)
REVERT: D  201 ASN cc_start: 0.8559 (p0) cc_final: 0.7953 (p0)
REVERT: D  203 SER cc_start: 0.8866 (p) cc_final: 0.8636 (t)
REVERT: D  237 LYS cc_start: 0.8368 (mtmm) cc_final: 0.8061 (mttm)
REVERT: D  281 ARG cc_start: 0.8796 (ttm-80) cc_final: 0.8501 (ttm110)
REVERT: D  288 LYS cc_start: 0.8473 (mttp) cc_final: 0.8103 (mmtm)
REVERT: E  113 MET cc_start: 0.8778 (ttp) cc_final: 0.8513 (ttp)
REVERT: E  149 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8838 (t)
REVERT: E  164 LYS cc_start: 0.8727 (pttp) cc_final: 0.8146 (ptmm)
REVERT: E  201 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.7759 (p0)
REVERT: E  237 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8094 (mttm)
REVERT: E  277 ARG cc_start: 0.8637 (mtp-110) cc_final: 0.8435 (mtp-110)
REVERT: E  281 ARG cc_start: 0.8712 (ttm-80) cc_final: 0.8170 (ttm-80)
REVERT: E  288 LYS cc_start: 0.8566 (mttm) cc_final: 0.8342 (mmtm)
REVERT: F   87 GLN cc_start: 0.8692 (pt0) cc_final: 0.8448 (pt0)
REVERT: F  101 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8414 (p90)
REVERT: F  164 LYS cc_start: 0.8587 (pttp) cc_final: 0.8081 (ptmm)
REVERT: F  198 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8004 (ttpt)
REVERT: F  227 ASP cc_start: 0.8222 (p0) cc_final: 0.7896 (p0)
REVERT: F  237 LYS cc_start: 0.8316 (mtmm) cc_final: 0.7895 (mmtt)
REVERT: F  281 ARG cc_start: 0.8821 (ttm-80) cc_final: 0.8520 (ttm110)
  outliers start: 44
  outliers final: 30
  residues processed: 352
  average time/residue: 0.1769
  time to fit residues: 86.2266
Evaluate side-chains
  358 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 316
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue   86 VAL
Chi-restraints excluded: chain G residue   87 GLN
Chi-restraints excluded: chain G residue  198 LYS
Chi-restraints excluded: chain G residue  257 GLN
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   36 LYS
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue   87 GLN
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue   36 LYS
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue   87 GLN
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain C residue    9 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   70 GLU
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   36 LYS
Chi-restraints excluded: chain D residue   75 LYS
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   87 GLN
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  198 LYS
Chi-restraints excluded: chain E residue   14 ILE
Chi-restraints excluded: chain E residue   36 LYS
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   87 GLN
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  201 ASN
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain F residue   36 LYS
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue  101 TYR
Chi-restraints excluded: chain F residue  198 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 105 optimal weight:    7.9990
   chunk 155 optimal weight:    1.9990
   chunk 167 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 126 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 71 optimal weight:    5.9990
   chunk 172 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 119 optimal weight:    6.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
G 178 ASN
A 178 ASN
B 178 ASN
E 178 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.116844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.099009 restraints weight = 18942.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 1.75
r_work: 0.3012 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.3249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  16779  Z= 0.116
  Angle     :  0.507   9.285  22715  Z= 0.273
  Chirality :  0.045   0.137   2429
  Planarity :  0.003   0.029   2933
  Dihedral  :  4.114  55.272   2221
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.76 %
    Favored  : 79.70 %
  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: -0.78 (0.18), residues: 2037
  helix: -4.27 (0.29), residues: 42
  sheet:  0.28 (0.15), residues: 1085
  loop : -1.30 (0.19), residues: 910

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 104 
 TYR   0.012   0.001   TYR D  65 
 PHE   0.010   0.001   PHE E 224 
 TRP   0.019   0.001   TRP G 260 
 HIS   0.004   0.001   HIS C 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (16779)
  covalent geometry    : angle       0.50713 (22715)
  hydrogen bonds       : bond        0.02772 (  558)
  hydrogen bonds       : angle       5.23627 ( 1518)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  366 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 320
  time to evaluate  : 0.615 
Fit side-chains
REVERT: G   29 ASP cc_start: 0.8335 (t0) cc_final: 0.7990 (t70)
REVERT: G  164 LYS cc_start: 0.8497 (pttp) cc_final: 0.7988 (ptmm)
REVERT: G  198 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8235 (ttpt)
REVERT: G  203 SER cc_start: 0.8886 (p) cc_final: 0.8645 (t)
REVERT: G  237 LYS cc_start: 0.8265 (mtmm) cc_final: 0.8046 (mttm)
REVERT: G  240 LYS cc_start: 0.7474 (ttpp) cc_final: 0.7255 (tttp)
REVERT: G  281 ARG cc_start: 0.8817 (ttm-80) cc_final: 0.8524 (ttm110)
REVERT: G  288 LYS cc_start: 0.8602 (mttm) cc_final: 0.8242 (mmtm)
REVERT: A    5 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.7956 (pt)
REVERT: A   87 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8425 (pt0)
REVERT: A  164 LYS cc_start: 0.8501 (pttp) cc_final: 0.8156 (ptmm)
REVERT: A  203 SER cc_start: 0.8993 (p) cc_final: 0.8724 (t)
REVERT: A  227 ASP cc_start: 0.8187 (p0) cc_final: 0.7897 (p0)
REVERT: B   30 LYS cc_start: 0.8544 (tttp) cc_final: 0.8239 (ttmt)
REVERT: B   36 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8447 (mtmm)
REVERT: B   46 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7491 (ptmm)
REVERT: B   87 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8420 (pt0)
REVERT: B  101 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.8375 (p90)
REVERT: B  164 LYS cc_start: 0.8537 (pttp) cc_final: 0.8113 (ptmm)
REVERT: B  231 VAL cc_start: 0.8772 (OUTLIER) cc_final: 0.8554 (t)
REVERT: B  237 LYS cc_start: 0.8457 (mtmm) cc_final: 0.8120 (mttm)
REVERT: B  240 LYS cc_start: 0.7254 (ttpp) cc_final: 0.7010 (tttt)
REVERT: B  281 ARG cc_start: 0.8723 (ttm-80) cc_final: 0.8444 (ttm110)
REVERT: B  288 LYS cc_start: 0.8607 (mttp) cc_final: 0.8332 (mmtm)
REVERT: C   29 ASP cc_start: 0.8412 (t0) cc_final: 0.8065 (t70)
REVERT: C   30 LYS cc_start: 0.8327 (tttp) cc_final: 0.8028 (tttm)
REVERT: C  106 SER cc_start: 0.9279 (OUTLIER) cc_final: 0.9035 (m)
REVERT: C  164 LYS cc_start: 0.8568 (pttp) cc_final: 0.8033 (ptmm)
REVERT: C  203 SER cc_start: 0.8814 (p) cc_final: 0.8599 (t)
REVERT: C  227 ASP cc_start: 0.8289 (p0) cc_final: 0.8077 (p0)
REVERT: C  237 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8007 (mmtt)
REVERT: C  277 ARG cc_start: 0.8481 (mtp-110) cc_final: 0.8216 (mtp-110)
REVERT: C  281 ARG cc_start: 0.8790 (ttm-80) cc_final: 0.8229 (ttm170)
REVERT: D  164 LYS cc_start: 0.8541 (pttp) cc_final: 0.8116 (ptmm)
REVERT: D  198 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8353 (ttpt)
REVERT: D  201 ASN cc_start: 0.8590 (p0) cc_final: 0.8001 (p0)
REVERT: D  203 SER cc_start: 0.8865 (p) cc_final: 0.8644 (t)
REVERT: D  237 LYS cc_start: 0.8371 (mtmm) cc_final: 0.7974 (mmtt)
REVERT: D  281 ARG cc_start: 0.8791 (ttm-80) cc_final: 0.8517 (ttm110)
REVERT: D  288 LYS cc_start: 0.8531 (mttp) cc_final: 0.8170 (mmtm)
REVERT: E  113 MET cc_start: 0.8789 (ttp) cc_final: 0.8541 (ttp)
REVERT: E  149 VAL cc_start: 0.9172 (OUTLIER) cc_final: 0.8840 (t)
REVERT: E  164 LYS cc_start: 0.8741 (pttp) cc_final: 0.8214 (ptmm)
REVERT: E  201 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.7807 (p0)
REVERT: E  237 LYS cc_start: 0.8413 (mtmm) cc_final: 0.8116 (mttm)
REVERT: E  281 ARG cc_start: 0.8727 (ttm-80) cc_final: 0.8198 (ttm-80)
REVERT: E  288 LYS cc_start: 0.8631 (mttm) cc_final: 0.8416 (mmtm)
REVERT: F   87 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8496 (pt0)
REVERT: F  101 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.8421 (p90)
REVERT: F  164 LYS cc_start: 0.8599 (pttp) cc_final: 0.8142 (ptmm)
REVERT: F  198 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8061 (ttpt)
REVERT: F  227 ASP cc_start: 0.8186 (p0) cc_final: 0.7888 (p0)
REVERT: F  237 LYS cc_start: 0.8325 (mtmm) cc_final: 0.7922 (mmtt)
REVERT: F  277 ARG cc_start: 0.8386 (mtp-110) cc_final: 0.8136 (mtp-110)
REVERT: F  281 ARG cc_start: 0.8835 (ttm-80) cc_final: 0.8549 (ttm110)
  outliers start: 46
  outliers final: 31
  residues processed: 355
  average time/residue: 0.1734
  time to fit residues: 85.3336
Evaluate side-chains
  362 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 317
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue   86 VAL
Chi-restraints excluded: chain G residue   87 GLN
Chi-restraints excluded: chain G residue  198 LYS
Chi-restraints excluded: chain G residue  257 GLN
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   36 LYS
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue   87 GLN
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue   36 LYS
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue   87 GLN
Chi-restraints excluded: chain B residue  101 TYR
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain C residue    9 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   70 GLU
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue   87 GLN
Chi-restraints excluded: chain C residue  101 TYR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain D residue   36 LYS
Chi-restraints excluded: chain D residue   75 LYS
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   87 GLN
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  198 LYS
Chi-restraints excluded: chain E residue   14 ILE
Chi-restraints excluded: chain E residue   36 LYS
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   87 GLN
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  201 ASN
Chi-restraints excluded: chain E residue  231 VAL
Chi-restraints excluded: chain F residue   36 LYS
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue   87 GLN
Chi-restraints excluded: chain F residue  101 TYR
Chi-restraints excluded: chain F residue  198 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 124 optimal weight:    0.7980
   chunk 119 optimal weight:    6.9990
   chunk 187 optimal weight:    6.9990
   chunk 157 optimal weight:    0.7980
   chunk 113 optimal weight:    0.7980
   chunk 155 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 95 optimal weight:    0.0570
   chunk 22 optimal weight:    0.6980
   chunk 141 optimal weight:    1.9990
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
G 178 ASN
B 178 ASN
E 178 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.120434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.103310 restraints weight = 18906.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 1.68
r_work: 0.3100 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.3321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  16779  Z= 0.091
  Angle     :  0.482   8.580  22715  Z= 0.262
  Chirality :  0.045   0.168   2429
  Planarity :  0.003   0.029   2933
  Dihedral  :  3.907  53.834   2221
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 17.93 %
    Favored  : 79.76 %
  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: -0.67 (0.18), residues: 2037
  helix: -4.24 (0.30), residues: 42
  sheet:  0.36 (0.15), residues: 1085
  loop : -1.22 (0.19), residues: 910

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 104 
 TYR   0.012   0.001   TYR B 101 
 PHE   0.010   0.001   PHE E 224 
 TRP   0.020   0.001   TRP G 260 
 HIS   0.004   0.001   HIS C 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 (16779)
  covalent geometry    : angle       0.48166 (22715)
  hydrogen bonds       : bond        0.02505 (  558)
  hydrogen bonds       : angle       5.05150 ( 1518)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3820.99 seconds
wall clock time: 66 minutes 35.42 seconds (3995.42 seconds total)