Starting phenix.real_space_refine
on Wed Apr 30 20:41:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g13_29660/04_2025/8g13_29660.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g13_29660/04_2025/8g13_29660.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g13_29660/04_2025/8g13_29660.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g13_29660/04_2025/8g13_29660.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g13_29660/04_2025/8g13_29660.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g13_29660/04_2025/8g13_29660.cif"
  }
  resolution = 2.3
  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=   0.001
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: 5
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    6316      2.51       5
     N    1736      2.21       5
     O    1896      1.98       5
     H      12      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10008
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2502
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2502
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 12, 'TRANS': 321}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 26
          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: 5.15, per 1000 atoms: 0.51
  Number of scatterers: 10008
  At special positions: 0
  Unit cell: (94.355, 99.365, 91.015, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     O    1896      8.00
     N    1736      7.00
     C    6316      6.00
     H      12      1.00
    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: 2.69
  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
      39.5% alpha, 31.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.55
  Creating SS restraints...
    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
      removed outlier: 3.552A  pdb=" N   ALA B  90 " --> pdb=" O   LYS B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 109
    Processing helix  chain 'B' and resid 109 through 114
      removed outlier: 3.998A  pdb=" N   GLN B 113 " --> pdb=" O   GLY B 109 " (cutoff:3.500A)
      removed outlier: 3.872A  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: 3.721A  pdb=" N   GLY B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
      removed outlier: 3.565A  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 335
    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
      removed outlier: 3.552A  pdb=" N   ALA A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 109
    Processing helix  chain 'A' and resid 109 through 114
      removed outlier: 3.999A  pdb=" N   GLN A 113 " --> pdb=" O   GLY A 109 " (cutoff:3.500A)
      removed outlier: 3.872A  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: 3.721A  pdb=" N   GLY A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
      removed outlier: 3.565A  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 335
    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
      removed outlier: 3.552A  pdb=" N   ALA C  90 " --> pdb=" O   LYS C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 109
    Processing helix  chain 'C' and resid 109 through 114
      removed outlier: 3.999A  pdb=" N   GLN C 113 " --> pdb=" O   GLY C 109 " (cutoff:3.500A)
      removed outlier: 3.872A  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: 3.721A  pdb=" N   GLY C 218 " --> pdb=" O   ALA C 214 " (cutoff:3.500A)
      removed outlier: 3.565A  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 335
    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
      removed outlier: 3.551A  pdb=" N   ALA D  90 " --> pdb=" O   LYS D  86 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 109
    Processing helix  chain 'D' and resid 109 through 114
      removed outlier: 3.999A  pdb=" N   GLN D 113 " --> pdb=" O   GLY D 109 " (cutoff:3.500A)
      removed outlier: 3.871A  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: 3.722A  pdb=" N   GLY D 218 " --> pdb=" O   ALA D 214 " (cutoff:3.500A)
      removed outlier: 3.565A  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 335
    Processing sheet with id=AA1, first strand: chain 'B' and resid 60 through 63
      removed outlier: 10.105A  pdb=" N   ASP B  29 " --> pdb=" O   PRO B  73 " (cutoff:3.500A)
      removed outlier: 9.829A  pdb=" N   THR B  75 " --> pdb=" O   ASP B  29 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   VAL B  31 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 8.159A  pdb=" N   PHE B  77 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ILE B  33 " --> pdb=" O   PHE B  77 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   VAL B   8 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ILE B  33 " --> pdb=" O   VAL B   8 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   VAL B  95 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   VAL B 119 " --> pdb=" O   ILE B 147 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 208 through 210
      removed outlier: 3.577A  pdb=" N   THR B 229 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ARG B 248 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   GLY B 173 " --> pdb=" O   THR B 246 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR B 246 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   MET B 175 " --> pdb=" O   ASP B 244 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ASP B 244 " --> pdb=" O   MET B 175 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   THR B 177 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL B 242 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   HIS B 179 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   VAL B 240 " --> pdb=" O   HIS B 179 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   ILE B 311 " --> pdb=" O   ASP B 296 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 208 through 210
      removed outlier: 3.577A  pdb=" N   THR B 229 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ARG B 248 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   GLY B 173 " --> pdb=" O   THR B 246 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR B 246 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   MET B 175 " --> pdb=" O   ASP B 244 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ASP B 244 " --> pdb=" O   MET B 175 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   THR B 177 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL B 242 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   HIS B 179 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   VAL B 240 " --> pdb=" O   HIS B 179 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   PHE B 307 " --> pdb=" O   LEU B 303 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 63
      removed outlier: 10.106A  pdb=" N   ASP A  29 " --> pdb=" O   PRO A  73 " (cutoff:3.500A)
      removed outlier: 9.830A  pdb=" N   THR A  75 " --> pdb=" O   ASP A  29 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL A  31 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 8.159A  pdb=" N   PHE A  77 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ILE A  33 " --> pdb=" O   PHE A  77 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   VAL A   8 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ILE A  33 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   VAL A  95 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   VAL A 119 " --> pdb=" O   ILE A 147 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 210
      removed outlier: 3.577A  pdb=" N   THR A 229 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ARG A 248 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   GLY A 173 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR A 246 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   MET A 175 " --> pdb=" O   ASP A 244 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ASP A 244 " --> pdb=" O   MET A 175 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   THR A 177 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL A 242 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   HIS A 179 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   VAL A 240 " --> pdb=" O   HIS A 179 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   ILE A 311 " --> pdb=" O   ASP A 296 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 208 through 210
      removed outlier: 3.577A  pdb=" N   THR A 229 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ARG A 248 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   GLY A 173 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR A 246 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   MET A 175 " --> pdb=" O   ASP A 244 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ASP A 244 " --> pdb=" O   MET A 175 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   THR A 177 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL A 242 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   HIS A 179 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   VAL A 240 " --> pdb=" O   HIS A 179 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   PHE A 307 " --> pdb=" O   LEU A 303 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 63
      removed outlier: 10.105A  pdb=" N   ASP C  29 " --> pdb=" O   PRO C  73 " (cutoff:3.500A)
      removed outlier: 9.830A  pdb=" N   THR C  75 " --> pdb=" O   ASP C  29 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL C  31 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 8.158A  pdb=" N   PHE C  77 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ILE C  33 " --> pdb=" O   PHE C  77 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   VAL C   8 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ILE C  33 " --> pdb=" O   VAL C   8 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   VAL C  95 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   VAL C 119 " --> pdb=" O   ILE C 147 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 208 through 210
      removed outlier: 3.577A  pdb=" N   THR C 229 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ARG C 248 " --> pdb=" O   VAL C 171 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   GLY C 173 " --> pdb=" O   THR C 246 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR C 246 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   MET C 175 " --> pdb=" O   ASP C 244 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ASP C 244 " --> pdb=" O   MET C 175 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   THR C 177 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL C 242 " --> pdb=" O   THR C 177 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   HIS C 179 " --> pdb=" O   VAL C 240 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   VAL C 240 " --> pdb=" O   HIS C 179 " (cutoff:3.500A)
      removed outlier: 4.783A  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: 3.577A  pdb=" N   THR C 229 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ARG C 248 " --> pdb=" O   VAL C 171 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   GLY C 173 " --> pdb=" O   THR C 246 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR C 246 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   MET C 175 " --> pdb=" O   ASP C 244 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ASP C 244 " --> pdb=" O   MET C 175 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   THR C 177 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL C 242 " --> pdb=" O   THR C 177 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   HIS C 179 " --> pdb=" O   VAL C 240 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   VAL C 240 " --> pdb=" O   HIS C 179 " (cutoff:3.500A)
      removed outlier: 6.768A  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: 10.105A  pdb=" N   ASP D  29 " --> pdb=" O   PRO D  73 " (cutoff:3.500A)
      removed outlier: 9.830A  pdb=" N   THR D  75 " --> pdb=" O   ASP D  29 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   VAL D  31 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 8.158A  pdb=" N   PHE D  77 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ILE D  33 " --> pdb=" O   PHE D  77 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   VAL D   8 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ILE D  33 " --> pdb=" O   VAL D   8 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   VAL D  95 " --> pdb=" O   ILE D 120 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   VAL D 119 " --> pdb=" O   ILE D 147 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 208 through 210
      removed outlier: 3.577A  pdb=" N   THR D 229 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ARG D 248 " --> pdb=" O   VAL D 171 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   GLY D 173 " --> pdb=" O   THR D 246 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   THR D 246 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   MET D 175 " --> pdb=" O   ASP D 244 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ASP D 244 " --> pdb=" O   MET D 175 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   THR D 177 " --> pdb=" O   VAL D 242 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL D 242 " --> pdb=" O   THR D 177 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   HIS D 179 " --> pdb=" O   VAL D 240 " (cutoff:3.500A)
      removed outlier: 7.527A  pdb=" N   VAL D 240 " --> pdb=" O   HIS D 179 " (cutoff:3.500A)
      removed outlier: 4.783A  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: 3.577A  pdb=" N   THR D 229 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ARG D 248 " --> pdb=" O   VAL D 171 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   GLY D 173 " --> pdb=" O   THR D 246 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   THR D 246 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   MET D 175 " --> pdb=" O   ASP D 244 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ASP D 244 " --> pdb=" O   MET D 175 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   THR D 177 " --> pdb=" O   VAL D 242 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL D 242 " --> pdb=" O   THR D 177 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   HIS D 179 " --> pdb=" O   VAL D 240 " (cutoff:3.500A)
      removed outlier: 7.527A  pdb=" N   VAL D 240 " --> pdb=" O   HIS D 179 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   PHE D 307 " --> pdb=" O   LEU D 303 " (cutoff:3.500A)

    512 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: 3.37

  Time building geometry restraints manager: 3.14 seconds

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

  Histogram of bond lengths:
        0.86 -     1.05: 8
        1.05 -     1.24: 1364
        1.24 -     1.43: 2899
        1.43 -     1.62: 5853
        1.62 -     1.81: 84
  Bond restraints: 10208
  Sorted by residual:
  bond pdb=" CA  CYS D 152 "
       pdb=" HA  CYS D 152 "
    ideal  model  delta    sigma   weight residual
    0.970  1.090 -0.120 2.00e-02 2.50e+03 3.59e+01
  bond pdb=" CA  CYS B 152 "
       pdb=" HA  CYS B 152 "
    ideal  model  delta    sigma   weight residual
    0.970  1.090 -0.120 2.00e-02 2.50e+03 3.59e+01
  bond pdb=" CA  CYS C 152 "
       pdb=" HA  CYS C 152 "
    ideal  model  delta    sigma   weight residual
    0.970  1.090 -0.120 2.00e-02 2.50e+03 3.59e+01
  bond pdb=" CA  CYS A 152 "
       pdb=" HA  CYS A 152 "
    ideal  model  delta    sigma   weight residual
    0.970  1.090 -0.120 2.00e-02 2.50e+03 3.58e+01
  bond pdb=" N   VAL C 188 "
       pdb=" CA  VAL C 188 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.11e-02 8.12e+03 1.22e+01
  ... (remaining 10203 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 13208
        1.25 -     2.51: 493
        2.51 -     3.76: 134
        3.76 -     5.02: 13
        5.02 -     6.27: 16
  Bond angle restraints: 13864
  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  110.36    6.27 1.16e+00 7.43e-01 2.92e+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  110.39    6.24 1.16e+00 7.43e-01 2.89e+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  110.40    6.23 1.16e+00 7.43e-01 2.88e+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  110.42    6.21 1.16e+00 7.43e-01 2.87e+01
  angle pdb=" N   ARG A  80 "
        pdb=" CA  ARG A  80 "
        pdb=" C   ARG A  80 "
      ideal   model   delta    sigma   weight residual
     113.41  108.74    4.67 1.22e+00 6.72e-01 1.46e+01
  ... (remaining 13859 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.09: 5375
       17.09 -    34.19: 461
       34.19 -    51.28: 147
       51.28 -    68.38: 33
       68.38 -    85.47: 8
  Dihedral angle restraints: 6024
    sinusoidal: 2248
      harmonic: 3776
  Sorted by residual:
  dihedral pdb=" CG  ARG D 197 "
           pdb=" CD  ARG D 197 "
           pdb=" NE  ARG D 197 "
           pdb=" CZ  ARG D 197 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -132.92   42.92     2      1.50e+01 4.44e-03 9.89e+00
  dihedral pdb=" CG  ARG C 197 "
           pdb=" CD  ARG C 197 "
           pdb=" NE  ARG C 197 "
           pdb=" CZ  ARG C 197 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -132.91   42.91     2      1.50e+01 4.44e-03 9.89e+00
  dihedral pdb=" CG  ARG A 197 "
           pdb=" CD  ARG A 197 "
           pdb=" NE  ARG A 197 "
           pdb=" CZ  ARG A 197 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -132.91   42.91     2      1.50e+01 4.44e-03 9.89e+00
  ... (remaining 6021 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1078
       0.041 -    0.081: 315
       0.081 -    0.122: 167
       0.122 -    0.163: 12
       0.163 -    0.203: 8
  Chirality restraints: 1580
  Sorted by residual:
  chirality pdb=" CA  VAL B 188 "
            pdb=" N   VAL B 188 "
            pdb=" C   VAL B 188 "
            pdb=" CB  VAL B 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  VAL C 188 "
            pdb=" N   VAL C 188 "
            pdb=" C   VAL C 188 "
            pdb=" CB  VAL C 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  VAL A 188 "
            pdb=" N   VAL A 188 "
            pdb=" C   VAL A 188 "
            pdb=" CB  VAL A 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 1577 not shown)

  Planarity restraints: 1800
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 268 "    0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO A 269 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 269 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 269 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C 268 "   -0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO C 269 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO C 269 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 269 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 268 "   -0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO B 269 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 269 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 269 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1797 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.59: 76
        2.59 -     3.09: 7050
        3.09 -     3.59: 11331
        3.59 -     4.10: 17078
        4.10 -     4.60: 25617
  Nonbonded interactions: 61152
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 118 "
            pdb=" OD1 ASN A 142 "
     model   vdw
     2.083 2.950
  nonbonded pdb=" NH2 ARG B 118 "
            pdb=" OD1 ASN B 142 "
     model   vdw
     2.083 2.950
  nonbonded pdb=" NH2 ARG C 118 "
            pdb=" OD1 ASN C 142 "
     model   vdw
     2.083 2.950
  nonbonded pdb=" NH2 ARG D 118 "
            pdb=" OD1 ASN D 142 "
     model   vdw
     2.083 2.950
  nonbonded pdb=" NZ  LYS D   3 "
            pdb=" O   GLY D  26 "
     model   vdw
     2.288 2.950
  ... (remaining 61147 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  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:             0.960
  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:             0.310
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.070
  Set scattering table:                    0.120
  Process input model:                     26.060
  Find NCS groups from input model:        0.220
  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:17.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8954
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   0.039  10196  Z= 0.285
  Angle     :  0.597   6.272  13832  Z= 0.407
  Chirality :  0.049   0.203   1580
  Planarity :  0.003   0.032   1796
  Dihedral  : 14.969  85.473   3612
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 13.21 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.94 (0.25), residues: 1328
  helix:  2.33 (0.26), residues: 368
  sheet:  0.27 (0.38), residues: 212
  loop : -0.10 (0.25), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 313 
 HIS   0.003   0.001   HIS A 137 
 PHE   0.007   0.001   PHE B 318 
 TYR   0.007   0.001   TYR D 314 
 ARG   0.002   0.000   ARG D 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20204 (  448)
  hydrogen bonds       : angle       7.75392 ( 1368)
  covalent geometry    : bond        0.00416 (10196)
  covalent geometry    : angle       0.59684 (13832)

*********************** 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
  94 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 1.063 
Fit side-chains
  outliers start: 9
  outliers final: 8
  residues processed: 94
  average time/residue: 1.5790
  time to fit residues: 157.5196
Evaluate side-chains
  77 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  243 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    9.9990
   chunk 100 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 67 optimal weight:    8.9990
   chunk 53 optimal weight:    7.9990
   chunk 103 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   chunk 62 optimal weight:    7.9990
   chunk 77 optimal weight:    0.9980
   chunk 119 optimal weight:    7.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
B 149 ASN
B 185 GLN
A 149 ASN
A 185 GLN
C 149 ASN
C 185 GLN
D 149 ASN
D 185 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.061699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.048573 restraints weight = 20055.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.2599 rms_B_bonded: 2.51
r_work: 0.2464 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2340 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9090
moved from start:          0.1124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034  10196  Z= 0.275
  Angle     :  0.567   7.471  13832  Z= 0.323
  Chirality :  0.048   0.172   1580
  Planarity :  0.005   0.051   1796
  Dihedral  :  4.984  33.192   1420
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 13.97 %
    Favored  : 84.79 %
  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:  0.53 (0.25), residues: 1328
  helix:  2.05 (0.27), residues: 372
  sheet: -0.72 (0.33), residues: 288
  loop : -0.03 (0.27), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  87 
 HIS   0.004   0.001   HIS B 137 
 PHE   0.014   0.002   PHE B 318 
 TYR   0.019   0.002   TYR B  42 
 ARG   0.007   0.001   ARG B  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06082 (  448)
  hydrogen bonds       : angle       5.83030 ( 1368)
  covalent geometry    : bond        0.00644 (10196)
  covalent geometry    : angle       0.56672 (13832)

*********************** 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
  77 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 1.199 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8720 (mp0) cc_final: 0.8447 (mp0)
REVERT: A  223 GLU cc_start: 0.8734 (mp0) cc_final: 0.8461 (mp0)
REVERT: C  223 GLU cc_start: 0.8727 (mp0) cc_final: 0.8453 (mp0)
REVERT: D  223 GLU cc_start: 0.8714 (mp0) cc_final: 0.8442 (mp0)
  outliers start: 13
  outliers final: 8
  residues processed: 77
  average time/residue: 1.4853
  time to fit residues: 122.3983
Evaluate side-chains
  72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  243 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 55 optimal weight:    0.0970
   chunk 11 optimal weight:    8.9990
   chunk 69 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 114 optimal weight:    0.9980
   chunk 126 optimal weight:    7.9990
   chunk 82 optimal weight:    0.6980
   chunk 89 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3002 r_free = 0.3002 target = 0.066662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.053660 restraints weight = 20085.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.2716 rms_B_bonded: 2.54
r_work: 0.2586 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2465 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8999
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015  10196  Z= 0.076
  Angle     :  0.403   4.788  13832  Z= 0.227
  Chirality :  0.042   0.125   1580
  Planarity :  0.004   0.038   1796
  Dihedral  :  3.967  22.191   1416
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 14.64 %
    Favored  : 84.60 %
  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:  0.87 (0.25), residues: 1328
  helix:  2.55 (0.27), residues: 396
  sheet: -0.68 (0.32), residues: 288
  loop :  0.02 (0.28), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP D 313 
 HIS   0.002   0.000   HIS A 137 
 PHE   0.005   0.001   PHE A 233 
 TYR   0.005   0.001   TYR C 314 
 ARG   0.007   0.001   ARG B  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03265 (  448)
  hydrogen bonds       : angle       5.01880 ( 1368)
  covalent geometry    : bond        0.00154 (10196)
  covalent geometry    : angle       0.40315 (13832)

*********************** 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
  76 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 1.274 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8668 (mp0) cc_final: 0.8377 (mp0)
REVERT: A  223 GLU cc_start: 0.8682 (mp0) cc_final: 0.8391 (mp0)
REVERT: C  223 GLU cc_start: 0.8674 (mp0) cc_final: 0.8383 (mp0)
REVERT: D  223 GLU cc_start: 0.8671 (mp0) cc_final: 0.8381 (mp0)
  outliers start: 8
  outliers final: 0
  residues processed: 76
  average time/residue: 1.8435
  time to fit residues: 148.3330
Evaluate side-chains
  68 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 16 optimal weight:    0.0980
   chunk 116 optimal weight:   10.0000
   chunk 112 optimal weight:    6.9990
   chunk 66 optimal weight:   10.0000
   chunk 91 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 1 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 55 optimal weight:    0.8980
   chunk 83 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    2.5986

-------------------------------------------------------------------------------
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 = 0.2930 r_free = 0.2930 target = 0.063002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.049823 restraints weight = 19927.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.2627 rms_B_bonded: 2.53
r_work: 0.2494 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2371 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9062
moved from start:          0.1183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022  10196  Z= 0.170
  Angle     :  0.467   6.301  13832  Z= 0.264
  Chirality :  0.045   0.135   1580
  Planarity :  0.004   0.042   1796
  Dihedral  :  4.019  14.427   1412
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 14.64 %
    Favored  : 84.41 %
  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:  0.71 (0.25), residues: 1328
  helix:  2.41 (0.27), residues: 372
  sheet: -0.64 (0.32), residues: 288
  loop : -0.06 (0.27), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D  87 
 HIS   0.003   0.001   HIS B 137 
 PHE   0.009   0.001   PHE B 286 
 TYR   0.010   0.001   TYR D 314 
 ARG   0.007   0.001   ARG B  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04546 (  448)
  hydrogen bonds       : angle       5.13915 ( 1368)
  covalent geometry    : bond        0.00394 (10196)
  covalent geometry    : angle       0.46676 (13832)

*********************** 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
  74 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 1.191 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8697 (mp0) cc_final: 0.8425 (mp0)
REVERT: A  223 GLU cc_start: 0.8703 (mp0) cc_final: 0.8433 (mp0)
REVERT: C  223 GLU cc_start: 0.8693 (mp0) cc_final: 0.8421 (mp0)
REVERT: D  223 GLU cc_start: 0.8687 (mp0) cc_final: 0.8418 (mp0)
  outliers start: 10
  outliers final: 6
  residues processed: 74
  average time/residue: 1.6970
  time to fit residues: 133.5436
Evaluate side-chains
  70 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain D residue  143 SER
Chi-restraints excluded: chain D residue  220 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 104 optimal weight:    8.9990
   chunk 2 optimal weight:    4.9990
   chunk 15 optimal weight:    8.9990
   chunk 78 optimal weight:   10.0000
   chunk 95 optimal weight:    9.9990
   chunk 91 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 67 optimal weight:    8.9990
   chunk 59 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    2.5786

-------------------------------------------------------------------------------
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 = 0.2926 r_free = 0.2926 target = 0.062841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.049696 restraints weight = 19864.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.2625 rms_B_bonded: 2.51
r_work: 0.2491 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2369 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9066
moved from start:          0.1203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022  10196  Z= 0.167
  Angle     :  0.467   6.266  13832  Z= 0.264
  Chirality :  0.045   0.135   1580
  Planarity :  0.004   0.048   1796
  Dihedral  :  4.063  16.395   1412
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 14.26 %
    Favored  : 84.79 %
  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:  0.59 (0.25), residues: 1328
  helix:  2.29 (0.27), residues: 372
  sheet: -0.70 (0.31), residues: 288
  loop : -0.11 (0.26), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 313 
 HIS   0.003   0.001   HIS A 137 
 PHE   0.009   0.001   PHE D 286 
 TYR   0.010   0.001   TYR D 314 
 ARG   0.008   0.001   ARG A  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04487 (  448)
  hydrogen bonds       : angle       5.08742 ( 1368)
  covalent geometry    : bond        0.00386 (10196)
  covalent geometry    : angle       0.46692 (13832)

*********************** 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
  74 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 1.268 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8710 (mp0) cc_final: 0.8430 (mp0)
REVERT: A  223 GLU cc_start: 0.8712 (mp0) cc_final: 0.8431 (mp0)
REVERT: C  223 GLU cc_start: 0.8707 (mp0) cc_final: 0.8428 (mp0)
REVERT: D  223 GLU cc_start: 0.8705 (mp0) cc_final: 0.8427 (mp0)
  outliers start: 10
  outliers final: 7
  residues processed: 74
  average time/residue: 1.5661
  time to fit residues: 123.8233
Evaluate side-chains
  71 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain D residue  143 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 21 optimal weight:    8.9990
   chunk 128 optimal weight:    9.9990
   chunk 108 optimal weight:    9.9990
   chunk 62 optimal weight:    0.0870
   chunk 12 optimal weight:   10.0000
   chunk 86 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 111 optimal weight:    0.5980
   chunk 97 optimal weight:    4.9990
   chunk 1 optimal weight:    8.9990
   chunk 85 optimal weight:    0.8980
   overall best weight:    1.5162

-------------------------------------------------------------------------------
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 = 0.2951 r_free = 0.2951 target = 0.064014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2669 r_free = 0.2669 target = 0.051057 restraints weight = 19826.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.2660 rms_B_bonded: 2.49
r_work: 0.2527 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2405 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9041
moved from start:          0.1240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018  10196  Z= 0.109
  Angle     :  0.425   5.641  13832  Z= 0.239
  Chirality :  0.043   0.124   1580
  Planarity :  0.004   0.043   1796
  Dihedral  :  3.870  16.605   1412
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 14.54 %
    Favored  : 84.79 %
  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:  0.77 (0.25), residues: 1328
  helix:  2.53 (0.27), residues: 372
  sheet: -0.64 (0.31), residues: 288
  loop : -0.04 (0.27), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 313 
 HIS   0.002   0.000   HIS B 137 
 PHE   0.006   0.001   PHE A 286 
 TYR   0.008   0.001   TYR A 314 
 ARG   0.009   0.001   ARG B  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03670 (  448)
  hydrogen bonds       : angle       4.86287 ( 1368)
  covalent geometry    : bond        0.00243 (10196)
  covalent geometry    : angle       0.42461 (13832)

*********************** 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
  71 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 1.117 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8687 (mp0) cc_final: 0.8401 (mp0)
REVERT: A  223 GLU cc_start: 0.8698 (mp0) cc_final: 0.8412 (mp0)
REVERT: C  223 GLU cc_start: 0.8682 (mp0) cc_final: 0.8397 (mp0)
REVERT: D  223 GLU cc_start: 0.8677 (mp0) cc_final: 0.8396 (mp0)
  outliers start: 7
  outliers final: 7
  residues processed: 71
  average time/residue: 1.6182
  time to fit residues: 122.2767
Evaluate side-chains
  71 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain D residue  143 SER
Chi-restraints excluded: chain D residue  220 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 102 optimal weight:    0.0870
   chunk 69 optimal weight:    0.7980
   chunk 125 optimal weight:    0.9990
   chunk 15 optimal weight:    8.9990
   chunk 66 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   chunk 62 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.7762

-------------------------------------------------------------------------------
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 = 0.2995 r_free = 0.2995 target = 0.066290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.053112 restraints weight = 19936.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.2705 rms_B_bonded: 2.56
r_work: 0.2576 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2455 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8999
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  10196  Z= 0.074
  Angle     :  0.394   4.954  13832  Z= 0.220
  Chirality :  0.042   0.122   1580
  Planarity :  0.004   0.043   1796
  Dihedral  :  3.580  15.443   1412
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 15.59 %
    Favored  : 84.13 %
  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:  1.00 (0.25), residues: 1328
  helix:  2.71 (0.27), residues: 396
  sheet: -0.56 (0.32), residues: 288
  loop :  0.03 (0.28), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP D 313 
 HIS   0.002   0.000   HIS A 137 
 PHE   0.004   0.001   PHE C 286 
 TYR   0.006   0.001   TYR B 314 
 ARG   0.009   0.001   ARG C  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02964 (  448)
  hydrogen bonds       : angle       4.56514 ( 1368)
  covalent geometry    : bond        0.00160 (10196)
  covalent geometry    : angle       0.39407 (13832)

*********************** 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
  79 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 1.118 
Fit side-chains
REVERT: B   78 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8918 (mm110)
REVERT: B  223 GLU cc_start: 0.8669 (mp0) cc_final: 0.8398 (mp0)
REVERT: A   78 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8909 (mm110)
REVERT: A  223 GLU cc_start: 0.8683 (mp0) cc_final: 0.8410 (mp0)
REVERT: C   78 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8919 (mm110)
REVERT: C  223 GLU cc_start: 0.8667 (mp0) cc_final: 0.8395 (mp0)
REVERT: D   78 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8914 (mm110)
REVERT: D  223 GLU cc_start: 0.8662 (mp0) cc_final: 0.8395 (mp0)
  outliers start: 3
  outliers final: 3
  residues processed: 79
  average time/residue: 1.5636
  time to fit residues: 131.4428
Evaluate side-chains
  71 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 1.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain D residue  220 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 120 optimal weight:    3.9990
   chunk 104 optimal weight:   10.0000
   chunk 131 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0010
   chunk 76 optimal weight:    0.3980
   chunk 2 optimal weight:    5.9990
   chunk 71 optimal weight:   10.0000
   chunk 15 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 85 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    2.4792

-------------------------------------------------------------------------------
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 = 0.2932 r_free = 0.2932 target = 0.063110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.049876 restraints weight = 20082.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.2630 rms_B_bonded: 2.54
r_work: 0.2494 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2371 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9061
moved from start:          0.1267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022  10196  Z= 0.160
  Angle     :  0.464   6.099  13832  Z= 0.267
  Chirality :  0.044   0.130   1580
  Planarity :  0.005   0.074   1796
  Dihedral  :  3.924  16.477   1412
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 14.92 %
    Favored  : 84.03 %
  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:  0.81 (0.25), residues: 1328
  helix:  2.54 (0.27), residues: 372
  sheet: -0.60 (0.31), residues: 288
  loop : -0.00 (0.27), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C  87 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.008   0.001   PHE A 286 
 TYR   0.010   0.001   TYR D 314 
 ARG   0.009   0.001   ARG C  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04266 (  448)
  hydrogen bonds       : angle       4.91424 ( 1368)
  covalent geometry    : bond        0.00371 (10196)
  covalent geometry    : angle       0.46393 (13832)

*********************** 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
  75 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 2.086 
Fit side-chains
REVERT: B   78 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8902 (mm110)
REVERT: B  223 GLU cc_start: 0.8705 (mp0) cc_final: 0.8426 (mp0)
REVERT: A   78 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8898 (mm110)
REVERT: A  223 GLU cc_start: 0.8715 (mp0) cc_final: 0.8435 (mp0)
REVERT: C   78 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8886 (mm110)
REVERT: C  223 GLU cc_start: 0.8704 (mp0) cc_final: 0.8423 (mp0)
REVERT: D   78 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8903 (mm110)
REVERT: D  223 GLU cc_start: 0.8702 (mp0) cc_final: 0.8424 (mp0)
  outliers start: 11
  outliers final: 7
  residues processed: 75
  average time/residue: 1.8612
  time to fit residues: 149.4112
Evaluate side-chains
  71 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 1.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain D residue  143 SER
Chi-restraints excluded: chain D residue  220 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 90 optimal weight:    8.9990
   chunk 98 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   chunk 106 optimal weight:   10.0000
   chunk 81 optimal weight:    6.9990
   chunk 48 optimal weight:    7.9990
   chunk 130 optimal weight:    6.9990
   chunk 77 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 68 optimal weight:    4.9990
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.061214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2598 r_free = 0.2598 target = 0.048087 restraints weight = 20082.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.2588 rms_B_bonded: 2.51
r_work: 0.2452 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2329 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9095
moved from start:          0.1326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034  10196  Z= 0.269
  Angle     :  0.551   7.280  13832  Z= 0.316
  Chirality :  0.047   0.166   1580
  Planarity :  0.006   0.080   1796
  Dihedral  :  4.270  17.755   1412
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 15.02 %
    Favored  : 84.22 %
  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:  0.48 (0.24), residues: 1328
  helix:  2.08 (0.26), residues: 372
  sheet: -0.67 (0.31), residues: 288
  loop : -0.15 (0.26), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  87 
 HIS   0.003   0.001   HIS D  53 
 PHE   0.012   0.002   PHE A 286 
 TYR   0.013   0.002   TYR C 314 
 ARG   0.010   0.001   ARG C  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05462 (  448)
  hydrogen bonds       : angle       5.25856 ( 1368)
  covalent geometry    : bond        0.00635 (10196)
  covalent geometry    : angle       0.55107 (13832)

*********************** 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
  72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 1.432 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8710 (mp0) cc_final: 0.8433 (mp0)
REVERT: A  223 GLU cc_start: 0.8715 (mp0) cc_final: 0.8439 (mp0)
REVERT: C  223 GLU cc_start: 0.8710 (mp0) cc_final: 0.8432 (mp0)
REVERT: D  223 GLU cc_start: 0.8707 (mp0) cc_final: 0.8433 (mp0)
  outliers start: 8
  outliers final: 8
  residues processed: 72
  average time/residue: 1.9880
  time to fit residues: 151.7716
Evaluate side-chains
  72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain D residue  143 SER
Chi-restraints excluded: chain D residue  220 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 94 optimal weight:    0.0060
   chunk 79 optimal weight:    0.8980
   chunk 87 optimal weight:    6.9990
   chunk 125 optimal weight:    0.6980
   chunk 73 optimal weight:    7.9990
   chunk 99 optimal weight:   10.0000
   chunk 114 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.9198

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

Flipped N/Q/H residues before XYZ refinement:
** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.065314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.052162 restraints weight = 19923.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.2681 rms_B_bonded: 2.54
r_work: 0.2550 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2429 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9020
moved from start:          0.1321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10196  Z= 0.087
  Angle     :  0.418   5.029  13832  Z= 0.241
  Chirality :  0.043   0.127   1580
  Planarity :  0.005   0.070   1796
  Dihedral  :  3.774  16.907   1412
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 15.21 %
    Favored  : 84.41 %
  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:  0.83 (0.25), residues: 1328
  helix:  2.60 (0.27), residues: 372
  sheet: -0.67 (0.31), residues: 288
  loop :  0.02 (0.27), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP C 313 
 HIS   0.002   0.000   HIS C 137 
 PHE   0.006   0.001   PHE A 286 
 TYR   0.006   0.001   TYR D 314 
 ARG   0.011   0.001   ARG C  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03190 (  448)
  hydrogen bonds       : angle       4.72139 ( 1368)
  covalent geometry    : bond        0.00186 (10196)
  covalent geometry    : angle       0.41846 (13832)

********************** 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
  72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 1.108 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8680 (mp0) cc_final: 0.8410 (mp0)
REVERT: A  223 GLU cc_start: 0.8690 (mp0) cc_final: 0.8420 (mp0)
REVERT: C   78 GLN cc_start: 0.9150 (mm-40) cc_final: 0.8885 (mm110)
REVERT: C  223 GLU cc_start: 0.8677 (mp0) cc_final: 0.8407 (mp0)
REVERT: D  223 GLU cc_start: 0.8676 (mp0) cc_final: 0.8409 (mp0)
  outliers start: 4
  outliers final: 3
  residues processed: 71
  average time/residue: 1.7934
  time to fit residues: 134.9084
Evaluate side-chains
  71 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 1.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain D residue  220 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 60 optimal weight:    7.9990
   chunk 46 optimal weight:    5.9990
   chunk 78 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 127 optimal weight:    0.5980
   chunk 52 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 81 optimal weight:    7.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.063133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.050116 restraints weight = 19911.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.2636 rms_B_bonded: 2.50
r_work: 0.2502 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2379 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9053
moved from start:          0.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  10196  Z= 0.144
  Angle     :  0.463   5.888  13832  Z= 0.266
  Chirality :  0.044   0.126   1580
  Planarity :  0.005   0.066   1796
  Dihedral  :  3.919  16.489   1412
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 15.11 %
    Favored  : 84.41 %
  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:  0.78 (0.25), residues: 1328
  helix:  2.49 (0.27), residues: 372
  sheet: -0.62 (0.31), residues: 288
  loop : -0.02 (0.27), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D 313 
 HIS   0.003   0.000   HIS C 137 
 PHE   0.008   0.001   PHE C 286 
 TYR   0.009   0.001   TYR C 314 
 ARG   0.013   0.001   ARG B  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04068 (  448)
  hydrogen bonds       : angle       4.87571 ( 1368)
  covalent geometry    : bond        0.00329 (10196)
  covalent geometry    : angle       0.46296 (13832)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7051.43 seconds
wall clock time: 123 minutes 34.69 seconds (7414.69 seconds total)