Starting phenix.real_space_refine
on Fri Feb 14 06:45:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g13_29660/02_2025/8g13_29660.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g13_29660/02_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_29660/02_2025/8g13_29660.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g13_29660/02_2025/8g13_29660.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g13_29660/02_2025/8g13_29660.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g13_29660/02_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-5592/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: 4.58, per 1000 atoms: 0.46
  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: 2.46
  Conformation dependent library (CDL) restraints added in 1.4 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: 1.40
  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: 3.04

  Time building geometry restraints manager: 2.85 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: 0.07
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:             0.750
  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:             0.220
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.310
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:10.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.920
-------------------------------------------------------------------------------
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= 0.288
  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 

*********************** 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  : 1.098 
Fit side-chains
  outliers start: 9
  outliers final: 8
  residues processed: 94
  average time/residue: 1.5713
  time to fit residues: 157.2588
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  : 1.129 
-------------------------------------------------------------------------------
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 = 0.2905 r_free = 0.2905 target = 0.061712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.048584 restraints weight = 20055.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.2599 rms_B_bonded: 2.51
r_work: 0.2463 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: 0.9089
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= 0.433
  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 

*********************** 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  : 1.152 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8720 (mp0) cc_final: 0.8447 (mp0)
REVERT: A  223 GLU cc_start: 0.8733 (mp0) cc_final: 0.8460 (mp0)
REVERT: C  223 GLU cc_start: 0.8727 (mp0) cc_final: 0.8452 (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: 1.5148
  time to fit residues: 124.6355
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  : 1.150 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 69 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 114 optimal weight:    0.8980
   chunk 126 optimal weight:    6.9990
   chunk 82 optimal weight:    0.6980
   chunk 89 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    1.3382

-------------------------------------------------------------------------------
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 = 0.2964 r_free = 0.2964 target = 0.064727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.051639 restraints weight = 20115.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.2667 rms_B_bonded: 2.54
r_work: 0.2535 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2413 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9035
moved from start:          0.1130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.013  10196  Z= 0.148
  Angle     :  0.431   5.554  13832  Z= 0.244
  Chirality :  0.043   0.124   1580
  Planarity :  0.004   0.041   1796
  Dihedral  :  4.222  25.775   1416
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  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:  0.68 (0.25), residues: 1328
  helix:  2.40 (0.27), residues: 372
  sheet: -0.70 (0.32), residues: 288
  loop : -0.06 (0.27), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 313 
 HIS   0.003   0.000   HIS B 137 
 PHE   0.006   0.001   PHE D 286 
 TYR   0.008   0.001   TYR D 314 
 ARG   0.007   0.000   ARG A  80 

*********************** 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
  74 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 1.030 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8687 (mp0) cc_final: 0.8416 (mp0)
REVERT: A  223 GLU cc_start: 0.8691 (mp0) cc_final: 0.8423 (mp0)
REVERT: C  223 GLU cc_start: 0.8686 (mp0) cc_final: 0.8418 (mp0)
REVERT: D  223 GLU cc_start: 0.8685 (mp0) cc_final: 0.8418 (mp0)
  outliers start: 10
  outliers final: 0
  residues processed: 74
  average time/residue: 1.6385
  time to fit residues: 129.1548
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  : 1.195 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 116 optimal weight:    9.9990
   chunk 112 optimal weight:    5.9990
   chunk 66 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 25 optimal weight:    0.3980
   chunk 1 optimal weight:    8.9990
   chunk 26 optimal weight:    3.9990
   chunk 55 optimal weight:    0.4980
   chunk 83 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    2.7786

-------------------------------------------------------------------------------
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 = 0.2920 r_free = 0.2920 target = 0.062512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.049405 restraints weight = 19890.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.2617 rms_B_bonded: 2.51
r_work: 0.2483 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2360 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9072
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024  10196  Z= 0.280
  Angle     :  0.478   6.455  13832  Z= 0.271
  Chirality :  0.045   0.139   1580
  Planarity :  0.004   0.045   1796
  Dihedral  :  4.147  15.606   1412
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 14.45 %
    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:  0.57 (0.25), residues: 1328
  helix:  2.23 (0.27), residues: 372
  sheet: -0.66 (0.32), residues: 288
  loop : -0.12 (0.26), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 313 
 HIS   0.003   0.001   HIS B 137 
 PHE   0.010   0.001   PHE A 286 
 TYR   0.011   0.001   TYR C 314 
 ARG   0.007   0.001   ARG B  80 

*********************** 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
  72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 1.210 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8714 (mp0) cc_final: 0.8437 (mp0)
REVERT: A  223 GLU cc_start: 0.8718 (mp0) cc_final: 0.8440 (mp0)
REVERT: C  223 GLU cc_start: 0.8706 (mp0) cc_final: 0.8429 (mp0)
REVERT: D  223 GLU cc_start: 0.8702 (mp0) cc_final: 0.8428 (mp0)
  outliers start: 8
  outliers final: 8
  residues processed: 72
  average time/residue: 1.7193
  time to fit residues: 131.6374
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  : 1.067 
-------------------------------------------------------------------------------
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=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:    4.9990
   chunk 78 optimal weight:    9.9990
   chunk 95 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   overall best weight:    2.7986

-------------------------------------------------------------------------------
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 = 0.2919 r_free = 0.2919 target = 0.062470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.049365 restraints weight = 19869.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.2616 rms_B_bonded: 2.50
r_work: 0.2481 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2359 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9073
moved from start:          0.1218

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= 0.279
  Angle     :  0.477   6.405  13832  Z= 0.270
  Chirality :  0.045   0.138   1580
  Planarity :  0.004   0.048   1796
  Dihedral  :  4.158  16.933   1412
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 13.21 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.24), residues: 1328
  helix:  2.18 (0.27), residues: 372
  sheet: -0.75 (0.31), residues: 288
  loop : -0.14 (0.26), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 313 
 HIS   0.003   0.001   HIS A 137 
 PHE   0.009   0.001   PHE A 286 
 TYR   0.011   0.001   TYR A 314 
 ARG   0.008   0.001   ARG C  80 

*********************** 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
  80 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 1.246 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8713 (mp0) cc_final: 0.8435 (mp0)
REVERT: A  223 GLU cc_start: 0.8723 (mp0) cc_final: 0.8445 (mp0)
REVERT: C  223 GLU cc_start: 0.8700 (mp0) cc_final: 0.8424 (mp0)
REVERT: D  223 GLU cc_start: 0.8708 (mp0) cc_final: 0.8433 (mp0)
  outliers start: 16
  outliers final: 12
  residues processed: 80
  average time/residue: 1.5533
  time to fit residues: 132.7957
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  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue  143 SER
Chi-restraints excluded: chain D residue  220 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 21 optimal weight:    1.9990
   chunk 128 optimal weight:   10.0000
   chunk 108 optimal weight:    8.9990
   chunk 62 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 86 optimal weight:    0.0970
   chunk 39 optimal weight:    0.8980
   chunk 111 optimal weight:    3.9990
   chunk 97 optimal weight:    0.2980
   chunk 1 optimal weight:    7.9990
   chunk 85 optimal weight:    0.0270
   overall best weight:    0.6638

-------------------------------------------------------------------------------
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 = 0.2994 r_free = 0.2994 target = 0.066268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.053259 restraints weight = 19753.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.2707 rms_B_bonded: 2.51
r_work: 0.2579 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2458 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8999
moved from start:          0.1343

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= 0.097
  Angle     :  0.395   4.942  13832  Z= 0.221
  Chirality :  0.042   0.124   1580
  Planarity :  0.004   0.044   1796
  Dihedral  :  3.696  15.740   1412
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 14.64 %
    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 (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:  0.92 (0.25), residues: 1328
  helix:  2.73 (0.27), residues: 372
  sheet: -0.64 (0.31), residues: 288
  loop :  0.05 (0.27), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP A 313 
 HIS   0.002   0.000   HIS B 137 
 PHE   0.004   0.000   PHE A 286 
 TYR   0.005   0.001   TYR A 276 
 ARG   0.009   0.001   ARG D  80 

*********************** 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
  73 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 1.243 
Fit side-chains
REVERT: B   78 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8892 (mm110)
REVERT: B  223 GLU cc_start: 0.8672 (mp0) cc_final: 0.8403 (mp0)
REVERT: A   78 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8890 (mm110)
REVERT: A  223 GLU cc_start: 0.8684 (mp0) cc_final: 0.8414 (mp0)
REVERT: C   78 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8882 (mm110)
REVERT: C  223 GLU cc_start: 0.8664 (mp0) cc_final: 0.8392 (mp0)
REVERT: D   78 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8892 (mm110)
REVERT: D  223 GLU cc_start: 0.8664 (mp0) cc_final: 0.8398 (mp0)
  outliers start: 5
  outliers final: 0
  residues processed: 73
  average time/residue: 1.7817
  time to fit residues: 137.8974
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  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    9.9990
   chunk 69 optimal weight:    7.9990
   chunk 125 optimal weight:    3.9990
   chunk 15 optimal weight:    8.9990
   chunk 66 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 64 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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 = 0.2893 r_free = 0.2893 target = 0.061197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2596 r_free = 0.2596 target = 0.048050 restraints weight = 20299.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.2586 rms_B_bonded: 2.53
r_work: 0.2448 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2324 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9097
moved from start:          0.1308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.035  10196  Z= 0.447
  Angle     :  0.541   7.316  13832  Z= 0.305
  Chirality :  0.048   0.165   1580
  Planarity :  0.004   0.047   1796
  Dihedral  :  4.273  16.339   1412
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 14.07 %
    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:  0.58 (0.24), residues: 1328
  helix:  2.15 (0.26), residues: 372
  sheet: -0.59 (0.32), residues: 288
  loop : -0.09 (0.26), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  87 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.013   0.002   PHE C 286 
 TYR   0.013   0.002   TYR D 314 
 ARG   0.009   0.001   ARG D  80 

*********************** 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
  78 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 1.215 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8729 (mp0) cc_final: 0.8449 (mp0)
REVERT: A  223 GLU cc_start: 0.8733 (mp0) cc_final: 0.8452 (mp0)
REVERT: C  223 GLU cc_start: 0.8705 (mp0) cc_final: 0.8428 (mp0)
REVERT: D  223 GLU cc_start: 0.8701 (mp0) cc_final: 0.8426 (mp0)
  outliers start: 14
  outliers final: 11
  residues processed: 75
  average time/residue: 1.6144
  time to fit residues: 128.8733
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  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain D residue  220 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 120 optimal weight:    6.9990
   chunk 104 optimal weight:    7.9990
   chunk 131 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 71 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 55 optimal weight:    0.3980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.2978 r_free = 0.2978 target = 0.065512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.052383 restraints weight = 19989.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.2687 rms_B_bonded: 2.54
r_work: 0.2557 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2434 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9018
moved from start:          0.1325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019  10196  Z= 0.117
  Angle     :  0.406   5.037  13832  Z= 0.227
  Chirality :  0.043   0.125   1580
  Planarity :  0.004   0.047   1796
  Dihedral  :  3.797  17.127   1412
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 14.73 %
    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:  0.89 (0.25), residues: 1328
  helix:  2.63 (0.27), residues: 372
  sheet: -0.59 (0.31), residues: 288
  loop :  0.05 (0.27), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP D 313 
 HIS   0.002   0.000   HIS B 137 
 PHE   0.005   0.001   PHE C 286 
 TYR   0.005   0.001   TYR D 314 
 ARG   0.010   0.001   ARG B  80 

*********************** 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
  81 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 1.154 
Fit side-chains
REVERT: B   78 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8900 (mm110)
REVERT: B  223 GLU cc_start: 0.8688 (mp0) cc_final: 0.8420 (mp0)
REVERT: A   78 GLN cc_start: 0.9150 (mm-40) cc_final: 0.8893 (mm110)
REVERT: A  223 GLU cc_start: 0.8694 (mp0) cc_final: 0.8426 (mp0)
REVERT: C   78 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8898 (mm110)
REVERT: C  223 GLU cc_start: 0.8670 (mp0) cc_final: 0.8402 (mp0)
REVERT: D   78 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8898 (mm110)
REVERT: D  223 GLU cc_start: 0.8674 (mp0) cc_final: 0.8410 (mp0)
  outliers start: 9
  outliers final: 8
  residues processed: 81
  average time/residue: 1.6417
  time to fit residues: 141.4410
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  : 1.191 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 90 optimal weight:    6.9990
   chunk 98 optimal weight:    9.9990
   chunk 1 optimal weight:    8.9990
   chunk 106 optimal weight:    9.9990
   chunk 81 optimal weight:    7.9990
   chunk 48 optimal weight:    8.9990
   chunk 130 optimal weight:    6.9990
   chunk 77 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 68 optimal weight:    0.6980
   overall best weight:    4.7388

-------------------------------------------------------------------------------
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 = 0.2890 r_free = 0.2890 target = 0.061055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2593 r_free = 0.2593 target = 0.047946 restraints weight = 20120.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.2583 rms_B_bonded: 2.51
r_work: 0.2445 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2322 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9098
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.035  10196  Z= 0.458
  Angle     :  0.556   7.183  13832  Z= 0.317
  Chirality :  0.048   0.164   1580
  Planarity :  0.005   0.051   1796
  Dihedral  :  4.303  16.813   1412
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 14.83 %
    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:  0.58 (0.24), residues: 1328
  helix:  2.11 (0.26), residues: 372
  sheet: -0.54 (0.32), residues: 288
  loop : -0.09 (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 C  53 
 PHE   0.013   0.002   PHE D 286 
 TYR   0.012   0.002   TYR D 314 
 ARG   0.010   0.001   ARG C  80 

*********************** 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
  75 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 1.176 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8714 (mp0) cc_final: 0.8437 (mp0)
REVERT: A  223 GLU cc_start: 0.8718 (mp0) cc_final: 0.8443 (mp0)
REVERT: C  223 GLU cc_start: 0.8724 (mp0) cc_final: 0.8444 (mp0)
REVERT: D  223 GLU cc_start: 0.8708 (mp0) cc_final: 0.8433 (mp0)
  outliers start: 11
  outliers final: 11
  residues processed: 73
  average time/residue: 1.6672
  time to fit residues: 129.4401
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  : 1.241 
-------------------------------------------------------------------------------
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 A residue  244 ASP
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain D residue  143 SER
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 94 optimal weight:    0.0670
   chunk 79 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 125 optimal weight:    0.9990
   chunk 73 optimal weight:    7.9990
   chunk 99 optimal weight:   10.0000
   chunk 114 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    1.6124

-------------------------------------------------------------------------------
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 = 0.2942 r_free = 0.2942 target = 0.063639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.050530 restraints weight = 19968.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.2644 rms_B_bonded: 2.51
r_work: 0.2510 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2387 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9052
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  10196  Z= 0.184
  Angle     :  0.453   5.904  13832  Z= 0.261
  Chirality :  0.043   0.126   1580
  Planarity :  0.004   0.051   1796
  Dihedral  :  4.008  17.840   1412
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 15.02 %
    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:  0.74 (0.25), residues: 1328
  helix:  2.38 (0.27), residues: 372
  sheet: -0.55 (0.31), residues: 288
  loop : -0.03 (0.27), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 313 
 HIS   0.002   0.000   HIS D 137 
 PHE   0.007   0.001   PHE D 286 
 TYR   0.008   0.001   TYR A 314 
 ARG   0.011   0.001   ARG C  80 

********************** 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
  73 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 1.093 
Fit side-chains
REVERT: B  223 GLU cc_start: 0.8722 (mp0) cc_final: 0.8445 (mp0)
REVERT: A  223 GLU cc_start: 0.8724 (mp0) cc_final: 0.8450 (mp0)
REVERT: C  223 GLU cc_start: 0.8693 (mp0) cc_final: 0.8417 (mp0)
REVERT: D  223 GLU cc_start: 0.8713 (mp0) cc_final: 0.8438 (mp0)
  outliers start: 9
  outliers final: 9
  residues processed: 72
  average time/residue: 1.6832
  time to fit residues: 128.8545
Evaluate side-chains
  73 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  244 ASP
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 59 optimal weight:    0.2980
   chunk 11 optimal weight:    0.2980
   chunk 60 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 78 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 127 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 10 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.2952 r_free = 0.2952 target = 0.064125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.050970 restraints weight = 19798.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.2654 rms_B_bonded: 2.52
r_work: 0.2521 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2399 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9042
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      :  0.003   0.022  10196  Z= 0.172
  Angle     :  0.442   5.777  13832  Z= 0.253
  Chirality :  0.043   0.123   1580
  Planarity :  0.004   0.050   1796
  Dihedral  :  3.880  16.761   1412
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 15.11 %
    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:  0.85 (0.25), residues: 1328
  helix:  2.53 (0.27), residues: 372
  sheet: -0.56 (0.31), residues: 288
  loop :  0.03 (0.27), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 313 
 HIS   0.002   0.000   HIS D 137 
 PHE   0.006   0.001   PHE D 286 
 TYR   0.008   0.001   TYR A 314 
 ARG   0.011   0.001   ARG C  80 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6453.42 seconds
wall clock time: 114 minutes 59.72 seconds (6899.72 seconds total)