Starting phenix.real_space_refine
on Fri Nov 15 23:28:55 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g17_29664/11_2024/8g17_29664.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g17_29664/11_2024/8g17_29664.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g17_29664/11_2024/8g17_29664.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g17_29664/11_2024/8g17_29664.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g17_29664/11_2024/8g17_29664.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g17_29664/11_2024/8g17_29664.cif"
  }
  resolution = 1.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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      48      5.16       5
     C    6328      2.51       5
     N    1744      2.21       5
     O    1896      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 10016
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2504
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 12, 'TRANS': 321}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 4.86, per 1000 atoms: 0.49
  Number of scatterers: 10016
  At special positions: 0
  Unit cell: (99.365, 101.035, 91.015, 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      48     16.00
     O    1896      8.00
     N    1744      7.00
     C    6328      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.62
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2408

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 12 sheets defined
      39.2% alpha, 30.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 26
    Processing helix  chain 'A' and resid 39 through 49
    Processing helix  chain 'A' and resid 81 through 85
    Processing helix  chain 'A' and resid 86 through 91
    Processing helix  chain 'A' and resid 104 through 109
    Processing helix  chain 'A' and resid 109 through 114
      removed outlier: 3.918A  pdb=" N   GLN A 113 " --> pdb=" O   GLY A 109 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLY A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 109 through 114'
    Processing helix  chain 'A' and resid 136 through 140
    Processing helix  chain 'A' and resid 151 through 169
      Proline residue:  A 159  - end of helix
    Processing helix  chain 'A' and resid 196 through 200
    Processing helix  chain 'A' and resid 212 through 221
      removed outlier: 3.816A  pdb=" N   GLY A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LYS A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 254 through 268
    Processing helix  chain 'A' and resid 282 through 287
    Processing helix  chain 'A' and resid 317 through 334
    Processing helix  chain 'B' and resid 12 through 26
    Processing helix  chain 'B' and resid 39 through 49
    Processing helix  chain 'B' and resid 81 through 85
    Processing helix  chain 'B' and resid 86 through 91
    Processing helix  chain 'B' and resid 104 through 109
    Processing helix  chain 'B' and resid 109 through 114
      removed outlier: 3.918A  pdb=" N   GLN B 113 " --> pdb=" O   GLY B 109 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLY B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 109 through 114'
    Processing helix  chain 'B' and resid 136 through 140
    Processing helix  chain 'B' and resid 151 through 169
      Proline residue:  B 159  - end of helix
    Processing helix  chain 'B' and resid 196 through 200
    Processing helix  chain 'B' and resid 212 through 221
      removed outlier: 3.816A  pdb=" N   GLY B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LYS B 219 " --> pdb=" O   LYS B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 254 through 268
    Processing helix  chain 'B' and resid 282 through 287
    Processing helix  chain 'B' and resid 317 through 334
    Processing helix  chain 'C' and resid 12 through 26
    Processing helix  chain 'C' and resid 39 through 49
    Processing helix  chain 'C' and resid 81 through 85
    Processing helix  chain 'C' and resid 86 through 91
    Processing helix  chain 'C' and resid 104 through 109
    Processing helix  chain 'C' and resid 109 through 114
      removed outlier: 3.919A  pdb=" N   GLN C 113 " --> pdb=" O   GLY C 109 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLY C 114 " --> pdb=" O   ALA C 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 109 through 114'
    Processing helix  chain 'C' and resid 136 through 140
    Processing helix  chain 'C' and resid 151 through 169
      Proline residue:  C 159  - end of helix
    Processing helix  chain 'C' and resid 196 through 200
    Processing helix  chain 'C' and resid 212 through 221
      removed outlier: 3.816A  pdb=" N   GLY C 218 " --> pdb=" O   ALA C 214 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS C 219 " --> pdb=" O   LYS C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 254 through 268
    Processing helix  chain 'C' and resid 282 through 287
    Processing helix  chain 'C' and resid 317 through 334
    Processing helix  chain 'D' and resid 12 through 26
    Processing helix  chain 'D' and resid 39 through 49
    Processing helix  chain 'D' and resid 81 through 85
    Processing helix  chain 'D' and resid 86 through 91
    Processing helix  chain 'D' and resid 104 through 109
    Processing helix  chain 'D' and resid 109 through 114
      removed outlier: 3.918A  pdb=" N   GLN D 113 " --> pdb=" O   GLY D 109 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLY D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 109 through 114'
    Processing helix  chain 'D' and resid 136 through 140
    Processing helix  chain 'D' and resid 151 through 169
      Proline residue:  D 159  - end of helix
    Processing helix  chain 'D' and resid 196 through 200
    Processing helix  chain 'D' and resid 212 through 221
      removed outlier: 3.816A  pdb=" N   GLY D 218 " --> pdb=" O   ALA D 214 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LYS D 219 " --> pdb=" O   LYS D 215 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 254 through 268
    Processing helix  chain 'D' and resid 282 through 287
    Processing helix  chain 'D' and resid 317 through 334
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63
      removed outlier: 10.277A  pdb=" N   ASP A  29 " --> pdb=" O   PRO A  73 " (cutoff:3.500A)
      removed outlier: 9.816A  pdb=" N   THR A  75 " --> pdb=" O   ASP A  29 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL A  31 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   PHE A  77 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE A  33 " --> pdb=" O   PHE A  77 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   VAL A   8 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ILE A  33 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   VAL A  95 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR A 229 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ARG A 248 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   GLY A 173 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR A 246 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET A 175 " --> pdb=" O   ASP A 244 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ASP A 244 " --> pdb=" O   MET A 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR A 177 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL A 242 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   ILE A 311 " --> pdb=" O   ASP A 296 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR A 229 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ARG A 248 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   GLY A 173 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR A 246 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET A 175 " --> pdb=" O   ASP A 244 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ASP A 244 " --> pdb=" O   MET A 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR A 177 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL A 242 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   PHE A 307 " --> pdb=" O   LEU A 303 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 63
      removed outlier: 10.277A  pdb=" N   ASP B  29 " --> pdb=" O   PRO B  73 " (cutoff:3.500A)
      removed outlier: 9.815A  pdb=" N   THR B  75 " --> pdb=" O   ASP B  29 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL B  31 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   PHE B  77 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE B  33 " --> pdb=" O   PHE B  77 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   VAL B   8 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ILE B  33 " --> pdb=" O   VAL B   8 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   VAL B  95 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR B 229 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ARG B 248 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY B 173 " --> pdb=" O   THR B 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR B 246 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET B 175 " --> pdb=" O   ASP B 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP B 244 " --> pdb=" O   MET B 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR B 177 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL B 242 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   ILE B 311 " --> pdb=" O   ASP B 296 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR B 229 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ARG B 248 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY B 173 " --> pdb=" O   THR B 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR B 246 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET B 175 " --> pdb=" O   ASP B 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP B 244 " --> pdb=" O   MET B 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR B 177 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL B 242 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   PHE B 307 " --> pdb=" O   LEU B 303 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 63
      removed outlier: 10.277A  pdb=" N   ASP C  29 " --> pdb=" O   PRO C  73 " (cutoff:3.500A)
      removed outlier: 9.815A  pdb=" N   THR C  75 " --> pdb=" O   ASP C  29 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL C  31 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   PHE C  77 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE C  33 " --> pdb=" O   PHE C  77 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   VAL C   8 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ILE C  33 " --> pdb=" O   VAL C   8 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   VAL C  95 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 208 through 210
      removed outlier: 3.605A  pdb=" N   THR C 229 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ARG C 248 " --> pdb=" O   VAL C 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY C 173 " --> pdb=" O   THR C 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR C 246 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET C 175 " --> pdb=" O   ASP C 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP C 244 " --> pdb=" O   MET C 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR C 177 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL C 242 " --> pdb=" O   THR C 177 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   ILE C 311 " --> pdb=" O   ASP C 296 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 208 through 210
      removed outlier: 3.605A  pdb=" N   THR C 229 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ARG C 248 " --> pdb=" O   VAL C 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY C 173 " --> pdb=" O   THR C 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR C 246 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET C 175 " --> pdb=" O   ASP C 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP C 244 " --> pdb=" O   MET C 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR C 177 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL C 242 " --> pdb=" O   THR C 177 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   PHE C 307 " --> pdb=" O   LEU C 303 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 60 through 63
      removed outlier: 10.277A  pdb=" N   ASP D  29 " --> pdb=" O   PRO D  73 " (cutoff:3.500A)
      removed outlier: 9.816A  pdb=" N   THR D  75 " --> pdb=" O   ASP D  29 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL D  31 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   PHE D  77 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE D  33 " --> pdb=" O   PHE D  77 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   VAL D   8 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ILE D  33 " --> pdb=" O   VAL D   8 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   VAL D  95 " --> pdb=" O   ILE D 120 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR D 229 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ARG D 248 " --> pdb=" O   VAL D 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY D 173 " --> pdb=" O   THR D 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR D 246 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET D 175 " --> pdb=" O   ASP D 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP D 244 " --> pdb=" O   MET D 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR D 177 " --> pdb=" O   VAL D 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL D 242 " --> pdb=" O   THR D 177 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   ILE D 311 " --> pdb=" O   ASP D 296 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR D 229 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ARG D 248 " --> pdb=" O   VAL D 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY D 173 " --> pdb=" O   THR D 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR D 246 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET D 175 " --> pdb=" O   ASP D 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP D 244 " --> pdb=" O   MET D 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR D 177 " --> pdb=" O   VAL D 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL D 242 " --> pdb=" O   THR D 177 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   PHE D 307 " --> pdb=" O   LEU D 303 " (cutoff:3.500A)

    520 hydrogen bonds defined for protein.
    1368 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.31

  Time building geometry restraints manager: 3.00 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: 3260
        1.34 -     1.46: 1385
        1.46 -     1.57: 5487
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 10216
  Sorted by residual:
  bond pdb=" N   VAL C 242 "
       pdb=" CA  VAL C 242 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.11e-02 8.12e+03 1.28e+01
  bond pdb=" N   VAL B 242 "
       pdb=" CA  VAL B 242 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.11e-02 8.12e+03 1.26e+01
  bond pdb=" N   VAL D 242 "
       pdb=" CA  VAL D 242 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.11e-02 8.12e+03 1.26e+01
  bond pdb=" N   VAL A 242 "
       pdb=" CA  VAL A 242 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.11e-02 8.12e+03 1.24e+01
  bond pdb=" N   VAL B 188 "
       pdb=" CA  VAL B 188 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.039 1.15e-02 7.56e+03 1.14e+01
  ... (remaining 10211 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 13361
        1.49 -     2.97: 386
        2.97 -     4.46: 73
        4.46 -     5.94: 16
        5.94 -     7.43: 12
  Bond angle restraints: 13848
  Sorted by residual:
  angle pdb=" C   ALA B 150 "
        pdb=" CA  ALA B 150 "
        pdb=" CB  ALA B 150 "
      ideal   model   delta    sigma   weight residual
     116.63  110.81    5.82 1.16e+00 7.43e-01 2.52e+01
  angle pdb=" C   ALA D 150 "
        pdb=" CA  ALA D 150 "
        pdb=" CB  ALA D 150 "
      ideal   model   delta    sigma   weight residual
     116.63  110.83    5.80 1.16e+00 7.43e-01 2.50e+01
  angle pdb=" C   ALA A 150 "
        pdb=" CA  ALA A 150 "
        pdb=" CB  ALA A 150 "
      ideal   model   delta    sigma   weight residual
     116.63  110.83    5.80 1.16e+00 7.43e-01 2.50e+01
  angle pdb=" C   ALA C 150 "
        pdb=" CA  ALA C 150 "
        pdb=" CB  ALA C 150 "
      ideal   model   delta    sigma   weight residual
     116.63  110.88    5.75 1.16e+00 7.43e-01 2.45e+01
  angle pdb=" N   ILE C 206 "
        pdb=" CA  ILE C 206 "
        pdb=" C   ILE C 206 "
      ideal   model   delta    sigma   weight residual
     113.39  107.89    5.50 1.47e+00 4.63e-01 1.40e+01
  ... (remaining 13843 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.89: 5408
       16.89 -    33.78: 408
       33.78 -    50.67: 160
       50.67 -    67.56: 60
       67.56 -    84.45: 8
  Dihedral angle restraints: 6044
    sinusoidal: 2268
      harmonic: 3776
  Sorted by residual:
  dihedral pdb=" CA  ASP A  50 "
           pdb=" CB  ASP A  50 "
           pdb=" CG  ASP A  50 "
           pdb=" OD1 ASP A  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.76   54.76     1      2.00e+01 2.50e-03 1.02e+01
  dihedral pdb=" CA  ASP D  50 "
           pdb=" CB  ASP D  50 "
           pdb=" CG  ASP D  50 "
           pdb=" OD1 ASP D  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.72   54.72     1      2.00e+01 2.50e-03 1.01e+01
  dihedral pdb=" CA  ASP B  50 "
           pdb=" CB  ASP B  50 "
           pdb=" CG  ASP B  50 "
           pdb=" OD1 ASP B  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.69   54.69     1      2.00e+01 2.50e-03 1.01e+01
  ... (remaining 6041 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1100
       0.042 -    0.084: 310
       0.084 -    0.127: 146
       0.127 -    0.169: 14
       0.169 -    0.211: 6
  Chirality restraints: 1576
  Sorted by residual:
  chirality pdb=" CA  ILE C 206 "
            pdb=" N   ILE C 206 "
            pdb=" C   ILE C 206 "
            pdb=" CB  ILE C 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  ILE D 206 "
            pdb=" N   ILE D 206 "
            pdb=" C   ILE D 206 "
            pdb=" CB  ILE D 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CA  ILE A 206 "
            pdb=" N   ILE A 206 "
            pdb=" C   ILE A 206 "
            pdb=" CB  ILE A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.08e+00
  ... (remaining 1573 not shown)

  Planarity restraints: 1796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 207 "   -0.045 5.00e-02 4.00e+02   6.77e-02 7.33e+00
        pdb=" N   PRO D 208 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO D 208 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO D 208 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 207 "   -0.045 5.00e-02 4.00e+02   6.76e-02 7.30e+00
        pdb=" N   PRO C 208 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO C 208 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO C 208 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 207 "    0.044 5.00e-02 4.00e+02   6.74e-02 7.27e+00
        pdb=" N   PRO B 208 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO B 208 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 208 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1793 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 301
        2.72 -     3.26: 9851
        3.26 -     3.81: 15900
        3.81 -     4.35: 20720
        4.35 -     4.90: 35089
  Nonbonded interactions: 81861
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C  94 "
            pdb=" OE2 GLU C 335 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OH  TYR B  94 "
            pdb=" OE2 GLU B 335 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OH  TYR D  94 "
            pdb=" OE2 GLU D 335 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OH  TYR A  94 "
            pdb=" OE2 GLU A 335 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OE2 GLU C 172 "
            pdb=" NH1 ARG C 248 "
     model   vdw
     2.238 3.120
  ... (remaining 81856 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     25.230
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
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      :  0.004   0.041  10216  Z= 0.272
  Angle     :  0.640   7.427  13848  Z= 0.418
  Chirality :  0.049   0.211   1576
  Planarity :  0.005   0.068   1796
  Dihedral  : 15.696  84.451   3636
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 13.64 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.25), residues: 1328
  helix:  1.79 (0.26), residues: 392
  sheet: -0.38 (0.36), residues: 232
  loop : -0.03 (0.27), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 313 
 HIS   0.002   0.001   HIS A  53 
 PHE   0.007   0.001   PHE C 233 
 TYR   0.008   0.001   TYR B 314 
 ARG   0.006   0.001   ARG A 234 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 170
  time to evaluate  : 1.185 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.6871 (m-30) cc_final: 0.6466 (m-30)
REVERT: A   37 PHE cc_start: 0.6293 (m-80) cc_final: 0.5841 (m-80)
REVERT: A   57 HIS cc_start: 0.5836 (m-70) cc_final: 0.5613 (m170)
REVERT: A  130 MET cc_start: 0.7661 (mtm) cc_final: 0.7311 (mtm)
REVERT: A  138 GLU cc_start: 0.6885 (mm-30) cc_final: 0.5028 (pm20)
REVERT: A  141 ASP cc_start: 0.5363 (p0) cc_final: 0.4807 (t0)
REVERT: A  145 LYS cc_start: 0.6942 (mtmt) cc_final: 0.6634 (mmtt)
REVERT: A  223 GLU cc_start: 0.5866 (mp0) cc_final: 0.5389 (mp0)
REVERT: A  239 ASN cc_start: 0.5141 (OUTLIER) cc_final: 0.4854 (t0)
REVERT: A  250 GLU cc_start: 0.6714 (tt0) cc_final: 0.5936 (tp30)
REVERT: A  264 GLN cc_start: 0.6574 (tt0) cc_final: 0.5998 (mt0)
REVERT: A  280 GLN cc_start: 0.6956 (mm-40) cc_final: 0.6736 (mm-40)
REVERT: A  331 MET cc_start: 0.6669 (mtp) cc_final: 0.6316 (mtp)
REVERT: B   29 ASP cc_start: 0.6852 (m-30) cc_final: 0.6456 (m-30)
REVERT: B   37 PHE cc_start: 0.6285 (m-80) cc_final: 0.5813 (m-80)
REVERT: B   57 HIS cc_start: 0.5823 (m-70) cc_final: 0.5607 (m170)
REVERT: B  106 GLU cc_start: 0.6206 (tm-30) cc_final: 0.5393 (tp30)
REVERT: B  130 MET cc_start: 0.7658 (mtm) cc_final: 0.7323 (mtm)
REVERT: B  138 GLU cc_start: 0.6884 (mm-30) cc_final: 0.5014 (pm20)
REVERT: B  141 ASP cc_start: 0.5326 (p0) cc_final: 0.4824 (t0)
REVERT: B  145 LYS cc_start: 0.6905 (mtmt) cc_final: 0.6627 (mmtt)
REVERT: B  223 GLU cc_start: 0.5876 (mp0) cc_final: 0.5383 (mp0)
REVERT: B  239 ASN cc_start: 0.5162 (OUTLIER) cc_final: 0.4897 (t0)
REVERT: B  250 GLU cc_start: 0.6646 (tt0) cc_final: 0.5889 (tp30)
REVERT: B  264 GLN cc_start: 0.6524 (tt0) cc_final: 0.5959 (mt0)
REVERT: B  280 GLN cc_start: 0.6962 (mm-40) cc_final: 0.6688 (mm-40)
REVERT: B  331 MET cc_start: 0.6676 (mtp) cc_final: 0.6327 (mtp)
REVERT: C   29 ASP cc_start: 0.6849 (m-30) cc_final: 0.6455 (m-30)
REVERT: C   37 PHE cc_start: 0.6276 (m-80) cc_final: 0.5804 (m-80)
REVERT: C   57 HIS cc_start: 0.5819 (m-70) cc_final: 0.5593 (m170)
REVERT: C  106 GLU cc_start: 0.6243 (tm-30) cc_final: 0.5420 (tp30)
REVERT: C  130 MET cc_start: 0.7657 (mtm) cc_final: 0.7322 (mtm)
REVERT: C  138 GLU cc_start: 0.6883 (mm-30) cc_final: 0.5007 (pm20)
REVERT: C  141 ASP cc_start: 0.5344 (p0) cc_final: 0.4828 (t0)
REVERT: C  145 LYS cc_start: 0.6895 (mtmt) cc_final: 0.6619 (mmtt)
REVERT: C  223 GLU cc_start: 0.5862 (mp0) cc_final: 0.5369 (mp0)
REVERT: C  234 ARG cc_start: 0.6996 (mtt-85) cc_final: 0.6795 (mtt-85)
REVERT: C  239 ASN cc_start: 0.5158 (OUTLIER) cc_final: 0.4883 (t0)
REVERT: C  250 GLU cc_start: 0.6676 (tt0) cc_final: 0.5936 (tp30)
REVERT: C  264 GLN cc_start: 0.6539 (tt0) cc_final: 0.5974 (mt0)
REVERT: C  280 GLN cc_start: 0.6959 (mm-40) cc_final: 0.6685 (mm-40)
REVERT: C  331 MET cc_start: 0.6664 (mtp) cc_final: 0.6313 (mtp)
REVERT: D   29 ASP cc_start: 0.6869 (m-30) cc_final: 0.6454 (m-30)
REVERT: D   37 PHE cc_start: 0.6305 (m-80) cc_final: 0.5828 (m-80)
REVERT: D   57 HIS cc_start: 0.5835 (m-70) cc_final: 0.5612 (m170)
REVERT: D  106 GLU cc_start: 0.6194 (tm-30) cc_final: 0.5380 (tp30)
REVERT: D  130 MET cc_start: 0.7671 (mtm) cc_final: 0.7318 (mtm)
REVERT: D  138 GLU cc_start: 0.6884 (mm-30) cc_final: 0.5019 (pm20)
REVERT: D  141 ASP cc_start: 0.5302 (p0) cc_final: 0.4801 (t0)
REVERT: D  145 LYS cc_start: 0.6869 (mtmt) cc_final: 0.6636 (mmtt)
REVERT: D  223 GLU cc_start: 0.5885 (mp0) cc_final: 0.5400 (mp0)
REVERT: D  239 ASN cc_start: 0.5162 (OUTLIER) cc_final: 0.4901 (t0)
REVERT: D  250 GLU cc_start: 0.6667 (tt0) cc_final: 0.5909 (tp30)
REVERT: D  264 GLN cc_start: 0.6546 (tt0) cc_final: 0.5981 (mt0)
REVERT: D  280 GLN cc_start: 0.6962 (mm-40) cc_final: 0.6691 (mm-40)
REVERT: D  331 MET cc_start: 0.6685 (mtp) cc_final: 0.6321 (mtp)
  outliers start: 8
  outliers final: 0
  residues processed: 174
  average time/residue: 1.5305
  time to fit residues: 282.1781
Evaluate side-chains
  132 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 128
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain C residue  239 ASN
Chi-restraints excluded: chain D residue  239 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 100 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 67 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 77 optimal weight:   20.0000
   chunk 119 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:
A 142 ASN
A 239 ASN
B 142 ASN
B 239 ASN
C 142 ASN
C 239 ASN
D 142 ASN
D 239 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10216  Z= 0.214
  Angle     :  0.653   7.867  13848  Z= 0.365
  Chirality :  0.050   0.241   1576
  Planarity :  0.006   0.060   1796
  Dihedral  :  4.820  19.111   1420
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 1.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 13.26 %
    Favored  : 85.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.25), residues: 1328
  helix:  1.55 (0.26), residues: 392
  sheet: -0.36 (0.38), residues: 204
  loop : -0.17 (0.26), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  87 
 HIS   0.005   0.001   HIS B  53 
 PHE   0.014   0.002   PHE A 233 
 TYR   0.017   0.002   TYR A 314 
 ARG   0.004   0.001   ARG C 234 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 1.211 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.6886 (m-30) cc_final: 0.6505 (m-30)
REVERT: A  107 LYS cc_start: 0.6281 (mttt) cc_final: 0.5985 (mtpp)
REVERT: A  130 MET cc_start: 0.7649 (mtm) cc_final: 0.7344 (mtm)
REVERT: A  138 GLU cc_start: 0.6825 (mm-30) cc_final: 0.5144 (pm20)
REVERT: A  142 ASN cc_start: 0.5907 (m-40) cc_final: 0.5653 (p0)
REVERT: A  143 SER cc_start: 0.6757 (m) cc_final: 0.6010 (p)
REVERT: A  250 GLU cc_start: 0.6754 (tt0) cc_final: 0.6068 (mt-10)
REVERT: A  264 GLN cc_start: 0.6564 (tt0) cc_final: 0.6023 (mt0)
REVERT: A  280 GLN cc_start: 0.7073 (mm-40) cc_final: 0.6843 (mm-40)
REVERT: A  331 MET cc_start: 0.6697 (mtp) cc_final: 0.6328 (mtp)
REVERT: B   29 ASP cc_start: 0.6887 (m-30) cc_final: 0.6511 (m-30)
REVERT: B  107 LYS cc_start: 0.6285 (mttt) cc_final: 0.5972 (mtpp)
REVERT: B  130 MET cc_start: 0.7648 (mtm) cc_final: 0.7345 (mtm)
REVERT: B  138 GLU cc_start: 0.6822 (mm-30) cc_final: 0.5139 (pm20)
REVERT: B  142 ASN cc_start: 0.5916 (m-40) cc_final: 0.5576 (p0)
REVERT: B  143 SER cc_start: 0.6741 (m) cc_final: 0.5991 (p)
REVERT: B  145 LYS cc_start: 0.7346 (mtmt) cc_final: 0.7031 (mmtt)
REVERT: B  250 GLU cc_start: 0.6752 (tt0) cc_final: 0.6126 (mm-30)
REVERT: B  264 GLN cc_start: 0.6561 (tt0) cc_final: 0.6022 (mt0)
REVERT: B  280 GLN cc_start: 0.7065 (mm-40) cc_final: 0.6835 (mm-40)
REVERT: B  331 MET cc_start: 0.6715 (mtp) cc_final: 0.6355 (mtp)
REVERT: C   29 ASP cc_start: 0.6887 (m-30) cc_final: 0.6509 (m-30)
REVERT: C  107 LYS cc_start: 0.6300 (mttt) cc_final: 0.5986 (mtpp)
REVERT: C  130 MET cc_start: 0.7652 (mtm) cc_final: 0.7349 (mtm)
REVERT: C  138 GLU cc_start: 0.6823 (mm-30) cc_final: 0.5149 (pm20)
REVERT: C  142 ASN cc_start: 0.5901 (m-40) cc_final: 0.5640 (p0)
REVERT: C  143 SER cc_start: 0.6756 (m) cc_final: 0.6011 (p)
REVERT: C  234 ARG cc_start: 0.7091 (mtt-85) cc_final: 0.6405 (mmt90)
REVERT: C  250 GLU cc_start: 0.6751 (tt0) cc_final: 0.6133 (mm-30)
REVERT: C  264 GLN cc_start: 0.6562 (tt0) cc_final: 0.6021 (mt0)
REVERT: C  280 GLN cc_start: 0.7066 (mm-40) cc_final: 0.6838 (mm-40)
REVERT: C  331 MET cc_start: 0.6714 (mtp) cc_final: 0.6352 (mtp)
REVERT: D   29 ASP cc_start: 0.6887 (m-30) cc_final: 0.6506 (m-30)
REVERT: D  107 LYS cc_start: 0.6301 (mttt) cc_final: 0.5989 (mtpp)
REVERT: D  130 MET cc_start: 0.7649 (mtm) cc_final: 0.7343 (mtm)
REVERT: D  138 GLU cc_start: 0.6821 (mm-30) cc_final: 0.5142 (pm20)
REVERT: D  142 ASN cc_start: 0.5892 (m-40) cc_final: 0.5656 (p0)
REVERT: D  143 SER cc_start: 0.6782 (m) cc_final: 0.6045 (p)
REVERT: D  250 GLU cc_start: 0.6752 (tt0) cc_final: 0.6125 (mm-30)
REVERT: D  264 GLN cc_start: 0.6557 (tt0) cc_final: 0.6038 (mt0)
REVERT: D  280 GLN cc_start: 0.7064 (mm-40) cc_final: 0.6835 (mm-40)
REVERT: D  331 MET cc_start: 0.6711 (mtp) cc_final: 0.6349 (mtp)
  outliers start: 13
  outliers final: 12
  residues processed: 142
  average time/residue: 1.4739
  time to fit residues: 222.9093
Evaluate side-chains
  137 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 1.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 66 optimal weight:   20.0000
   chunk 37 optimal weight:    7.9990
   chunk 99 optimal weight:   20.0000
   chunk 81 optimal weight:    0.9980
   chunk 33 optimal weight:   20.0000
   chunk 120 optimal weight:    0.5980
   chunk 129 optimal weight:   10.0000
   chunk 106 optimal weight:    8.9990
   chunk 119 optimal weight:    1.9990
   chunk 40 optimal weight:    8.9990
   chunk 96 optimal weight:    9.9990
   overall best weight:    4.1186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10216  Z= 0.291
  Angle     :  0.763   8.954  13848  Z= 0.428
  Chirality :  0.054   0.322   1576
  Planarity :  0.007   0.064   1796
  Dihedral  :  5.085  17.495   1412
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 1.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.69 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.24), residues: 1328
  helix:  1.23 (0.26), residues: 392
  sheet: -0.46 (0.39), residues: 176
  loop : -0.04 (0.24), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C 313 
 HIS   0.006   0.001   HIS A  53 
 PHE   0.016   0.003   PHE A 233 
 TYR   0.018   0.003   TYR D 314 
 ARG   0.003   0.001   ARG C 234 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 1.345 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.6846 (m-30) cc_final: 0.6543 (m-30)
REVERT: A  107 LYS cc_start: 0.6195 (mttt) cc_final: 0.5953 (mtpp)
REVERT: A  130 MET cc_start: 0.7641 (mtm) cc_final: 0.7402 (mtm)
REVERT: A  138 GLU cc_start: 0.6867 (mm-30) cc_final: 0.5253 (pm20)
REVERT: A  143 SER cc_start: 0.6684 (m) cc_final: 0.6370 (p)
REVERT: A  250 GLU cc_start: 0.6747 (tt0) cc_final: 0.6079 (mt-10)
REVERT: A  264 GLN cc_start: 0.6514 (tt0) cc_final: 0.5992 (mt0)
REVERT: A  280 GLN cc_start: 0.7123 (mm-40) cc_final: 0.6855 (mm-40)
REVERT: A  331 MET cc_start: 0.6707 (mtp) cc_final: 0.6357 (mtp)
REVERT: B   29 ASP cc_start: 0.6849 (m-30) cc_final: 0.6548 (m-30)
REVERT: B  107 LYS cc_start: 0.6189 (mttt) cc_final: 0.5877 (mtpp)
REVERT: B  130 MET cc_start: 0.7654 (mtm) cc_final: 0.7415 (mtm)
REVERT: B  138 GLU cc_start: 0.6870 (mm-30) cc_final: 0.5286 (pm20)
REVERT: B  143 SER cc_start: 0.6682 (OUTLIER) cc_final: 0.6363 (p)
REVERT: B  145 LYS cc_start: 0.7454 (mtmt) cc_final: 0.7065 (mmtm)
REVERT: B  250 GLU cc_start: 0.6748 (tt0) cc_final: 0.6078 (mt-10)
REVERT: B  264 GLN cc_start: 0.6494 (tt0) cc_final: 0.5976 (mt0)
REVERT: B  280 GLN cc_start: 0.7122 (mm-40) cc_final: 0.6853 (mm-40)
REVERT: B  331 MET cc_start: 0.6708 (mtp) cc_final: 0.6328 (mtp)
REVERT: C   29 ASP cc_start: 0.6848 (m-30) cc_final: 0.6546 (m-30)
REVERT: C  107 LYS cc_start: 0.6190 (mttt) cc_final: 0.5878 (mtpp)
REVERT: C  130 MET cc_start: 0.7657 (mtm) cc_final: 0.7418 (mtm)
REVERT: C  138 GLU cc_start: 0.6868 (mm-30) cc_final: 0.5283 (pm20)
REVERT: C  143 SER cc_start: 0.6683 (m) cc_final: 0.6368 (p)
REVERT: C  250 GLU cc_start: 0.6747 (tt0) cc_final: 0.6079 (mt-10)
REVERT: C  264 GLN cc_start: 0.6512 (tt0) cc_final: 0.5989 (mt0)
REVERT: C  280 GLN cc_start: 0.7122 (mm-40) cc_final: 0.6855 (mm-40)
REVERT: C  331 MET cc_start: 0.6706 (mtp) cc_final: 0.6357 (mtp)
REVERT: D   29 ASP cc_start: 0.6849 (m-30) cc_final: 0.6545 (m-30)
REVERT: D  107 LYS cc_start: 0.6183 (mttt) cc_final: 0.5870 (mtpp)
REVERT: D  130 MET cc_start: 0.7655 (mtm) cc_final: 0.7416 (mtm)
REVERT: D  138 GLU cc_start: 0.6866 (mm-30) cc_final: 0.5294 (pm20)
REVERT: D  143 SER cc_start: 0.6688 (m) cc_final: 0.6369 (p)
REVERT: D  250 GLU cc_start: 0.6745 (tt0) cc_final: 0.6077 (mt-10)
REVERT: D  264 GLN cc_start: 0.6512 (tt0) cc_final: 0.5989 (mt0)
REVERT: D  280 GLN cc_start: 0.7111 (mm-40) cc_final: 0.6844 (mm-40)
REVERT: D  331 MET cc_start: 0.6710 (mtp) cc_final: 0.6360 (mtp)
  outliers start: 17
  outliers final: 13
  residues processed: 130
  average time/residue: 1.6446
  time to fit residues: 226.2808
Evaluate side-chains
  128 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  271 LYS
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  271 LYS
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 118 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9980
   chunk 62 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 57 optimal weight:   40.0000
   chunk 80 optimal weight:    0.3980
   chunk 120 optimal weight:    4.9990
   chunk 127 optimal weight:    0.5980
   chunk 114 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 106 optimal weight:    0.8980
   overall best weight:    1.1782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017  10216  Z= 0.153
  Angle     :  0.562   6.960  13848  Z= 0.313
  Chirality :  0.047   0.203   1576
  Planarity :  0.005   0.058   1796
  Dihedral  :  4.658  19.138   1412
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.93 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.24), residues: 1328
  helix:  1.57 (0.26), residues: 396
  sheet: -0.15 (0.40), residues: 176
  loop : -0.12 (0.24), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  87 
 HIS   0.003   0.001   HIS D  53 
 PHE   0.013   0.001   PHE D 233 
 TYR   0.012   0.001   TYR A 314 
 ARG   0.001   0.000   ARG A  16 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 1.163 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.6854 (m-30) cc_final: 0.6516 (m-30)
REVERT: A  107 LYS cc_start: 0.6076 (mttt) cc_final: 0.5869 (mtpp)
REVERT: A  130 MET cc_start: 0.7655 (mtm) cc_final: 0.7405 (mtm)
REVERT: A  138 GLU cc_start: 0.6723 (mm-30) cc_final: 0.5158 (pm20)
REVERT: A  143 SER cc_start: 0.6662 (m) cc_final: 0.6378 (p)
REVERT: A  223 GLU cc_start: 0.5765 (mp0) cc_final: 0.5392 (mp0)
REVERT: A  250 GLU cc_start: 0.6758 (tt0) cc_final: 0.6042 (mt-10)
REVERT: A  264 GLN cc_start: 0.6454 (tt0) cc_final: 0.5927 (mt0)
REVERT: A  280 GLN cc_start: 0.7111 (mm-40) cc_final: 0.6862 (mm-40)
REVERT: A  331 MET cc_start: 0.6699 (mtp) cc_final: 0.6359 (mtp)
REVERT: B   29 ASP cc_start: 0.6856 (m-30) cc_final: 0.6521 (m-30)
REVERT: B  107 LYS cc_start: 0.6052 (mttt) cc_final: 0.5850 (mtpp)
REVERT: B  130 MET cc_start: 0.7654 (mtm) cc_final: 0.7403 (mtm)
REVERT: B  138 GLU cc_start: 0.6723 (mm-30) cc_final: 0.5158 (pm20)
REVERT: B  143 SER cc_start: 0.6660 (m) cc_final: 0.6382 (p)
REVERT: B  223 GLU cc_start: 0.5778 (mp0) cc_final: 0.5382 (mp0)
REVERT: B  250 GLU cc_start: 0.6767 (tt0) cc_final: 0.6044 (mt-10)
REVERT: B  264 GLN cc_start: 0.6453 (tt0) cc_final: 0.5926 (mt0)
REVERT: B  280 GLN cc_start: 0.7111 (mm-40) cc_final: 0.6860 (mm-40)
REVERT: B  331 MET cc_start: 0.6700 (mtp) cc_final: 0.6362 (mtp)
REVERT: C   29 ASP cc_start: 0.6865 (m-30) cc_final: 0.6520 (m-30)
REVERT: C  107 LYS cc_start: 0.6054 (mttt) cc_final: 0.5850 (mtpp)
REVERT: C  130 MET cc_start: 0.7657 (mtm) cc_final: 0.7406 (mtm)
REVERT: C  138 GLU cc_start: 0.6724 (mm-30) cc_final: 0.5160 (pm20)
REVERT: C  143 SER cc_start: 0.6660 (m) cc_final: 0.6376 (p)
REVERT: C  223 GLU cc_start: 0.5778 (mp0) cc_final: 0.5381 (mp0)
REVERT: C  250 GLU cc_start: 0.6760 (tt0) cc_final: 0.6036 (mt-10)
REVERT: C  264 GLN cc_start: 0.6452 (tt0) cc_final: 0.5926 (mt0)
REVERT: C  280 GLN cc_start: 0.7111 (mm-40) cc_final: 0.6861 (mm-40)
REVERT: C  331 MET cc_start: 0.6699 (mtp) cc_final: 0.6359 (mtp)
REVERT: D   29 ASP cc_start: 0.6831 (m-30) cc_final: 0.6520 (m-30)
REVERT: D  107 LYS cc_start: 0.6055 (mttt) cc_final: 0.5852 (mtpp)
REVERT: D  130 MET cc_start: 0.7662 (mtm) cc_final: 0.7407 (mtm)
REVERT: D  138 GLU cc_start: 0.6720 (mm-30) cc_final: 0.5158 (pm20)
REVERT: D  143 SER cc_start: 0.6664 (m) cc_final: 0.6378 (p)
REVERT: D  223 GLU cc_start: 0.5775 (mp0) cc_final: 0.5380 (mp0)
REVERT: D  250 GLU cc_start: 0.6758 (tt0) cc_final: 0.6042 (mt-10)
REVERT: D  264 GLN cc_start: 0.6450 (tt0) cc_final: 0.5918 (mt0)
REVERT: D  280 GLN cc_start: 0.7111 (mm-40) cc_final: 0.6861 (mm-40)
REVERT: D  331 MET cc_start: 0.6698 (mtp) cc_final: 0.6361 (mtp)
  outliers start: 20
  outliers final: 8
  residues processed: 137
  average time/residue: 1.5942
  time to fit residues: 231.9312
Evaluate side-chains
  128 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 72 optimal weight:    8.9990
   chunk 1 optimal weight:    9.9990
   chunk 95 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 108 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0070
   chunk 0 optimal weight:   20.0000
   chunk 65 optimal weight:    5.9990
   chunk 114 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    1.4004

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019  10216  Z= 0.160
  Angle     :  0.570   7.125  13848  Z= 0.319
  Chirality :  0.047   0.208   1576
  Planarity :  0.005   0.060   1796
  Dihedral  :  4.664  19.730   1412
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.88 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.24), residues: 1328
  helix:  1.59 (0.26), residues: 396
  sheet: -0.17 (0.39), residues: 176
  loop : -0.15 (0.24), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  87 
 HIS   0.003   0.001   HIS D  53 
 PHE   0.013   0.001   PHE C 233 
 TYR   0.013   0.002   TYR C 314 
 ARG   0.001   0.000   ARG C  16 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 1.220 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.6849 (m-30) cc_final: 0.6534 (m-30)
REVERT: A  130 MET cc_start: 0.7661 (mtm) cc_final: 0.7403 (mtm)
REVERT: A  138 GLU cc_start: 0.6688 (mm-30) cc_final: 0.5093 (pm20)
REVERT: A  143 SER cc_start: 0.6661 (m) cc_final: 0.6402 (p)
REVERT: A  223 GLU cc_start: 0.5785 (mp0) cc_final: 0.5408 (mp0)
REVERT: A  250 GLU cc_start: 0.6809 (tt0) cc_final: 0.6066 (mt-10)
REVERT: A  264 GLN cc_start: 0.6449 (tt0) cc_final: 0.5921 (mt0)
REVERT: A  280 GLN cc_start: 0.7117 (mm-40) cc_final: 0.6857 (mm-40)
REVERT: A  331 MET cc_start: 0.6701 (mtp) cc_final: 0.6269 (mtp)
REVERT: B   29 ASP cc_start: 0.6874 (m-30) cc_final: 0.6537 (m-30)
REVERT: B  130 MET cc_start: 0.7661 (mtm) cc_final: 0.7406 (mtm)
REVERT: B  138 GLU cc_start: 0.6689 (mm-30) cc_final: 0.5095 (pm20)
REVERT: B  143 SER cc_start: 0.6659 (m) cc_final: 0.6405 (p)
REVERT: B  223 GLU cc_start: 0.5795 (mp0) cc_final: 0.5405 (mp0)
REVERT: B  250 GLU cc_start: 0.6810 (tt0) cc_final: 0.6064 (mt-10)
REVERT: B  264 GLN cc_start: 0.6448 (tt0) cc_final: 0.5920 (mt0)
REVERT: B  280 GLN cc_start: 0.7116 (mm-40) cc_final: 0.6855 (mm-40)
REVERT: B  331 MET cc_start: 0.6704 (mtp) cc_final: 0.6273 (mtp)
REVERT: C   29 ASP cc_start: 0.6850 (m-30) cc_final: 0.6535 (m-30)
REVERT: C  130 MET cc_start: 0.7664 (mtm) cc_final: 0.7407 (mtm)
REVERT: C  138 GLU cc_start: 0.6689 (mm-30) cc_final: 0.5127 (pm20)
REVERT: C  143 SER cc_start: 0.6660 (m) cc_final: 0.6399 (p)
REVERT: C  223 GLU cc_start: 0.5796 (mp0) cc_final: 0.5406 (mp0)
REVERT: C  250 GLU cc_start: 0.6811 (tt0) cc_final: 0.6067 (mt-10)
REVERT: C  264 GLN cc_start: 0.6448 (tt0) cc_final: 0.5920 (mt0)
REVERT: C  280 GLN cc_start: 0.7116 (mm-40) cc_final: 0.6855 (mm-40)
REVERT: C  331 MET cc_start: 0.6702 (mtp) cc_final: 0.6270 (mtp)
REVERT: D   29 ASP cc_start: 0.6857 (m-30) cc_final: 0.6543 (m-30)
REVERT: D  130 MET cc_start: 0.7663 (mtm) cc_final: 0.7406 (mtm)
REVERT: D  138 GLU cc_start: 0.6688 (mm-30) cc_final: 0.5126 (pm20)
REVERT: D  143 SER cc_start: 0.6662 (m) cc_final: 0.6401 (p)
REVERT: D  223 GLU cc_start: 0.5793 (mp0) cc_final: 0.5405 (mp0)
REVERT: D  250 GLU cc_start: 0.6812 (tt0) cc_final: 0.6062 (mt-10)
REVERT: D  264 GLN cc_start: 0.6457 (tt0) cc_final: 0.5929 (mt0)
REVERT: D  280 GLN cc_start: 0.7115 (mm-40) cc_final: 0.6855 (mm-40)
REVERT: D  331 MET cc_start: 0.6700 (mtp) cc_final: 0.6269 (mtp)
  outliers start: 21
  outliers final: 16
  residues processed: 133
  average time/residue: 1.5145
  time to fit residues: 214.4131
Evaluate side-chains
  128 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 114 optimal weight:    6.9990
   chunk 25 optimal weight:    8.9990
   chunk 74 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   chunk 127 optimal weight:    0.4980
   chunk 106 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   chunk 42 optimal weight:    0.7980
   chunk 67 optimal weight:    9.9990
   chunk 123 optimal weight:    0.6980
   overall best weight:    1.5982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019  10216  Z= 0.169
  Angle     :  0.582   7.341  13848  Z= 0.326
  Chirality :  0.048   0.215   1576
  Planarity :  0.005   0.059   1796
  Dihedral  :  4.713  20.189   1412
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 1.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 13.83 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.24), residues: 1328
  helix:  1.58 (0.26), residues: 392
  sheet: -0.17 (0.40), residues: 176
  loop : -0.05 (0.25), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  87 
 HIS   0.003   0.001   HIS D  53 
 PHE   0.013   0.001   PHE A 233 
 TYR   0.013   0.002   TYR D 314 
 ARG   0.001   0.000   ARG B  16 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 116
  time to evaluate  : 1.206 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.6869 (m-30) cc_final: 0.6542 (m-30)
REVERT: A  130 MET cc_start: 0.7660 (mtm) cc_final: 0.7400 (mtm)
REVERT: A  138 GLU cc_start: 0.6688 (mm-30) cc_final: 0.5128 (pm20)
REVERT: A  143 SER cc_start: 0.6651 (m) cc_final: 0.6383 (p)
REVERT: A  223 GLU cc_start: 0.5783 (mp0) cc_final: 0.5402 (mp0)
REVERT: A  250 GLU cc_start: 0.6838 (tt0) cc_final: 0.6146 (tm-30)
REVERT: A  264 GLN cc_start: 0.6451 (tt0) cc_final: 0.5921 (mt0)
REVERT: A  280 GLN cc_start: 0.7109 (mm-40) cc_final: 0.6848 (mm-40)
REVERT: A  331 MET cc_start: 0.6704 (mtp) cc_final: 0.6293 (mtp)
REVERT: B   29 ASP cc_start: 0.6871 (m-30) cc_final: 0.6544 (m-30)
REVERT: B  130 MET cc_start: 0.7667 (mtm) cc_final: 0.7408 (mtm)
REVERT: B  138 GLU cc_start: 0.6688 (mm-30) cc_final: 0.5128 (pm20)
REVERT: B  143 SER cc_start: 0.6653 (m) cc_final: 0.6407 (p)
REVERT: B  223 GLU cc_start: 0.5795 (mp0) cc_final: 0.5392 (mp0)
REVERT: B  250 GLU cc_start: 0.6844 (tt0) cc_final: 0.6147 (tm-30)
REVERT: B  264 GLN cc_start: 0.6450 (tt0) cc_final: 0.5920 (mt0)
REVERT: B  280 GLN cc_start: 0.7108 (mm-40) cc_final: 0.6847 (mm-40)
REVERT: B  331 MET cc_start: 0.6709 (mtp) cc_final: 0.6302 (mtp)
REVERT: C   29 ASP cc_start: 0.6872 (m-30) cc_final: 0.6543 (m-30)
REVERT: C  130 MET cc_start: 0.7670 (mtm) cc_final: 0.7410 (mtm)
REVERT: C  138 GLU cc_start: 0.6689 (mm-30) cc_final: 0.5129 (pm20)
REVERT: C  143 SER cc_start: 0.6650 (m) cc_final: 0.6382 (p)
REVERT: C  223 GLU cc_start: 0.5793 (mp0) cc_final: 0.5390 (mp0)
REVERT: C  250 GLU cc_start: 0.6840 (tt0) cc_final: 0.6149 (tm-30)
REVERT: C  264 GLN cc_start: 0.6450 (tt0) cc_final: 0.5920 (mt0)
REVERT: C  280 GLN cc_start: 0.7108 (mm-40) cc_final: 0.6848 (mm-40)
REVERT: C  331 MET cc_start: 0.6707 (mtp) cc_final: 0.6301 (mtp)
REVERT: D   29 ASP cc_start: 0.6871 (m-30) cc_final: 0.6543 (m-30)
REVERT: D  130 MET cc_start: 0.7660 (mtm) cc_final: 0.7400 (mtm)
REVERT: D  138 GLU cc_start: 0.6687 (mm-30) cc_final: 0.5129 (pm20)
REVERT: D  143 SER cc_start: 0.6653 (m) cc_final: 0.6384 (p)
REVERT: D  223 GLU cc_start: 0.5799 (mp0) cc_final: 0.5401 (mp0)
REVERT: D  250 GLU cc_start: 0.6841 (tt0) cc_final: 0.6144 (tm-30)
REVERT: D  264 GLN cc_start: 0.6451 (tt0) cc_final: 0.5919 (mt0)
REVERT: D  280 GLN cc_start: 0.7108 (mm-40) cc_final: 0.6847 (mm-40)
REVERT: D  331 MET cc_start: 0.6704 (mtp) cc_final: 0.6299 (mtp)
  outliers start: 22
  outliers final: 20
  residues processed: 134
  average time/residue: 1.4260
  time to fit residues: 204.0757
Evaluate side-chains
  136 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 1.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 14 optimal weight:    0.2980
   chunk 72 optimal weight:   10.0000
   chunk 93 optimal weight:    4.9990
   chunk 107 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 127 optimal weight:    0.3980
   chunk 79 optimal weight:    2.9990
   chunk 77 optimal weight:    0.2980
   chunk 58 optimal weight:    6.9990
   chunk 78 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   overall best weight:    1.5984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019  10216  Z= 0.168
  Angle     :  0.583   7.522  13848  Z= 0.326
  Chirality :  0.048   0.222   1576
  Planarity :  0.005   0.064   1796
  Dihedral  :  4.716  20.175   1412
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 1.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.83 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.24), residues: 1328
  helix:  1.60 (0.27), residues: 392
  sheet: -0.20 (0.39), residues: 176
  loop : -0.06 (0.25), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  87 
 HIS   0.003   0.001   HIS C  53 
 PHE   0.013   0.001   PHE A 233 
 TYR   0.014   0.002   TYR D 314 
 ARG   0.001   0.000   ARG C  16 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 1.128 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.6867 (m-30) cc_final: 0.6542 (m-30)
REVERT: A  130 MET cc_start: 0.7659 (mtm) cc_final: 0.7399 (mtm)
REVERT: A  138 GLU cc_start: 0.6685 (mm-30) cc_final: 0.5112 (pm20)
REVERT: A  143 SER cc_start: 0.6651 (m) cc_final: 0.6382 (p)
REVERT: A  223 GLU cc_start: 0.5783 (mp0) cc_final: 0.5400 (mp0)
REVERT: A  250 GLU cc_start: 0.6830 (tt0) cc_final: 0.6120 (tm-30)
REVERT: A  264 GLN cc_start: 0.6454 (tt0) cc_final: 0.5922 (mt0)
REVERT: A  280 GLN cc_start: 0.7128 (mm-40) cc_final: 0.6855 (mm-40)
REVERT: A  331 MET cc_start: 0.6701 (mtp) cc_final: 0.6306 (mtp)
REVERT: B   29 ASP cc_start: 0.6868 (m-30) cc_final: 0.6544 (m-30)
REVERT: B  130 MET cc_start: 0.7657 (mtm) cc_final: 0.7397 (mtm)
REVERT: B  138 GLU cc_start: 0.6686 (mm-30) cc_final: 0.5113 (pm20)
REVERT: B  143 SER cc_start: 0.6655 (m) cc_final: 0.6408 (p)
REVERT: B  223 GLU cc_start: 0.5795 (mp0) cc_final: 0.5389 (mp0)
REVERT: B  250 GLU cc_start: 0.6832 (tt0) cc_final: 0.6121 (tm-30)
REVERT: B  264 GLN cc_start: 0.6453 (tt0) cc_final: 0.5920 (mt0)
REVERT: B  280 GLN cc_start: 0.7134 (mm-40) cc_final: 0.6864 (mm-40)
REVERT: B  331 MET cc_start: 0.6704 (mtp) cc_final: 0.6313 (mtp)
REVERT: C   29 ASP cc_start: 0.6844 (m-30) cc_final: 0.6543 (m-30)
REVERT: C  130 MET cc_start: 0.7661 (mtm) cc_final: 0.7400 (mtm)
REVERT: C  138 GLU cc_start: 0.6686 (mm-30) cc_final: 0.5114 (pm20)
REVERT: C  143 SER cc_start: 0.6651 (m) cc_final: 0.6381 (p)
REVERT: C  223 GLU cc_start: 0.5794 (mp0) cc_final: 0.5388 (mp0)
REVERT: C  250 GLU cc_start: 0.6832 (tt0) cc_final: 0.6121 (tm-30)
REVERT: C  264 GLN cc_start: 0.6453 (tt0) cc_final: 0.5922 (mt0)
REVERT: C  280 GLN cc_start: 0.7133 (mm-40) cc_final: 0.6865 (mm-40)
REVERT: C  331 MET cc_start: 0.6703 (mtp) cc_final: 0.6311 (mtp)
REVERT: D   29 ASP cc_start: 0.6868 (m-30) cc_final: 0.6544 (m-30)
REVERT: D  130 MET cc_start: 0.7660 (mtm) cc_final: 0.7398 (mtm)
REVERT: D  138 GLU cc_start: 0.6685 (mm-30) cc_final: 0.5114 (pm20)
REVERT: D  143 SER cc_start: 0.6653 (m) cc_final: 0.6384 (p)
REVERT: D  223 GLU cc_start: 0.5791 (mp0) cc_final: 0.5396 (mp0)
REVERT: D  250 GLU cc_start: 0.6829 (tt0) cc_final: 0.6119 (tm-30)
REVERT: D  264 GLN cc_start: 0.6462 (tt0) cc_final: 0.5931 (mt0)
REVERT: D  280 GLN cc_start: 0.7133 (mm-40) cc_final: 0.6864 (mm-40)
REVERT: D  331 MET cc_start: 0.6701 (mtp) cc_final: 0.6311 (mtp)
  outliers start: 20
  outliers final: 20
  residues processed: 132
  average time/residue: 1.4641
  time to fit residues: 205.7357
Evaluate side-chains
  136 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 24 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9990
   chunk 86 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 11 optimal weight:   20.0000
   chunk 100 optimal weight:    2.9990
   chunk 115 optimal weight:    2.9990
   chunk 121 optimal weight:    1.9990
   chunk 111 optimal weight:    5.9990
   overall best weight:    1.9388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  10216  Z= 0.185
  Angle     :  0.611   7.982  13848  Z= 0.342
  Chirality :  0.049   0.240   1576
  Planarity :  0.006   0.066   1796
  Dihedral  :  4.790  19.924   1412
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 1.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 13.83 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.24), residues: 1328
  helix:  1.55 (0.26), residues: 392
  sheet: -0.25 (0.39), residues: 176
  loop : -0.05 (0.25), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  87 
 HIS   0.004   0.001   HIS D  53 
 PHE   0.013   0.002   PHE B 233 
 TYR   0.015   0.002   TYR D 314 
 ARG   0.002   0.000   ARG A  16 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 1.242 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.6810 (m-30) cc_final: 0.6496 (m-30)
REVERT: A  130 MET cc_start: 0.7656 (mtm) cc_final: 0.7393 (mtm)
REVERT: A  138 GLU cc_start: 0.6695 (mm-30) cc_final: 0.5134 (pm20)
REVERT: A  143 SER cc_start: 0.6655 (m) cc_final: 0.6374 (p)
REVERT: A  223 GLU cc_start: 0.5754 (mp0) cc_final: 0.5385 (mp0)
REVERT: A  250 GLU cc_start: 0.6829 (tt0) cc_final: 0.6302 (mm-30)
REVERT: A  260 LYS cc_start: 0.6604 (ttmm) cc_final: 0.5801 (ttpp)
REVERT: A  264 GLN cc_start: 0.6426 (tt0) cc_final: 0.5892 (mt0)
REVERT: A  280 GLN cc_start: 0.7131 (mm-40) cc_final: 0.6872 (mm-40)
REVERT: A  331 MET cc_start: 0.6700 (mtp) cc_final: 0.6314 (mtp)
REVERT: B   29 ASP cc_start: 0.6812 (m-30) cc_final: 0.6499 (m-30)
REVERT: B  130 MET cc_start: 0.7655 (mtm) cc_final: 0.7392 (mtm)
REVERT: B  138 GLU cc_start: 0.6696 (mm-30) cc_final: 0.5135 (pm20)
REVERT: B  143 SER cc_start: 0.6658 (m) cc_final: 0.6401 (p)
REVERT: B  223 GLU cc_start: 0.5767 (mp0) cc_final: 0.5394 (mp0)
REVERT: B  250 GLU cc_start: 0.6830 (tt0) cc_final: 0.6119 (tm-30)
REVERT: B  264 GLN cc_start: 0.6426 (tt0) cc_final: 0.5890 (mt0)
REVERT: B  280 GLN cc_start: 0.7130 (mm-40) cc_final: 0.6872 (mm-40)
REVERT: B  331 MET cc_start: 0.6703 (mtp) cc_final: 0.6319 (mtp)
REVERT: C   29 ASP cc_start: 0.6811 (m-30) cc_final: 0.6498 (m-30)
REVERT: C  130 MET cc_start: 0.7657 (mtm) cc_final: 0.7394 (mtm)
REVERT: C  138 GLU cc_start: 0.6696 (mm-30) cc_final: 0.5135 (pm20)
REVERT: C  143 SER cc_start: 0.6654 (m) cc_final: 0.6373 (p)
REVERT: C  223 GLU cc_start: 0.5766 (mp0) cc_final: 0.5394 (mp0)
REVERT: C  250 GLU cc_start: 0.6831 (tt0) cc_final: 0.6120 (tm-30)
REVERT: C  264 GLN cc_start: 0.6425 (tt0) cc_final: 0.5891 (mt0)
REVERT: C  280 GLN cc_start: 0.7131 (mm-40) cc_final: 0.6874 (mm-40)
REVERT: C  331 MET cc_start: 0.6701 (mtp) cc_final: 0.6317 (mtp)
REVERT: D   29 ASP cc_start: 0.6811 (m-30) cc_final: 0.6499 (m-30)
REVERT: D  130 MET cc_start: 0.7657 (mtm) cc_final: 0.7393 (mtm)
REVERT: D  138 GLU cc_start: 0.6694 (mm-30) cc_final: 0.5135 (pm20)
REVERT: D  143 SER cc_start: 0.6656 (m) cc_final: 0.6375 (p)
REVERT: D  223 GLU cc_start: 0.5762 (mp0) cc_final: 0.5352 (mp0)
REVERT: D  250 GLU cc_start: 0.6828 (tt0) cc_final: 0.6117 (tm-30)
REVERT: D  264 GLN cc_start: 0.6426 (tt0) cc_final: 0.5889 (mt0)
REVERT: D  280 GLN cc_start: 0.7129 (mm-40) cc_final: 0.6872 (mm-40)
REVERT: D  331 MET cc_start: 0.6700 (mtp) cc_final: 0.6318 (mtp)
  outliers start: 24
  outliers final: 20
  residues processed: 137
  average time/residue: 1.4487
  time to fit residues: 211.9671
Evaluate side-chains
  137 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 118 optimal weight:    5.9990
   chunk 121 optimal weight:    0.2980
   chunk 71 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 93 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 107 optimal weight:    3.9990
   chunk 112 optimal weight:    3.9990
   chunk 77 optimal weight:   10.0000
   chunk 125 optimal weight:    6.9990
   chunk 76 optimal weight:    7.9990
   overall best weight:    3.8588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10216  Z= 0.277
  Angle     :  0.740   9.466  13848  Z= 0.417
  Chirality :  0.053   0.311   1576
  Planarity :  0.007   0.070   1796
  Dihedral  :  5.105  18.962   1412
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 13.83 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.24), residues: 1328
  helix:  1.28 (0.26), residues: 392
  sheet: -0.50 (0.38), residues: 176
  loop : -0.08 (0.24), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 313 
 HIS   0.006   0.001   HIS B  53 
 PHE   0.017   0.003   PHE D 233 
 TYR   0.020   0.003   TYR D 314 
 ARG   0.004   0.001   ARG C 323 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 1.176 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.6888 (m-30) cc_final: 0.6585 (m-30)
REVERT: A  138 GLU cc_start: 0.6852 (mm-30) cc_final: 0.5268 (pm20)
REVERT: A  143 SER cc_start: 0.6694 (m) cc_final: 0.6368 (p)
REVERT: A  194 LYS cc_start: 0.5284 (OUTLIER) cc_final: 0.4966 (mmmm)
REVERT: A  250 GLU cc_start: 0.6823 (tt0) cc_final: 0.6315 (mm-30)
REVERT: A  260 LYS cc_start: 0.6623 (ttmm) cc_final: 0.6046 (tttp)
REVERT: A  264 GLN cc_start: 0.6414 (tt0) cc_final: 0.5857 (mt0)
REVERT: A  280 GLN cc_start: 0.7179 (mm-40) cc_final: 0.6853 (mm-40)
REVERT: A  331 MET cc_start: 0.6752 (mtp) cc_final: 0.6387 (mtp)
REVERT: B   29 ASP cc_start: 0.6889 (m-30) cc_final: 0.6587 (m-30)
REVERT: B  138 GLU cc_start: 0.6854 (mm-30) cc_final: 0.5269 (pm20)
REVERT: B  143 SER cc_start: 0.6683 (m) cc_final: 0.6377 (p)
REVERT: B  194 LYS cc_start: 0.5278 (OUTLIER) cc_final: 0.4954 (mmmm)
REVERT: B  250 GLU cc_start: 0.6835 (tt0) cc_final: 0.6138 (tm-30)
REVERT: B  260 LYS cc_start: 0.6622 (ttmm) cc_final: 0.6045 (tttp)
REVERT: B  264 GLN cc_start: 0.6413 (tt0) cc_final: 0.5855 (mt0)
REVERT: B  280 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6884 (mm-40)
REVERT: B  331 MET cc_start: 0.6750 (mtp) cc_final: 0.6388 (mtp)
REVERT: C   29 ASP cc_start: 0.6889 (m-30) cc_final: 0.6585 (m-30)
REVERT: C  130 MET cc_start: 0.7661 (mtm) cc_final: 0.7405 (mtm)
REVERT: C  138 GLU cc_start: 0.6854 (mm-30) cc_final: 0.5269 (pm20)
REVERT: C  143 SER cc_start: 0.6693 (m) cc_final: 0.6367 (p)
REVERT: C  194 LYS cc_start: 0.5267 (OUTLIER) cc_final: 0.4941 (mmmm)
REVERT: C  250 GLU cc_start: 0.6824 (tt0) cc_final: 0.6134 (tm-30)
REVERT: C  260 LYS cc_start: 0.6621 (ttmm) cc_final: 0.6045 (tttp)
REVERT: C  264 GLN cc_start: 0.6413 (tt0) cc_final: 0.5855 (mt0)
REVERT: C  280 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6885 (mm-40)
REVERT: C  331 MET cc_start: 0.6750 (mtp) cc_final: 0.6387 (mtp)
REVERT: D   29 ASP cc_start: 0.6888 (m-30) cc_final: 0.6586 (m-30)
REVERT: D  138 GLU cc_start: 0.6852 (mm-30) cc_final: 0.5269 (pm20)
REVERT: D  143 SER cc_start: 0.6697 (m) cc_final: 0.6368 (p)
REVERT: D  194 LYS cc_start: 0.5277 (OUTLIER) cc_final: 0.4954 (mmmm)
REVERT: D  250 GLU cc_start: 0.6832 (tt0) cc_final: 0.6138 (tm-30)
REVERT: D  260 LYS cc_start: 0.6620 (ttmm) cc_final: 0.6043 (tttp)
REVERT: D  264 GLN cc_start: 0.6415 (tt0) cc_final: 0.5856 (mt0)
REVERT: D  280 GLN cc_start: 0.7206 (mm-40) cc_final: 0.6884 (mm-40)
REVERT: D  331 MET cc_start: 0.6749 (mtp) cc_final: 0.6391 (mtp)
  outliers start: 24
  outliers final: 12
  residues processed: 136
  average time/residue: 1.5462
  time to fit residues: 223.3564
Evaluate side-chains
  136 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  194 LYS
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  194 LYS
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  194 LYS
Chi-restraints excluded: chain D residue  244 ASP
Chi-restraints excluded: chain D residue  318 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 87 optimal weight:    3.9990
   chunk 131 optimal weight:    4.9990
   chunk 121 optimal weight:    0.0010
   chunk 104 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 80 optimal weight:    8.9990
   chunk 64 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   chunk 111 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    2.3792

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10216  Z= 0.207
  Angle     :  0.644   8.679  13848  Z= 0.362
  Chirality :  0.050   0.244   1576
  Planarity :  0.006   0.070   1796
  Dihedral  :  4.958  19.422   1412
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 1.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 15.06 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.24), residues: 1328
  helix:  1.44 (0.26), residues: 392
  sheet: -0.35 (0.39), residues: 176
  loop : -0.07 (0.24), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  87 
 HIS   0.004   0.001   HIS D  53 
 PHE   0.014   0.002   PHE B 233 
 TYR   0.017   0.002   TYR D 314 
 ARG   0.002   0.000   ARG D  16 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 1.201 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.6896 (m-30) cc_final: 0.6589 (m-30)
REVERT: A  138 GLU cc_start: 0.6745 (mm-30) cc_final: 0.5146 (pm20)
REVERT: A  143 SER cc_start: 0.6689 (m) cc_final: 0.6383 (p)
REVERT: A  194 LYS cc_start: 0.5280 (OUTLIER) cc_final: 0.4958 (mmmm)
REVERT: A  250 GLU cc_start: 0.6844 (tt0) cc_final: 0.6317 (mm-30)
REVERT: A  260 LYS cc_start: 0.6610 (ttmm) cc_final: 0.5801 (ttpp)
REVERT: A  264 GLN cc_start: 0.6495 (tt0) cc_final: 0.5950 (mt0)
REVERT: A  280 GLN cc_start: 0.7180 (mm-40) cc_final: 0.6846 (mm-40)
REVERT: A  331 MET cc_start: 0.6724 (mtp) cc_final: 0.6348 (mtp)
REVERT: B   29 ASP cc_start: 0.6898 (m-30) cc_final: 0.6591 (m-30)
REVERT: B  138 GLU cc_start: 0.6746 (mm-30) cc_final: 0.5148 (pm20)
REVERT: B  143 SER cc_start: 0.6685 (m) cc_final: 0.6399 (p)
REVERT: B  194 LYS cc_start: 0.5219 (OUTLIER) cc_final: 0.4900 (mmmm)
REVERT: B  250 GLU cc_start: 0.6846 (tt0) cc_final: 0.6137 (tm-30)
REVERT: B  260 LYS cc_start: 0.6617 (ttmm) cc_final: 0.5810 (ttpp)
REVERT: B  264 GLN cc_start: 0.6495 (tt0) cc_final: 0.5949 (mt0)
REVERT: B  280 GLN cc_start: 0.7180 (mm-40) cc_final: 0.6846 (mm-40)
REVERT: B  331 MET cc_start: 0.6727 (mtp) cc_final: 0.6354 (mtp)
REVERT: C   29 ASP cc_start: 0.6898 (m-30) cc_final: 0.6588 (m-30)
REVERT: C  130 MET cc_start: 0.7673 (mtm) cc_final: 0.7405 (mtm)
REVERT: C  138 GLU cc_start: 0.6746 (mm-30) cc_final: 0.5148 (pm20)
REVERT: C  143 SER cc_start: 0.6688 (m) cc_final: 0.6381 (p)
REVERT: C  250 GLU cc_start: 0.6847 (tt0) cc_final: 0.6138 (tm-30)
REVERT: C  260 LYS cc_start: 0.6615 (ttmm) cc_final: 0.5810 (ttpp)
REVERT: C  264 GLN cc_start: 0.6492 (tt0) cc_final: 0.5965 (mt0)
REVERT: C  280 GLN cc_start: 0.7181 (mm-40) cc_final: 0.6848 (mm-40)
REVERT: C  331 MET cc_start: 0.6721 (mtp) cc_final: 0.6348 (mtp)
REVERT: D   29 ASP cc_start: 0.6898 (m-30) cc_final: 0.6591 (m-30)
REVERT: D  138 GLU cc_start: 0.6744 (mm-30) cc_final: 0.5146 (pm20)
REVERT: D  143 SER cc_start: 0.6691 (m) cc_final: 0.6385 (p)
REVERT: D  194 LYS cc_start: 0.5218 (OUTLIER) cc_final: 0.4900 (mmmm)
REVERT: D  250 GLU cc_start: 0.6844 (tt0) cc_final: 0.6135 (tm-30)
REVERT: D  260 LYS cc_start: 0.6616 (ttmm) cc_final: 0.5810 (ttpp)
REVERT: D  264 GLN cc_start: 0.6578 (tt0) cc_final: 0.6037 (mt0)
REVERT: D  280 GLN cc_start: 0.7180 (mm-40) cc_final: 0.6847 (mm-40)
REVERT: D  331 MET cc_start: 0.6722 (mtp) cc_final: 0.6352 (mtp)
  outliers start: 11
  outliers final: 8
  residues processed: 127
  average time/residue: 1.6357
  time to fit residues: 220.1366
Evaluate side-chains
  131 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 1.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  194 LYS
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  194 LYS
Chi-restraints excluded: chain D residue  318 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 104 optimal weight:    0.0570
   chunk 43 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 92 optimal weight:    0.7980
   chunk 5 optimal weight:    5.9990
   chunk 75 optimal weight:    9.9990
   overall best weight:    2.3704

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.152797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.134271 restraints weight = 7138.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 0.63
r_work: 0.3342 rms_B_bonded: 1.11 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 1.90 restraints_weight: 0.2500
r_work: 0.3087 rms_B_bonded: 4.87 restraints_weight: 0.1250
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10216  Z= 0.205
  Angle     :  0.648   9.037  13848  Z= 0.364
  Chirality :  0.049   0.249   1576
  Planarity :  0.006   0.069   1796
  Dihedral  :  4.946  19.686   1412
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 1.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 15.06 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.24), residues: 1328
  helix:  1.45 (0.26), residues: 392
  sheet: -0.36 (0.39), residues: 176
  loop : -0.08 (0.24), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  87 
 HIS   0.004   0.001   HIS D  53 
 PHE   0.014   0.002   PHE A 233 
 TYR   0.016   0.002   TYR D 314 
 ARG   0.002   0.000   ARG C  16 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4265.89 seconds
wall clock time: 77 minutes 0.75 seconds (4620.75 seconds total)