Starting phenix.real_space_refine
on Sat Aug 23 05:07:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g13_29660/08_2025/8g13_29660.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g13_29660/08_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_29660/08_2025/8g13_29660.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g13_29660/08_2025/8g13_29660.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g13_29660/08_2025/8g13_29660.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g13_29660/08_2025/8g13_29660.cif"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10008
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      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:
    A, C, D
  Time building chain proxies: 1.30, per 1000 atoms: 0.13
  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: 0.70
  Conformation dependent library (CDL) restraints added in 330.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.40
  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: 1.24

  Time building geometry restraints manager: 0.91 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  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:             0.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.090
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     7.620
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.820
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG D 234 
 TYR   0.007   0.001   TYR D 314 
 PHE   0.007   0.001   PHE B 318 
 TRP   0.004   0.001   TRP D 313 
 HIS   0.003   0.001   HIS A 137 

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

*********************** 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  : 0.348 
Fit side-chains
  outliers start: 9
  outliers final: 8
  residues processed: 94
  average time/residue: 0.6908
  time to fit residues: 68.8113
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  : 0.247 
-------------------------------------------------------------------------------
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 98 optimal weight:    8.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    0.4980
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    2.6586

-------------------------------------------------------------------------------
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 = 0.2939 r_free = 0.2939 target = 0.063362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.050338 restraints weight = 20033.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.2642 rms_B_bonded: 2.52
r_work: 0.2507 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2384 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9061
moved from start:          0.1042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021  10196  Z= 0.179
  Angle     :  0.496   6.581  13832  Z= 0.283
  Chirality :  0.045   0.143   1580
  Planarity :  0.004   0.047   1796
  Dihedral  :  4.653  29.637   1420
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 14.83 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.25), residues: 1328
  helix:  2.28 (0.27), residues: 372
  sheet: -0.44 (0.35), residues: 232
  loop : -0.25 (0.26), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  80 
 TYR   0.014   0.002   TYR D  42 
 PHE   0.011   0.001   PHE B 318 
 TRP   0.004   0.001   TRP C 313 
 HIS   0.003   0.001   HIS C 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (10196)
  covalent geometry    : angle       0.49636 (13832)
  hydrogen bonds       : bond        0.04979 (  448)
  hydrogen bonds       : angle       5.58805 ( 1368)

*********************** 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
  72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.492 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8718 (mp0) cc_final: 0.8423 (mp0)
REVERT: A  223 GLU cc_start: 0.8719 (mp0) cc_final: 0.8423 (mp0)
REVERT: C  223 GLU cc_start: 0.8723 (mp0) cc_final: 0.8427 (mp0)
REVERT: D  223 GLU cc_start: 0.8709 (mp0) cc_final: 0.8419 (mp0)
  outliers start: 8
  outliers final: 8
  residues processed: 72
  average time/residue: 0.7727
  time to fit residues: 58.9971
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  : 0.397 
-------------------------------------------------------------------------------
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 124 optimal weight:    5.9990
   chunk 120 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 43 optimal weight:    8.9990
   chunk 63 optimal weight:    7.9990
   chunk 88 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 104 optimal weight:   10.0000
   chunk 97 optimal weight:    5.9990
   chunk 85 optimal weight:    6.9990
   chunk 83 optimal weight:    0.9980
   overall best weight:    3.1986

-------------------------------------------------------------------------------
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 = 0.2918 r_free = 0.2918 target = 0.062381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.049233 restraints weight = 20027.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.2614 rms_B_bonded: 2.52
r_work: 0.2478 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2356 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9077
moved from start:          0.1153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027  10196  Z= 0.203
  Angle     :  0.500   6.692  13832  Z= 0.283
  Chirality :  0.046   0.147   1580
  Planarity :  0.004   0.041   1796
  Dihedral  :  4.489  28.487   1416
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 14.83 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.24), residues: 1328
  helix:  2.09 (0.27), residues: 372
  sheet: -0.67 (0.32), residues: 288
  loop : -0.13 (0.26), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  80 
 TYR   0.011   0.002   TYR D 314 
 PHE   0.011   0.001   PHE B 318 
 TRP   0.004   0.001   TRP D  87 
 HIS   0.003   0.001   HIS A 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 (10196)
  covalent geometry    : angle       0.49965 (13832)
  hydrogen bonds       : bond        0.05160 (  448)
  hydrogen bonds       : angle       5.37505 ( 1368)

*********************** 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
  72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.464 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8718 (mp0) cc_final: 0.8440 (mp0)
REVERT: A  223 GLU cc_start: 0.8719 (mp0) cc_final: 0.8441 (mp0)
REVERT: C  223 GLU cc_start: 0.8719 (mp0) cc_final: 0.8443 (mp0)
REVERT: D  223 GLU cc_start: 0.8711 (mp0) cc_final: 0.8435 (mp0)
  outliers start: 8
  outliers final: 0
  residues processed: 72
  average time/residue: 0.7343
  time to fit residues: 56.1423
Evaluate side-chains
  64 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 80 optimal weight:    0.0050
   chunk 33 optimal weight:   10.0000
   chunk 107 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 117 optimal weight:    6.9990
   chunk 96 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 94 optimal weight:    6.9990
   chunk 129 optimal weight:    5.9990
   chunk 50 optimal weight:    9.9990
   overall best weight:    2.6002

-------------------------------------------------------------------------------
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 = 0.062795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.049654 restraints weight = 20085.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.2623 rms_B_bonded: 2.52
r_work: 0.2488 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2365 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9069
moved from start:          0.1178

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= 0.168
  Angle     :  0.470   6.339  13832  Z= 0.266
  Chirality :  0.045   0.134   1580
  Planarity :  0.004   0.043   1796
  Dihedral  :  4.136  16.474   1412
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 13.69 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.24), residues: 1328
  helix:  2.17 (0.27), residues: 372
  sheet: -0.67 (0.32), residues: 288
  loop : -0.16 (0.26), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  80 
 TYR   0.010   0.001   TYR D 314 
 PHE   0.009   0.001   PHE A 286 
 TRP   0.004   0.001   TRP C 313 
 HIS   0.003   0.001   HIS C 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (10196)
  covalent geometry    : angle       0.47004 (13832)
  hydrogen bonds       : bond        0.04558 (  448)
  hydrogen bonds       : angle       5.18122 ( 1368)

*********************** 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
  76 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.399 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8712 (mp0) cc_final: 0.8434 (mp0)
REVERT: A  223 GLU cc_start: 0.8711 (mp0) cc_final: 0.8433 (mp0)
REVERT: C  223 GLU cc_start: 0.8707 (mp0) cc_final: 0.8432 (mp0)
REVERT: D  223 GLU cc_start: 0.8709 (mp0) cc_final: 0.8432 (mp0)
  outliers start: 12
  outliers final: 8
  residues processed: 76
  average time/residue: 0.6709
  time to fit residues: 54.2458
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  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue  143 SER
Chi-restraints excluded: chain D residue  243 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 66 optimal weight:   10.0000
   chunk 87 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9990
   chunk 11 optimal weight:    8.9990
   chunk 67 optimal weight:    6.9990
   chunk 85 optimal weight:    5.9990
   chunk 115 optimal weight:    0.0980
   overall best weight:    1.2186

-------------------------------------------------------------------------------
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 = 0.2966 r_free = 0.2966 target = 0.064842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.051685 restraints weight = 19761.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.2672 rms_B_bonded: 2.53
r_work: 0.2540 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2418 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9029
moved from start:          0.1233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016  10196  Z= 0.095
  Angle     :  0.413   5.388  13832  Z= 0.232
  Chirality :  0.043   0.123   1580
  Planarity :  0.004   0.039   1796
  Dihedral  :  3.820  16.221   1412
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 14.26 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.25), residues: 1328
  helix:  2.53 (0.27), residues: 372
  sheet: -0.69 (0.31), residues: 288
  loop :  0.01 (0.27), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  80 
 TYR   0.007   0.001   TYR D 314 
 PHE   0.006   0.001   PHE D 286 
 TRP   0.004   0.001   TRP C 313 
 HIS   0.002   0.000   HIS B 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 (10196)
  covalent geometry    : angle       0.41267 (13832)
  hydrogen bonds       : bond        0.03467 (  448)
  hydrogen bonds       : angle       4.84287 ( 1368)

*********************** 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
  76 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.411 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8681 (mp0) cc_final: 0.8409 (mp0)
REVERT: A  223 GLU cc_start: 0.8694 (mp0) cc_final: 0.8421 (mp0)
REVERT: C  223 GLU cc_start: 0.8680 (mp0) cc_final: 0.8408 (mp0)
REVERT: D  223 GLU cc_start: 0.8680 (mp0) cc_final: 0.8411 (mp0)
  outliers start: 12
  outliers final: 4
  residues processed: 76
  average time/residue: 0.7826
  time to fit residues: 63.1186
Evaluate side-chains
  68 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue  243 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 91 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 1 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 108 optimal weight:    4.9990
   chunk 127 optimal weight:    0.0970
   chunk 38 optimal weight:    9.9990
   overall best weight:    3.2186

-------------------------------------------------------------------------------
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 = 0.2913 r_free = 0.2913 target = 0.062136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.048909 restraints weight = 20138.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.2607 rms_B_bonded: 2.53
r_work: 0.2470 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2347 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9081
moved from start:          0.1245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026  10196  Z= 0.203
  Angle     :  0.492   6.780  13832  Z= 0.278
  Chirality :  0.046   0.148   1580
  Planarity :  0.004   0.042   1796
  Dihedral  :  4.146  17.044   1412
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 13.59 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.24), residues: 1328
  helix:  2.20 (0.26), residues: 372
  sheet: -0.66 (0.32), residues: 288
  loop : -0.11 (0.26), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  80 
 TYR   0.011   0.001   TYR C 314 
 PHE   0.010   0.001   PHE A 286 
 TRP   0.003   0.001   TRP D  87 
 HIS   0.003   0.001   HIS B 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (10196)
  covalent geometry    : angle       0.49217 (13832)
  hydrogen bonds       : bond        0.04852 (  448)
  hydrogen bonds       : angle       5.15313 ( 1368)

*********************** 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
  80 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.408 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8711 (mp0) cc_final: 0.8432 (mp0)
REVERT: A  223 GLU cc_start: 0.8705 (mp0) cc_final: 0.8429 (mp0)
REVERT: C  223 GLU cc_start: 0.8697 (mp0) cc_final: 0.8422 (mp0)
REVERT: D  223 GLU cc_start: 0.8704 (mp0) cc_final: 0.8430 (mp0)
  outliers start: 16
  outliers final: 8
  residues processed: 80
  average time/residue: 0.7317
  time to fit residues: 62.4114
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  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue  143 SER
Chi-restraints excluded: chain D residue  243 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 107 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 81 optimal weight:    7.9990
   chunk 101 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 131 optimal weight:    6.9990
   chunk 48 optimal weight:    7.9990
   chunk 49 optimal weight:    0.7980
   chunk 27 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    3.3588

-------------------------------------------------------------------------------
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 = 0.2908 r_free = 0.2908 target = 0.061877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.048738 restraints weight = 20108.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.2603 rms_B_bonded: 2.52
r_work: 0.2467 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2343 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9085
moved from start:          0.1269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027  10196  Z= 0.210
  Angle     :  0.501   6.831  13832  Z= 0.283
  Chirality :  0.046   0.149   1580
  Planarity :  0.004   0.045   1796
  Dihedral  :  4.206  17.914   1412
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 14.26 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.24), residues: 1328
  helix:  2.13 (0.26), residues: 372
  sheet: -0.72 (0.31), residues: 288
  loop : -0.20 (0.26), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  80 
 TYR   0.011   0.001   TYR D 314 
 PHE   0.011   0.001   PHE A 286 
 TRP   0.003   0.001   TRP A  87 
 HIS   0.003   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 (10196)
  covalent geometry    : angle       0.50111 (13832)
  hydrogen bonds       : bond        0.04935 (  448)
  hydrogen bonds       : angle       5.17666 ( 1368)

*********************** 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
  70 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.401 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8713 (mp0) cc_final: 0.8434 (mp0)
REVERT: A  223 GLU cc_start: 0.8711 (mp0) cc_final: 0.8434 (mp0)
REVERT: C  223 GLU cc_start: 0.8706 (mp0) cc_final: 0.8429 (mp0)
REVERT: D  223 GLU cc_start: 0.8709 (mp0) cc_final: 0.8433 (mp0)
  outliers start: 6
  outliers final: 6
  residues processed: 70
  average time/residue: 0.8400
  time to fit residues: 62.1614
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  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue  243 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 120 optimal weight:    0.9990
   chunk 27 optimal weight:    0.4980
   chunk 92 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0970
   chunk 98 optimal weight:    7.9990
   chunk 79 optimal weight:    3.9990
   chunk 131 optimal weight:    0.9980
   chunk 127 optimal weight:    0.0670
   chunk 60 optimal weight:    0.0670
   overall best weight:    0.3054

-------------------------------------------------------------------------------
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 = 0.3027 r_free = 0.3027 target = 0.067980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.054950 restraints weight = 19799.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.2750 rms_B_bonded: 2.55
r_work: 0.2621 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2499 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8973
moved from start:          0.1496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.019  10196  Z= 0.062
  Angle     :  0.386   4.143  13832  Z= 0.214
  Chirality :  0.042   0.125   1580
  Planarity :  0.003   0.042   1796
  Dihedral  :  3.550  17.330   1412
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 14.64 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.25), residues: 1328
  helix:  2.74 (0.27), residues: 396
  sheet: -0.70 (0.31), residues: 288
  loop :  0.10 (0.28), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  80 
 TYR   0.006   0.001   TYR D  49 
 PHE   0.004   0.000   PHE A 286 
 TRP   0.005   0.001   TRP C 313 
 HIS   0.002   0.000   HIS D 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00126 (10196)
  covalent geometry    : angle       0.38644 (13832)
  hydrogen bonds       : bond        0.02531 (  448)
  hydrogen bonds       : angle       4.53946 ( 1368)

*********************** 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
  78 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.408 
Fit side-chains
REVERT: B   78 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8922 (mm110)
REVERT: A   78 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8918 (mm110)
REVERT: C   78 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8888 (mm110)
REVERT: D   78 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8898 (mm110)
  outliers start: 6
  outliers final: 6
  residues processed: 78
  average time/residue: 0.7548
  time to fit residues: 62.6779
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  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue  143 SER
Chi-restraints excluded: chain D residue  243 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   chunk 92 optimal weight:    4.9990
   chunk 66 optimal weight:   10.0000
   chunk 13 optimal weight:    0.0980
   chunk 36 optimal weight:    9.9990
   chunk 117 optimal weight:    7.9990
   chunk 64 optimal weight:    6.9990
   chunk 120 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 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 = 0.2939 r_free = 0.2939 target = 0.063473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.050219 restraints weight = 19879.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.2636 rms_B_bonded: 2.54
r_work: 0.2501 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2378 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9057
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023  10196  Z= 0.153
  Angle     :  0.459   5.885  13832  Z= 0.263
  Chirality :  0.044   0.124   1580
  Planarity :  0.005   0.064   1796
  Dihedral  :  3.878  14.782   1412
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 15.40 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.25), residues: 1328
  helix:  2.67 (0.27), residues: 372
  sheet: -0.63 (0.32), residues: 288
  loop :  0.06 (0.27), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  80 
 TYR   0.009   0.001   TYR B 314 
 PHE   0.008   0.001   PHE C 286 
 TRP   0.004   0.001   TRP A 313 
 HIS   0.003   0.001   HIS A 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (10196)
  covalent geometry    : angle       0.45871 (13832)
  hydrogen bonds       : bond        0.04082 (  448)
  hydrogen bonds       : angle       4.85685 ( 1368)

*********************** 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
  70 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.298 
Fit side-chains
REVERT: B   78 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8929 (mm110)
REVERT: B  223 GLU cc_start: 0.8720 (mp0) cc_final: 0.8438 (mp0)
REVERT: A   78 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8917 (mm110)
REVERT: A  223 GLU cc_start: 0.8718 (mp0) cc_final: 0.8437 (mp0)
REVERT: C   78 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8894 (mm110)
REVERT: C  223 GLU cc_start: 0.8705 (mp0) cc_final: 0.8426 (mp0)
REVERT: D  223 GLU cc_start: 0.8717 (mp0) cc_final: 0.8436 (mp0)
  outliers start: 6
  outliers final: 6
  residues processed: 70
  average time/residue: 0.7094
  time to fit residues: 52.5383
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  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue  243 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 121 optimal weight:    6.9990
   chunk 64 optimal weight:    6.9990
   chunk 100 optimal weight:    6.9990
   chunk 95 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   chunk 86 optimal weight:    0.0970
   chunk 104 optimal weight:    8.9990
   overall best weight:    3.0186

-------------------------------------------------------------------------------
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 = 0.2917 r_free = 0.2917 target = 0.062371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.049246 restraints weight = 19758.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.2614 rms_B_bonded: 2.49
r_work: 0.2480 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2357 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9076
moved from start:          0.1292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025  10196  Z= 0.192
  Angle     :  0.501   6.701  13832  Z= 0.288
  Chirality :  0.045   0.144   1580
  Planarity :  0.005   0.073   1796
  Dihedral  :  4.121  17.512   1412
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 15.40 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.24), residues: 1328
  helix:  2.33 (0.26), residues: 372
  sheet: -0.70 (0.31), residues: 288
  loop : -0.07 (0.26), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D  80 
 TYR   0.010   0.001   TYR D 314 
 PHE   0.009   0.001   PHE A 286 
 TRP   0.003   0.001   TRP D  87 
 HIS   0.003   0.001   HIS C  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 (10196)
  covalent geometry    : angle       0.50142 (13832)
  hydrogen bonds       : bond        0.04709 (  448)
  hydrogen bonds       : angle       5.06390 ( 1368)

********************** 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
  70 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.427 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8724 (mp0) cc_final: 0.8439 (mp0)
REVERT: A  223 GLU cc_start: 0.8709 (mp0) cc_final: 0.8429 (mp0)
REVERT: C  223 GLU cc_start: 0.8714 (mp0) cc_final: 0.8431 (mp0)
REVERT: D  223 GLU cc_start: 0.8714 (mp0) cc_final: 0.8432 (mp0)
  outliers start: 6
  outliers final: 6
  residues processed: 70
  average time/residue: 0.7023
  time to fit residues: 52.1354
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  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue  243 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0970
   chunk 119 optimal weight:    4.9990
   chunk 99 optimal weight:   10.0000
   chunk 111 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 61 optimal weight:    0.2980
   chunk 131 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 116 optimal weight:    7.9990
   chunk 31 optimal weight:    7.9990
   overall best weight:    1.6784

-------------------------------------------------------------------------------
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 = 0.2947 r_free = 0.2947 target = 0.063939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.050753 restraints weight = 19883.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.2648 rms_B_bonded: 2.53
r_work: 0.2514 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2391 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9049
moved from start:          0.1285

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= 0.121
  Angle     :  0.448   5.723  13832  Z= 0.257
  Chirality :  0.043   0.125   1580
  Planarity :  0.005   0.066   1796
  Dihedral  :  3.920  17.467   1412
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 6.85
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.25), residues: 1328
  helix:  2.55 (0.27), residues: 372
  sheet: -0.72 (0.31), residues: 288
  loop :  0.01 (0.27), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D  80 
 TYR   0.008   0.001   TYR A 314 
 PHE   0.007   0.001   PHE D 286 
 TRP   0.004   0.001   TRP A 313 
 HIS   0.002   0.000   HIS B 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (10196)
  covalent geometry    : angle       0.44789 (13832)
  hydrogen bonds       : bond        0.03801 (  448)
  hydrogen bonds       : angle       4.86125 ( 1368)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3225.39 seconds
wall clock time: 55 minutes 52.73 seconds (3352.73 seconds total)