Starting phenix.real_space_refine
on Wed Mar  4 06:01:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zgk_11209/03_2026/6zgk_11209.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zgk_11209/03_2026/6zgk_11209.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zgk_11209/03_2026/6zgk_11209.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zgk_11209/03_2026/6zgk_11209.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zgk_11209/03_2026/6zgk_11209.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zgk_11209/03_2026/6zgk_11209.map"
  }
  resolution = 3.6
  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=   0.007
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      20      5.16       5
     C    7710      2.51       5
     N    1875      2.21       5
     O    2025      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11630
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2326
          Classifications: {'peptide': 307}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 288}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 170
          Unresolved non-hydrogen angles: 218
          Unresolved non-hydrogen dihedrals: 136
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 9, 'ASN:plan1': 4, 'TRP:plan': 1, 'ARG:plan': 4, 'PHE:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 127
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 1.77, per 1000 atoms: 0.15
  Number of scatterers: 11630
  At special positions: 0
  Unit cell: (92.66, 91.02, 115.62, 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      20     16.00
     O    2025      8.00
     N    1875      7.00
     C    7710      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.98
  Conformation dependent library (CDL) restraints added in 588.6 milliseconds
  

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3010

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 10 sheets defined
      34.2% alpha, 25.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 196 through 201
    Processing helix  chain 'A' and resid 201 through 214
      removed outlier: 3.744A  pdb=" N   MET A 205 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU A 209 " --> pdb=" O   MET A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 243
      removed outlier: 4.027A  pdb=" N   THR A 226 " --> pdb=" O   GLU A 222 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   THR A 231 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 282
      removed outlier: 3.674A  pdb=" N   PHE A 260 " --> pdb=" O   GLY A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 315
      removed outlier: 3.984A  pdb=" N   ILE A 297 " --> pdb=" O   ARG A 293 " (cutoff:3.500A)
      Proline residue:  A 300  - end of helix
    Processing helix  chain 'B' and resid 196 through 201
    Processing helix  chain 'B' and resid 201 through 214
      removed outlier: 3.744A  pdb=" N   MET B 205 " --> pdb=" O   ILE B 201 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU B 209 " --> pdb=" O   MET B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 243
      removed outlier: 4.027A  pdb=" N   THR B 226 " --> pdb=" O   GLU B 222 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   THR B 231 " --> pdb=" O   LEU B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 282
      removed outlier: 3.673A  pdb=" N   PHE B 260 " --> pdb=" O   GLY B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 315
      removed outlier: 3.985A  pdb=" N   ILE B 297 " --> pdb=" O   ARG B 293 " (cutoff:3.500A)
      Proline residue:  B 300  - end of helix
    Processing helix  chain 'C' and resid 196 through 201
    Processing helix  chain 'C' and resid 201 through 214
      removed outlier: 3.744A  pdb=" N   MET C 205 " --> pdb=" O   ILE C 201 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU C 209 " --> pdb=" O   MET C 205 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 243
      removed outlier: 4.027A  pdb=" N   THR C 226 " --> pdb=" O   GLU C 222 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   THR C 231 " --> pdb=" O   LEU C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 254 through 282
      removed outlier: 3.673A  pdb=" N   PHE C 260 " --> pdb=" O   GLY C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 284 through 315
      removed outlier: 3.985A  pdb=" N   ILE C 297 " --> pdb=" O   ARG C 293 " (cutoff:3.500A)
      Proline residue:  C 300  - end of helix
    Processing helix  chain 'D' and resid 196 through 201
    Processing helix  chain 'D' and resid 201 through 214
      removed outlier: 3.744A  pdb=" N   MET D 205 " --> pdb=" O   ILE D 201 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU D 209 " --> pdb=" O   MET D 205 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 220 through 243
      removed outlier: 4.028A  pdb=" N   THR D 226 " --> pdb=" O   GLU D 222 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   THR D 231 " --> pdb=" O   LEU D 227 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 254 through 282
      removed outlier: 3.673A  pdb=" N   PHE D 260 " --> pdb=" O   GLY D 256 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 284 through 315
      removed outlier: 3.985A  pdb=" N   ILE D 297 " --> pdb=" O   ARG D 293 " (cutoff:3.500A)
      Proline residue:  D 300  - end of helix
    Processing helix  chain 'E' and resid 196 through 201
    Processing helix  chain 'E' and resid 201 through 214
      removed outlier: 3.743A  pdb=" N   MET E 205 " --> pdb=" O   ILE E 201 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU E 209 " --> pdb=" O   MET E 205 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 220 through 243
      removed outlier: 4.028A  pdb=" N   THR E 226 " --> pdb=" O   GLU E 222 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   THR E 231 " --> pdb=" O   LEU E 227 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 254 through 282
      removed outlier: 3.673A  pdb=" N   PHE E 260 " --> pdb=" O   GLY E 256 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 284 through 315
      removed outlier: 3.984A  pdb=" N   ILE E 297 " --> pdb=" O   ARG E 293 " (cutoff:3.500A)
      Proline residue:  E 300  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 95
      removed outlier: 4.900A  pdb=" N   ALA A  87 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   SER A 107 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   VAL A  89 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   ARG A 105 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   THR A  36 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   LEU A  30 " --> pdb=" O   THR A  36 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   LYS A  38 " --> pdb=" O   TYR A  28 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   PHE A  42 " --> pdb=" O   LEU A  24 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   LEU A  24 " --> pdb=" O   PHE A  42 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   SER A  44 " --> pdb=" O   ILE A  22 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   ILE A  22 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   SER A  46 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   THR A  20 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
      removed outlier: 8.305A  pdb=" N   LYS A  48 " --> pdb=" O   VAL A  18 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   VAL A  18 " --> pdb=" O   LYS A  48 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   LEU A  16 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   ALA A 143 " --> pdb=" O   LEU A  16 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   VAL A  18 " --> pdb=" O   ALA A 143 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.685A  pdb=" N   ASP A 185 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ALA A 167 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLN A 187 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   PHE A 165 " --> pdb=" O   GLN A 187 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ARG A 189 " --> pdb=" O   GLU A 163 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 86 through 95
      removed outlier: 4.900A  pdb=" N   ALA B  87 " --> pdb=" O   SER B 107 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   SER B 107 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   VAL B  89 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   ARG B 105 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   THR B  36 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   LEU B  30 " --> pdb=" O   THR B  36 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   LYS B  38 " --> pdb=" O   TYR B  28 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   PHE B  42 " --> pdb=" O   LEU B  24 " (cutoff:3.500A)
      removed outlier: 5.705A  pdb=" N   LEU B  24 " --> pdb=" O   PHE B  42 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   SER B  44 " --> pdb=" O   ILE B  22 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   ILE B  22 " --> pdb=" O   SER B  44 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   SER B  46 " --> pdb=" O   THR B  20 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   THR B  20 " --> pdb=" O   SER B  46 " (cutoff:3.500A)
      removed outlier: 8.306A  pdb=" N   LYS B  48 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   VAL B  18 " --> pdb=" O   LYS B  48 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   LEU B  16 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   ALA B 143 " --> pdb=" O   LEU B  16 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   VAL B  18 " --> pdb=" O   ALA B 143 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.686A  pdb=" N   ASP B 185 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ALA B 167 " --> pdb=" O   ASP B 185 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   GLN B 187 " --> pdb=" O   PHE B 165 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   PHE B 165 " --> pdb=" O   GLN B 187 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ARG B 189 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 86 through 95
      removed outlier: 4.899A  pdb=" N   ALA C  87 " --> pdb=" O   SER C 107 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   SER C 107 " --> pdb=" O   ALA C  87 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   VAL C  89 " --> pdb=" O   ARG C 105 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   ARG C 105 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   THR C  36 " --> pdb=" O   LEU C  30 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   LEU C  30 " --> pdb=" O   THR C  36 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   LYS C  38 " --> pdb=" O   TYR C  28 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   PHE C  42 " --> pdb=" O   LEU C  24 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   LEU C  24 " --> pdb=" O   PHE C  42 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   SER C  44 " --> pdb=" O   ILE C  22 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   ILE C  22 " --> pdb=" O   SER C  44 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   SER C  46 " --> pdb=" O   THR C  20 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   THR C  20 " --> pdb=" O   SER C  46 " (cutoff:3.500A)
      removed outlier: 8.306A  pdb=" N   LYS C  48 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   VAL C  18 " --> pdb=" O   LYS C  48 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   LEU C  16 " --> pdb=" O   VAL C 141 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   ALA C 143 " --> pdb=" O   LEU C  16 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   VAL C  18 " --> pdb=" O   ALA C 143 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.685A  pdb=" N   ASP C 185 " --> pdb=" O   ALA C 167 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ALA C 167 " --> pdb=" O   ASP C 185 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   GLN C 187 " --> pdb=" O   PHE C 165 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   PHE C 165 " --> pdb=" O   GLN C 187 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   ARG C 189 " --> pdb=" O   GLU C 163 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 86 through 95
      removed outlier: 4.899A  pdb=" N   ALA D  87 " --> pdb=" O   SER D 107 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   SER D 107 " --> pdb=" O   ALA D  87 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   VAL D  89 " --> pdb=" O   ARG D 105 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   ARG D 105 " --> pdb=" O   VAL D  89 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   THR D  36 " --> pdb=" O   LEU D  30 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   LEU D  30 " --> pdb=" O   THR D  36 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   LYS D  38 " --> pdb=" O   TYR D  28 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   PHE D  42 " --> pdb=" O   LEU D  24 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   LEU D  24 " --> pdb=" O   PHE D  42 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   SER D  44 " --> pdb=" O   ILE D  22 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   ILE D  22 " --> pdb=" O   SER D  44 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   SER D  46 " --> pdb=" O   THR D  20 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   THR D  20 " --> pdb=" O   SER D  46 " (cutoff:3.500A)
      removed outlier: 8.305A  pdb=" N   LYS D  48 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   VAL D  18 " --> pdb=" O   LYS D  48 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   LEU D  16 " --> pdb=" O   VAL D 141 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   ALA D 143 " --> pdb=" O   LEU D  16 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   VAL D  18 " --> pdb=" O   ALA D 143 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.684A  pdb=" N   ASP D 185 " --> pdb=" O   ALA D 167 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ALA D 167 " --> pdb=" O   ASP D 185 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLN D 187 " --> pdb=" O   PHE D 165 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   PHE D 165 " --> pdb=" O   GLN D 187 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ARG D 189 " --> pdb=" O   GLU D 163 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 86 through 95
      removed outlier: 4.899A  pdb=" N   ALA E  87 " --> pdb=" O   SER E 107 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   SER E 107 " --> pdb=" O   ALA E  87 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   VAL E  89 " --> pdb=" O   ARG E 105 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   ARG E 105 " --> pdb=" O   VAL E  89 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   THR E  36 " --> pdb=" O   LEU E  30 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   LEU E  30 " --> pdb=" O   THR E  36 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   LYS E  38 " --> pdb=" O   TYR E  28 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   PHE E  42 " --> pdb=" O   LEU E  24 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   LEU E  24 " --> pdb=" O   PHE E  42 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   SER E  44 " --> pdb=" O   ILE E  22 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   ILE E  22 " --> pdb=" O   SER E  44 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   SER E  46 " --> pdb=" O   THR E  20 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   THR E  20 " --> pdb=" O   SER E  46 " (cutoff:3.500A)
      removed outlier: 8.305A  pdb=" N   LYS E  48 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   VAL E  18 " --> pdb=" O   LYS E  48 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   LEU E  16 " --> pdb=" O   VAL E 141 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   ALA E 143 " --> pdb=" O   LEU E  16 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   VAL E  18 " --> pdb=" O   ALA E 143 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.685A  pdb=" N   ASP E 185 " --> pdb=" O   ALA E 167 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ALA E 167 " --> pdb=" O   ASP E 185 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLN E 187 " --> pdb=" O   PHE E 165 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   PHE E 165 " --> pdb=" O   GLN E 187 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ARG E 189 " --> pdb=" O   GLU E 163 " (cutoff:3.500A)

    550 hydrogen bonds defined for protein.
    1620 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.59

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3570
        1.34 -     1.46: 2515
        1.46 -     1.58: 5820
        1.58 -     1.69: 0
        1.69 -     1.81: 35
  Bond restraints: 11940
  Sorted by residual:
  bond pdb=" N   THR B 158 "
       pdb=" CA  THR B 158 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.27e-02 6.20e+03 6.02e+00
  bond pdb=" N   THR D 158 "
       pdb=" CA  THR D 158 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.27e-02 6.20e+03 5.83e+00
  bond pdb=" N   THR A 158 "
       pdb=" CA  THR A 158 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.27e-02 6.20e+03 5.81e+00
  bond pdb=" N   THR E 158 "
       pdb=" CA  THR E 158 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.27e-02 6.20e+03 5.70e+00
  bond pdb=" N   TRP A 160 "
       pdb=" CA  TRP A 160 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.29e-02 6.01e+03 5.66e+00
  ... (remaining 11935 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.10: 15238
        1.10 -     2.19: 862
        2.19 -     3.29: 184
        3.29 -     4.39: 76
        4.39 -     5.48: 35
  Bond angle restraints: 16395
  Sorted by residual:
  angle pdb=" CA  LEU E 157 "
        pdb=" C   LEU E 157 "
        pdb=" O   LEU E 157 "
      ideal   model   delta    sigma   weight residual
     122.44  118.20    4.24 1.32e+00 5.74e-01 1.03e+01
  angle pdb=" CA  LEU B 157 "
        pdb=" C   LEU B 157 "
        pdb=" O   LEU B 157 "
      ideal   model   delta    sigma   weight residual
     122.44  118.21    4.23 1.32e+00 5.74e-01 1.03e+01
  angle pdb=" CA  LEU C 157 "
        pdb=" C   LEU C 157 "
        pdb=" O   LEU C 157 "
      ideal   model   delta    sigma   weight residual
     122.44  118.21    4.23 1.32e+00 5.74e-01 1.03e+01
  angle pdb=" CA  LEU D 157 "
        pdb=" C   LEU D 157 "
        pdb=" O   LEU D 157 "
      ideal   model   delta    sigma   weight residual
     122.44  118.23    4.21 1.32e+00 5.74e-01 1.02e+01
  angle pdb=" CA  LEU A 157 "
        pdb=" C   LEU A 157 "
        pdb=" O   LEU A 157 "
      ideal   model   delta    sigma   weight residual
     122.44  118.25    4.19 1.32e+00 5.74e-01 1.01e+01
  ... (remaining 16390 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.88: 6011
       10.88 -    21.77: 639
       21.77 -    32.65: 245
       32.65 -    43.53: 105
       43.53 -    54.42: 20
  Dihedral angle restraints: 7020
    sinusoidal: 2415
      harmonic: 4605
  Sorted by residual:
  dihedral pdb=" CA  CYS D  27 "
           pdb=" C   CYS D  27 "
           pdb=" N   TYR D  28 "
           pdb=" CA  TYR D  28 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.38  -25.62     0      5.00e+00 4.00e-02 2.62e+01
  dihedral pdb=" CA  CYS B  27 "
           pdb=" C   CYS B  27 "
           pdb=" N   TYR B  28 "
           pdb=" CA  TYR B  28 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.39  -25.61     0      5.00e+00 4.00e-02 2.62e+01
  dihedral pdb=" CA  CYS A  27 "
           pdb=" C   CYS A  27 "
           pdb=" N   TYR A  28 "
           pdb=" CA  TYR A  28 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.40  -25.60     0      5.00e+00 4.00e-02 2.62e+01
  ... (remaining 7017 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1162
       0.034 -    0.068: 520
       0.068 -    0.102: 237
       0.102 -    0.135: 67
       0.135 -    0.169: 14
  Chirality restraints: 2000
  Sorted by residual:
  chirality pdb=" CA  THR B 158 "
            pdb=" N   THR B 158 "
            pdb=" C   THR B 158 "
            pdb=" CB  THR B 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.70   -0.17 2.00e-01 2.50e+01 7.16e-01
  chirality pdb=" CA  THR C 158 "
            pdb=" N   THR C 158 "
            pdb=" C   THR C 158 "
            pdb=" CB  THR C 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.69   -0.16 2.00e-01 2.50e+01 6.68e-01
  chirality pdb=" CA  THR E 158 "
            pdb=" N   THR E 158 "
            pdb=" C   THR E 158 "
            pdb=" CB  THR E 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.69   -0.16 2.00e-01 2.50e+01 6.67e-01
  ... (remaining 1997 not shown)

  Planarity restraints: 2035
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E  73 "    0.032 5.00e-02 4.00e+02   4.92e-02 3.87e+00
        pdb=" N   PRO E  74 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO E  74 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO E  74 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D  73 "    0.032 5.00e-02 4.00e+02   4.92e-02 3.87e+00
        pdb=" N   PRO D  74 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO D  74 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D  74 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  73 "    0.032 5.00e-02 4.00e+02   4.92e-02 3.87e+00
        pdb=" N   PRO A  74 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A  74 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  74 "    0.027 5.00e-02 4.00e+02
  ... (remaining 2032 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 173
        2.67 -     3.23: 11401
        3.23 -     3.78: 17409
        3.78 -     4.34: 22585
        4.34 -     4.90: 37951
  Nonbonded interactions: 89519
  Sorted by model distance:
  nonbonded pdb=" O   VAL A  90 "
            pdb=" NH1 ARG B 133 "
     model   vdw
     2.111 3.120
  nonbonded pdb=" O   VAL B  90 "
            pdb=" NH1 ARG C 133 "
     model   vdw
     2.186 3.120
  nonbonded pdb=" O   VAL C  90 "
            pdb=" NH1 ARG D 133 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" O   VAL D  90 "
            pdb=" NH1 ARG E 133 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" NH1 ARG A 133 "
            pdb=" O   VAL E  90 "
     model   vdw
     2.212 3.120
  ... (remaining 89514 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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 group one per residue
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:             1.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.510
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5283
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      :  0.006   0.049  11940  Z= 0.266
  Angle     :  0.681   5.483  16395  Z= 0.389
  Chirality :  0.047   0.169   2000
  Planarity :  0.005   0.049   2035
  Dihedral  : 12.304  54.417   4010
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.58 (0.22), residues: 1515
  helix:  0.81 (0.22), residues: 480
  sheet: -0.76 (0.27), residues: 420
  loop : -0.95 (0.26), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 287 
 TYR   0.012   0.002   TYR D 102 
 PHE   0.014   0.002   PHE C 121 
 TRP   0.023   0.002   TRP B 160 
 HIS   0.002   0.001   HIS C 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00600 (11940)
  covalent geometry    : angle       0.68145 (16395)
  hydrogen bonds       : bond        0.09469 (  550)
  hydrogen bonds       : angle       6.73101 ( 1620)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.423 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.1221
  time to fit residues: 36.4305
Evaluate side-chains
  151 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    0.4980
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.3980
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    0.0870
   chunk 149 optimal weight:    0.7980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
C 127 HIS
D 127 HIS
E 127 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.201889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.155137 restraints weight = 12413.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.151814 restraints weight = 15087.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.153656 restraints weight = 13820.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.153660 restraints weight = 8808.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.154078 restraints weight = 8020.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6148
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  11940  Z= 0.152
  Angle     :  0.615   6.709  16395  Z= 0.316
  Chirality :  0.044   0.172   2000
  Planarity :  0.006   0.064   2035
  Dihedral  :  4.692  26.282   1660
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.07 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.33 (0.22), residues: 1515
  helix:  1.51 (0.22), residues: 510
  sheet: -0.75 (0.29), residues: 370
  loop : -1.29 (0.24), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  77 
 TYR   0.013   0.002   TYR E  23 
 PHE   0.013   0.001   PHE C 265 
 TRP   0.021   0.002   TRP C 160 
 HIS   0.004   0.002   HIS D 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (11940)
  covalent geometry    : angle       0.61469 (16395)
  hydrogen bonds       : bond        0.03895 (  550)
  hydrogen bonds       : angle       5.03801 ( 1620)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 194
  time to evaluate  : 0.413 
Fit side-chains
REVERT: A  185 ASP cc_start: 0.7003 (t70) cc_final: 0.6609 (t0)
REVERT: B  185 ASP cc_start: 0.6690 (OUTLIER) cc_final: 0.6321 (t0)
REVERT: B  309 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7279 (mm)
REVERT: C  115 ASP cc_start: 0.7319 (p0) cc_final: 0.6835 (p0)
REVERT: C  230 SER cc_start: 0.7163 (m) cc_final: 0.6937 (t)
REVERT: C  302 VAL cc_start: 0.6608 (t) cc_final: 0.6348 (t)
REVERT: D  230 SER cc_start: 0.7162 (m) cc_final: 0.6921 (t)
REVERT: D  261 MET cc_start: 0.4700 (mmm) cc_final: 0.4471 (mmt)
REVERT: E  230 SER cc_start: 0.7240 (m) cc_final: 0.6990 (t)
REVERT: E  302 VAL cc_start: 0.6628 (t) cc_final: 0.6320 (t)
  outliers start: 22
  outliers final: 10
  residues processed: 212
  average time/residue: 0.1078
  time to fit residues: 32.5727
Evaluate side-chains
  164 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  185 ASP
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  127 HIS
Chi-restraints excluded: chain E residue  178 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 131 optimal weight:    4.9990
   chunk 103 optimal weight:   20.0000
   chunk 31 optimal weight:    5.9990
   chunk 107 optimal weight:    1.9990
   chunk 117 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9980
   chunk 104 optimal weight:   20.0000
   chunk 105 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B 127 HIS
B 235 HIS
C 127 HIS
D 127 HIS
** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.197827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.150296 restraints weight = 12860.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.145720 restraints weight = 15718.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.147741 restraints weight = 14054.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.148005 restraints weight = 8931.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.148105 restraints weight = 8781.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.5477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  11940  Z= 0.214
  Angle     :  0.673  11.307  16395  Z= 0.356
  Chirality :  0.047   0.330   2000
  Planarity :  0.006   0.091   2035
  Dihedral  :  4.576  30.058   1660
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 14.68 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.22), residues: 1515
  helix:  1.27 (0.22), residues: 510
  sheet: -0.22 (0.30), residues: 370
  loop : -1.62 (0.24), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  77 
 TYR   0.014   0.002   TYR A 102 
 PHE   0.018   0.002   PHE D 195 
 TRP   0.026   0.003   TRP A 160 
 HIS   0.073   0.005   HIS E 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 (11940)
  covalent geometry    : angle       0.67279 (16395)
  hydrogen bonds       : bond        0.05019 (  550)
  hydrogen bonds       : angle       5.24212 ( 1620)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 162
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7004 (mm-30)
REVERT: A  115 ASP cc_start: 0.7786 (p0) cc_final: 0.7402 (p0)
REVERT: A  185 ASP cc_start: 0.7386 (t70) cc_final: 0.6863 (t0)
REVERT: B  115 ASP cc_start: 0.7671 (p0) cc_final: 0.7263 (p0)
REVERT: B  185 ASP cc_start: 0.6929 (t70) cc_final: 0.6710 (t70)
REVERT: B  224 ASN cc_start: 0.8034 (t0) cc_final: 0.7635 (m-40)
REVERT: B  309 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8059 (mp)
REVERT: B  314 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7412 (t80)
REVERT: C   75 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6800 (mm-30)
REVERT: C  115 ASP cc_start: 0.7748 (p0) cc_final: 0.7356 (p0)
REVERT: C  185 ASP cc_start: 0.6937 (t70) cc_final: 0.6359 (t70)
REVERT: C  314 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7268 (t80)
REVERT: D  115 ASP cc_start: 0.7605 (p0) cc_final: 0.7220 (p0)
REVERT: D  314 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7384 (t80)
REVERT: E  115 ASP cc_start: 0.7681 (p0) cc_final: 0.7243 (p0)
REVERT: E  127 HIS cc_start: 0.8536 (OUTLIER) cc_final: 0.8285 (m-70)
REVERT: E  314 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7448 (t80)
  outliers start: 46
  outliers final: 32
  residues processed: 199
  average time/residue: 0.1006
  time to fit residues: 29.2948
Evaluate side-chains
  162 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 124
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  314 PHE
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  187 GLN
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  281 VAL
Chi-restraints excluded: chain C residue  314 PHE
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain D residue  130 LEU
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  314 PHE
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  127 HIS
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  281 VAL
Chi-restraints excluded: chain E residue  299 PHE
Chi-restraints excluded: chain E residue  314 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 149 optimal weight:    0.3980
   chunk 50 optimal weight:    0.5980
   chunk 87 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 140 optimal weight:    0.7980
   chunk 34 optimal weight:    8.9990
   chunk 70 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 117 optimal weight:    7.9990
   chunk 94 optimal weight:   10.0000
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C 127 HIS
D 127 HIS
E 127 HIS
E 235 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.198744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.151078 restraints weight = 12842.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.146031 restraints weight = 13876.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.147819 restraints weight = 13117.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.148155 restraints weight = 8436.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.148271 restraints weight = 8066.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.5960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11940  Z= 0.118
  Angle     :  0.561   9.972  16395  Z= 0.282
  Chirality :  0.043   0.134   2000
  Planarity :  0.005   0.043   2035
  Dihedral  :  4.314  27.999   1660
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 18.11 %
    Favored  : 78.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.16 (0.22), residues: 1515
  helix:  1.67 (0.22), residues: 510
  sheet: -0.04 (0.30), residues: 370
  loop : -1.66 (0.24), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  77 
 TYR   0.011   0.001   TYR A  23 
 PHE   0.012   0.001   PHE A 265 
 TRP   0.007   0.001   TRP A 160 
 HIS   0.011   0.001   HIS E 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (11940)
  covalent geometry    : angle       0.56079 (16395)
  hydrogen bonds       : bond        0.03818 (  550)
  hydrogen bonds       : angle       4.71244 ( 1620)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 128
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.7513 (mm-30) cc_final: 0.6923 (mm-30)
REVERT: A  115 ASP cc_start: 0.7739 (p0) cc_final: 0.7435 (p0)
REVERT: A  185 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.6938 (t0)
REVERT: B  115 ASP cc_start: 0.7719 (p0) cc_final: 0.7398 (p0)
REVERT: B  185 ASP cc_start: 0.7129 (t70) cc_final: 0.6837 (t0)
REVERT: B  224 ASN cc_start: 0.8326 (t0) cc_final: 0.8116 (t0)
REVERT: B  309 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8078 (mp)
REVERT: B  314 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7414 (t80)
REVERT: C  115 ASP cc_start: 0.7693 (p0) cc_final: 0.7439 (p0)
REVERT: C  314 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7252 (t80)
REVERT: D  115 ASP cc_start: 0.7692 (p0) cc_final: 0.7336 (p0)
REVERT: D  185 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6745 (t0)
REVERT: E  115 ASP cc_start: 0.7718 (p0) cc_final: 0.7381 (p0)
REVERT: E  314 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.7242 (t80)
  outliers start: 41
  outliers final: 23
  residues processed: 159
  average time/residue: 0.0838
  time to fit residues: 20.7272
Evaluate side-chains
  144 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  185 ASP
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  314 PHE
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  314 PHE
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain D residue  130 LEU
Chi-restraints excluded: chain D residue  185 ASP
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  281 VAL
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  299 PHE
Chi-restraints excluded: chain E residue  314 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 124 optimal weight:    9.9990
   chunk 126 optimal weight:    3.9990
   chunk 100 optimal weight:    8.9990
   chunk 143 optimal weight:    0.0470
   chunk 39 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 80 optimal weight:    0.7980
   chunk 111 optimal weight:    0.7980
   chunk 127 optimal weight:    0.0170
   chunk 11 optimal weight:    5.9990
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
C 127 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.198741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.152546 restraints weight = 12851.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.150242 restraints weight = 15414.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.151519 restraints weight = 16499.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.151966 restraints weight = 9566.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.152715 restraints weight = 8627.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.6823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11940  Z= 0.120
  Angle     :  0.548   8.883  16395  Z= 0.276
  Chirality :  0.043   0.142   2000
  Planarity :  0.005   0.041   2035
  Dihedral  :  4.166  31.261   1660
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 16.14 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

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: -0.06 (0.22), residues: 1515
  helix:  1.87 (0.22), residues: 510
  sheet:  0.04 (0.29), residues: 375
  loop : -1.75 (0.24), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 133 
 TYR   0.011   0.001   TYR E 102 
 PHE   0.013   0.001   PHE A 265 
 TRP   0.006   0.001   TRP C 160 
 HIS   0.003   0.001   HIS E 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (11940)
  covalent geometry    : angle       0.54850 (16395)
  hydrogen bonds       : bond        0.03300 (  550)
  hydrogen bonds       : angle       4.46610 ( 1620)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 128
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
REVERT: B  309 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8060 (mp)
REVERT: C  185 ASP cc_start: 0.7485 (t0) cc_final: 0.7138 (t70)
REVERT: D  115 ASP cc_start: 0.7756 (p0) cc_final: 0.7518 (p0)
REVERT: E  115 ASP cc_start: 0.7752 (p0) cc_final: 0.7509 (p0)
  outliers start: 50
  outliers final: 42
  residues processed: 169
  average time/residue: 0.0931
  time to fit residues: 23.4880
Evaluate side-chains
  151 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 108
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  205 MET
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  281 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain D residue   92 ILE
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain D residue  130 LEU
Chi-restraints excluded: chain D residue  144 VAL
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  281 VAL
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  144 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  281 VAL
Chi-restraints excluded: chain E residue  299 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 4 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 130 optimal weight:    7.9990
   chunk 112 optimal weight:    0.9980
   chunk 125 optimal weight:   30.0000
   chunk 48 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
C 127 HIS
D 127 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.193225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.149109 restraints weight = 13215.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.141367 restraints weight = 16205.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.144107 restraints weight = 14975.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.144708 restraints weight = 8188.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.145394 restraints weight = 7201.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.8331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  11940  Z= 0.242
  Angle     :  0.669   8.527  16395  Z= 0.349
  Chirality :  0.046   0.162   2000
  Planarity :  0.005   0.071   2035
  Dihedral  :  4.466  27.430   1660
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 16.91 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.41 (0.21), residues: 1515
  helix:  1.31 (0.21), residues: 490
  sheet:  0.09 (0.30), residues: 370
  loop : -1.76 (0.23), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 133 
 TYR   0.018   0.002   TYR A  28 
 PHE   0.020   0.002   PHE A 195 
 TRP   0.008   0.002   TRP E 213 
 HIS   0.006   0.002   HIS D 277 

Details of bonding type rmsd
  covalent geometry    : bond        0.00580 (11940)
  covalent geometry    : angle       0.66853 (16395)
  hydrogen bonds       : bond        0.04409 (  550)
  hydrogen bonds       : angle       4.83508 ( 1620)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 175
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: B  130 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7597 (mp)
REVERT: B  185 ASP cc_start: 0.7557 (t70) cc_final: 0.7278 (t0)
REVERT: B  193 GLN cc_start: 0.8668 (mt0) cc_final: 0.8389 (mt0)
REVERT: B  309 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8295 (mt)
REVERT: C   75 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7016 (mm-30)
REVERT: C   77 ARG cc_start: 0.8042 (mtt-85) cc_final: 0.7631 (mtt-85)
REVERT: D   75 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7169 (mm-30)
REVERT: D   77 ARG cc_start: 0.8016 (mtt-85) cc_final: 0.7568 (mtt-85)
REVERT: D  130 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7389 (mp)
REVERT: D  193 GLN cc_start: 0.8739 (mt0) cc_final: 0.8443 (mt0)
REVERT: D  224 ASN cc_start: 0.8604 (t0) cc_final: 0.8403 (t0)
REVERT: E  130 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7603 (mp)
  outliers start: 53
  outliers final: 36
  residues processed: 219
  average time/residue: 0.0926
  time to fit residues: 29.9445
Evaluate side-chains
  185 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 145
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  281 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  130 LEU
Chi-restraints excluded: chain D residue  144 VAL
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  270 VAL
Chi-restraints excluded: chain D residue  281 VAL
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain E residue  130 LEU
Chi-restraints excluded: chain E residue  144 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  205 MET
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  281 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 114 optimal weight:    0.8980
   chunk 31 optimal weight:    7.9990
   chunk 71 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 19 optimal weight:    0.3980
   chunk 135 optimal weight:    6.9990
   chunk 59 optimal weight:    0.6980
   chunk 1 optimal weight:    0.3980
   chunk 118 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
D 127 HIS
E 193 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.195449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.150905 restraints weight = 12827.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.144719 restraints weight = 16682.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.147316 restraints weight = 14874.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.147549 restraints weight = 8905.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.148160 restraints weight = 8006.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.8482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11940  Z= 0.114
  Angle     :  0.557   7.806  16395  Z= 0.285
  Chirality :  0.043   0.146   2000
  Planarity :  0.005   0.051   2035
  Dihedral  :  4.314  30.858   1660
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 20.94 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.22), residues: 1515
  helix:  1.79 (0.22), residues: 490
  sheet:  0.10 (0.29), residues: 375
  loop : -1.77 (0.23), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 133 
 TYR   0.010   0.001   TYR E  23 
 PHE   0.013   0.001   PHE C  78 
 TRP   0.008   0.001   TRP B 213 
 HIS   0.002   0.001   HIS B 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (11940)
  covalent geometry    : angle       0.55741 (16395)
  hydrogen bonds       : bond        0.03457 (  550)
  hydrogen bonds       : angle       4.61972 ( 1620)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 130
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
REVERT: B  193 GLN cc_start: 0.8743 (mt0) cc_final: 0.8525 (mt0)
REVERT: B  309 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8130 (mt)
REVERT: C   75 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7370 (mm-30)
REVERT: C   77 ARG cc_start: 0.7996 (mtt-85) cc_final: 0.7652 (mtt-85)
REVERT: E   75 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6636 (mm-30)
REVERT: E   77 ARG cc_start: 0.7998 (mtt-85) cc_final: 0.7679 (mmt-90)
REVERT: E  193 GLN cc_start: 0.8788 (mt0) cc_final: 0.8333 (mp10)
  outliers start: 27
  outliers final: 22
  residues processed: 153
  average time/residue: 0.0997
  time to fit residues: 22.6270
Evaluate side-chains
  143 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  281 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  130 LEU
Chi-restraints excluded: chain D residue  144 VAL
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  281 VAL
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain E residue  144 VAL
Chi-restraints excluded: chain E residue  178 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 132 optimal weight:    1.9990
   chunk 44 optimal weight:   20.0000
   chunk 15 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 73 optimal weight:    9.9990
   chunk 117 optimal weight:    3.9990
   chunk 119 optimal weight:    0.7980
   chunk 142 optimal weight:    1.9990
   chunk 93 optimal weight:    5.9990
   chunk 50 optimal weight:    0.6980
   chunk 8 optimal weight:    0.3980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 127 HIS
D 127 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.195645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.152178 restraints weight = 12877.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.148111 restraints weight = 16715.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.150347 restraints weight = 14102.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.150455 restraints weight = 8625.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.151071 restraints weight = 7960.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.8741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11940  Z= 0.127
  Angle     :  0.555   7.035  16395  Z= 0.284
  Chirality :  0.043   0.159   2000
  Planarity :  0.005   0.054   2035
  Dihedral  :  4.159  27.603   1660
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 20.86 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.22), residues: 1515
  helix:  1.94 (0.22), residues: 490
  sheet: -0.57 (0.26), residues: 420
  loop : -1.42 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  77 
 TYR   0.012   0.001   TYR D  23 
 PHE   0.013   0.001   PHE C  42 
 TRP   0.006   0.001   TRP D 160 
 HIS   0.002   0.001   HIS D 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (11940)
  covalent geometry    : angle       0.55513 (16395)
  hydrogen bonds       : bond        0.03349 (  550)
  hydrogen bonds       : angle       4.45245 ( 1620)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 119
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7443 (mm-30)
REVERT: A   77 ARG cc_start: 0.8172 (mtt-85) cc_final: 0.7942 (mtt-85)
REVERT: A  293 ARG cc_start: 0.7672 (mtm110) cc_final: 0.7240 (ttm-80)
REVERT: B  309 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8118 (mt)
REVERT: C   75 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7325 (mm-30)
REVERT: C   77 ARG cc_start: 0.8001 (mtt-85) cc_final: 0.7689 (mtt-85)
REVERT: C  293 ARG cc_start: 0.7484 (mtm110) cc_final: 0.7221 (ttm-80)
REVERT: E   75 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6961 (mm-30)
  outliers start: 32
  outliers final: 27
  residues processed: 146
  average time/residue: 0.0944
  time to fit residues: 20.7183
Evaluate side-chains
  144 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 116
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  281 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  130 LEU
Chi-restraints excluded: chain D residue  144 VAL
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  281 VAL
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain E residue  144 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  205 MET
Chi-restraints excluded: chain E residue  242 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 91 optimal weight:    7.9990
   chunk 149 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 109 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 96 optimal weight:    6.9990
   chunk 75 optimal weight:    6.9990
   chunk 17 optimal weight:    0.5980
   chunk 121 optimal weight:    0.5980
   chunk 140 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
D 127 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.196569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.150580 restraints weight = 12793.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.143161 restraints weight = 12679.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.145910 restraints weight = 14159.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.145976 restraints weight = 8284.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.146398 restraints weight = 7410.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.8962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11940  Z= 0.115
  Angle     :  0.540   6.877  16395  Z= 0.277
  Chirality :  0.042   0.140   2000
  Planarity :  0.005   0.042   2035
  Dihedral  :  4.179  31.047   1660
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 21.37 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

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: -0.00 (0.22), residues: 1515
  helix:  2.05 (0.22), residues: 490
  sheet: -0.49 (0.27), residues: 420
  loop : -1.36 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  77 
 TYR   0.012   0.001   TYR C  23 
 PHE   0.011   0.001   PHE B  42 
 TRP   0.005   0.001   TRP B 160 
 HIS   0.001   0.001   HIS C 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (11940)
  covalent geometry    : angle       0.54040 (16395)
  hydrogen bonds       : bond        0.03134 (  550)
  hydrogen bonds       : angle       4.37965 ( 1620)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 117
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.7665 (mtm110) cc_final: 0.7177 (ttm-80)
REVERT: B   75 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7547 (mm-30)
REVERT: B  293 ARG cc_start: 0.7593 (mtm110) cc_final: 0.7113 (ttm-80)
REVERT: B  309 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8094 (mt)
REVERT: C   75 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7432 (mm-30)
REVERT: C   77 ARG cc_start: 0.8031 (mtt-85) cc_final: 0.7650 (mtt-85)
REVERT: C  293 ARG cc_start: 0.7466 (mtm110) cc_final: 0.7144 (ttm-80)
  outliers start: 29
  outliers final: 26
  residues processed: 143
  average time/residue: 0.1036
  time to fit residues: 21.5583
Evaluate side-chains
  139 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue  132 VAL
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  130 LEU
Chi-restraints excluded: chain D residue  144 VAL
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain E residue  144 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  242 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 140 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9980
   chunk 91 optimal weight:    5.9990
   chunk 118 optimal weight:    5.9990
   chunk 104 optimal weight:    7.9990
   chunk 78 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 119 optimal weight:    1.9990
   chunk 117 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
D 127 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.192522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.148148 restraints weight = 13042.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.141963 restraints weight = 20050.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.144369 restraints weight = 15907.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.144941 restraints weight = 9510.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.145338 restraints weight = 8446.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.9315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  11940  Z= 0.172
  Angle     :  0.585   6.567  16395  Z= 0.303
  Chirality :  0.043   0.161   2000
  Planarity :  0.005   0.055   2035
  Dihedral  :  4.253  28.257   1660
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 21.20 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.14 (0.22), residues: 1515
  helix:  1.85 (0.21), residues: 490
  sheet: -0.51 (0.27), residues: 420
  loop : -1.40 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  77 
 TYR   0.014   0.002   TYR C  23 
 PHE   0.013   0.002   PHE E 195 
 TRP   0.004   0.001   TRP E 217 
 HIS   0.003   0.001   HIS B 277 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (11940)
  covalent geometry    : angle       0.58523 (16395)
  hydrogen bonds       : bond        0.03607 (  550)
  hydrogen bonds       : angle       4.51275 ( 1620)

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

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

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 138
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.7727 (mtm110) cc_final: 0.7282 (ttm-80)
REVERT: B  293 ARG cc_start: 0.7696 (mtm110) cc_final: 0.7260 (ttm-80)
REVERT: B  309 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8193 (mt)
REVERT: C   75 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7309 (mm-30)
REVERT: C   77 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7621 (mtt-85)
REVERT: C  293 ARG cc_start: 0.7563 (mtm110) cc_final: 0.7272 (ttm-80)
  outliers start: 33
  outliers final: 25
  residues processed: 167
  average time/residue: 0.1063
  time to fit residues: 25.3813
Evaluate side-chains
  161 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue  132 VAL
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  144 VAL
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain E residue  132 VAL
Chi-restraints excluded: chain E residue  144 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  242 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 121 optimal weight:   20.0000
   chunk 147 optimal weight:    0.4980
   chunk 48 optimal weight:    2.9990
   chunk 140 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 110 optimal weight:    0.7980
   chunk 130 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 49 optimal weight:    0.4980
   chunk 31 optimal weight:    0.0030
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
D 127 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.195741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.151216 restraints weight = 12839.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.145739 restraints weight = 18387.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.148244 restraints weight = 16500.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.148166 restraints weight = 9859.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.148893 restraints weight = 9101.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.9403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11940  Z= 0.106
  Angle     :  0.545   6.733  16395  Z= 0.279
  Chirality :  0.042   0.154   2000
  Planarity :  0.005   0.041   2035
  Dihedral  :  4.222  29.946   1660
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 21.63 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.01 (0.22), residues: 1515
  helix:  2.06 (0.22), residues: 485
  sheet: -0.44 (0.26), residues: 420
  loop : -1.35 (0.25), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 133 
 TYR   0.017   0.001   TYR C  23 
 PHE   0.010   0.001   PHE B 265 
 TRP   0.006   0.001   TRP B 213 
 HIS   0.001   0.001   HIS B 277 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (11940)
  covalent geometry    : angle       0.54486 (16395)
  hydrogen bonds       : bond        0.03183 (  550)
  hydrogen bonds       : angle       4.37681 ( 1620)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1612.22 seconds
wall clock time: 28 minutes 31.15 seconds (1711.15 seconds total)