Starting phenix.real_space_refine
on Wed Mar  4 22:43:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lto_0976/03_2026/6lto_0976.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lto_0976/03_2026/6lto_0976.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lto_0976/03_2026/6lto_0976.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lto_0976/03_2026/6lto_0976.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lto_0976/03_2026/6lto_0976.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lto_0976/03_2026/6lto_0976.map"
  }
  resolution = 3.1
  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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      70      5.16       5
     C   11494      2.51       5
     N    2674      2.21       5
     O    3017      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17255
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2465
          Classifications: {'peptide': 308}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 14, 'TRANS': 293}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 13
  Restraints were copied for chains:
    B, C, D, E, F, G
  Time building chain proxies: 1.83, per 1000 atoms: 0.11
  Number of scatterers: 17255
  At special positions: 0
  Unit cell: (111.961, 111.961, 120.657, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      70     16.00
     O    3017      8.00
     N    2674      7.00
     C   11494      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  66 " - pdb=" SG  CYS A 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  84 " - pdb=" SG  CYS A 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  66 " - pdb=" SG  CYS B 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  66 " - pdb=" SG  CYS C 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  66 " - pdb=" SG  CYS D 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  66 " - pdb=" SG  CYS E 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  66 " - pdb=" SG  CYS F 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  66 " - pdb=" SG  CYS G 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  84 " - pdb=" SG  CYS B 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  84 " - pdb=" SG  CYS C 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  84 " - pdb=" SG  CYS D 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  84 " - pdb=" SG  CYS E 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  84 " - pdb=" SG  CYS F 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  84 " - pdb=" SG  CYS G 246 " distance=2.03

  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: 1.34
  Conformation dependent library (CDL) restraints added in 671.1 milliseconds
  

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4200

  Finding SS restraints...
    Secondary structure from input PDB file:
      98 helices and 7 sheets defined
      66.6% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 60
      removed outlier: 3.732A  pdb=" N   LYS A  36 " --> pdb=" O   LEU A  32 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   MET A  37 " --> pdb=" O   ALA A  33 " (cutoff:3.500A)
      Proline residue:  A  46  - end of helix
    Processing helix  chain 'A' and resid 73 through 87
      removed outlier: 3.554A  pdb=" N   ALA A  77 " --> pdb=" O   SER A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 98
      No H-bonds generated for 'chain 'A' and resid 96 through 98'
    Processing helix  chain 'A' and resid 99 through 120
      removed outlier: 3.961A  pdb=" N   LYS A 107 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   PHE A 108 " --> pdb=" O   TRP A 104 " (cutoff:3.500A)
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 121 through 131
    Processing helix  chain 'A' and resid 131 through 157
      removed outlier: 3.843A  pdb=" N   ILE A 135 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ASN A 151 " --> pdb=" O   ASP A 147 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ARG A 152 " --> pdb=" O   LYS A 148 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   ALA A 153 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   ILE A 154 " --> pdb=" O   TYR A 150 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   LYS A 155 " --> pdb=" O   ASN A 151 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA A 156 " --> pdb=" O   ARG A 152 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA A 157 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 203
      removed outlier: 3.888A  pdb=" N   LYS A 201 " --> pdb=" O   GLU A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 206
      No H-bonds generated for 'chain 'A' and resid 204 through 206'
    Processing helix  chain 'A' and resid 209 through 238
      removed outlier: 4.462A  pdb=" N   SER A 238 " --> pdb=" O   TYR A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 294
      removed outlier: 3.502A  pdb=" N   PHE A 273 " --> pdb=" O   ALA A 269 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LEU A 275 " --> pdb=" O   GLY A 271 " (cutoff:3.500A)
      Proline residue:  A 289  - end of helix
    Processing helix  chain 'A' and resid 306 through 312
      removed outlier: 3.824A  pdb=" N   GLU A 310 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ILE A 311 " --> pdb=" O   VAL A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 335
      removed outlier: 3.596A  pdb=" N   LEU A 330 " --> pdb=" O   ASN A 326 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU A 333 " --> pdb=" O   SER A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 339
      removed outlier: 4.198A  pdb=" N   ILE A 339 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 336 through 339'
    Processing helix  chain 'A' and resid 342 through 350
      removed outlier: 3.800A  pdb=" N   LYS A 346 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   VAL A 350 " --> pdb=" O   LYS A 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 60
      removed outlier: 3.732A  pdb=" N   LYS B  36 " --> pdb=" O   LEU B  32 " (cutoff:3.500A)
      Proline residue:  B  46  - end of helix
    Processing helix  chain 'B' and resid 73 through 87
      removed outlier: 3.554A  pdb=" N   ALA B  77 " --> pdb=" O   SER B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 98
      No H-bonds generated for 'chain 'B' and resid 96 through 98'
    Processing helix  chain 'B' and resid 99 through 120
      removed outlier: 3.961A  pdb=" N   LYS B 107 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   PHE B 108 " --> pdb=" O   TRP B 104 " (cutoff:3.500A)
      Proline residue:  B 110  - end of helix
    Processing helix  chain 'B' and resid 121 through 131
    Processing helix  chain 'B' and resid 131 through 157
      removed outlier: 3.843A  pdb=" N   ILE B 135 " --> pdb=" O   ALA B 131 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ASN B 151 " --> pdb=" O   ASP B 147 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ARG B 152 " --> pdb=" O   LYS B 148 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   ALA B 153 " --> pdb=" O   VAL B 149 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ILE B 154 " --> pdb=" O   TYR B 150 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   LYS B 155 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA B 156 " --> pdb=" O   ARG B 152 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA B 157 " --> pdb=" O   ALA B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 203
      removed outlier: 3.888A  pdb=" N   LYS B 201 " --> pdb=" O   GLU B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 206
      No H-bonds generated for 'chain 'B' and resid 204 through 206'
    Processing helix  chain 'B' and resid 209 through 238
      removed outlier: 4.462A  pdb=" N   SER B 238 " --> pdb=" O   TYR B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 294
      removed outlier: 3.503A  pdb=" N   PHE B 273 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LEU B 275 " --> pdb=" O   GLY B 271 " (cutoff:3.500A)
      Proline residue:  B 289  - end of helix
    Processing helix  chain 'B' and resid 306 through 312
      removed outlier: 3.823A  pdb=" N   GLU B 310 " --> pdb=" O   LYS B 307 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ILE B 311 " --> pdb=" O   VAL B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 335
      removed outlier: 3.596A  pdb=" N   LEU B 330 " --> pdb=" O   ASN B 326 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU B 333 " --> pdb=" O   SER B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 339
      removed outlier: 4.198A  pdb=" N   ILE B 339 " --> pdb=" O   GLU B 336 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 336 through 339'
    Processing helix  chain 'B' and resid 342 through 350
      removed outlier: 3.800A  pdb=" N   LYS B 346 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   VAL B 350 " --> pdb=" O   LYS B 346 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 32 through 60
      removed outlier: 3.732A  pdb=" N   LYS C  36 " --> pdb=" O   LEU C  32 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   MET C  37 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
      Proline residue:  C  46  - end of helix
    Processing helix  chain 'C' and resid 73 through 87
      removed outlier: 3.553A  pdb=" N   ALA C  77 " --> pdb=" O   SER C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 98
      No H-bonds generated for 'chain 'C' and resid 96 through 98'
    Processing helix  chain 'C' and resid 99 through 120
      removed outlier: 3.961A  pdb=" N   LYS C 107 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   PHE C 108 " --> pdb=" O   TRP C 104 " (cutoff:3.500A)
      Proline residue:  C 110  - end of helix
    Processing helix  chain 'C' and resid 121 through 131
    Processing helix  chain 'C' and resid 131 through 157
      removed outlier: 3.844A  pdb=" N   ILE C 135 " --> pdb=" O   ALA C 131 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ASN C 151 " --> pdb=" O   ASP C 147 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ARG C 152 " --> pdb=" O   LYS C 148 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ALA C 153 " --> pdb=" O   VAL C 149 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ILE C 154 " --> pdb=" O   TYR C 150 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   LYS C 155 " --> pdb=" O   ASN C 151 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA C 156 " --> pdb=" O   ARG C 152 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA C 157 " --> pdb=" O   ALA C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 203
      removed outlier: 3.888A  pdb=" N   LYS C 201 " --> pdb=" O   GLU C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 206
      No H-bonds generated for 'chain 'C' and resid 204 through 206'
    Processing helix  chain 'C' and resid 209 through 238
      removed outlier: 4.461A  pdb=" N   SER C 238 " --> pdb=" O   TYR C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 294
      removed outlier: 3.502A  pdb=" N   PHE C 273 " --> pdb=" O   ALA C 269 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LEU C 275 " --> pdb=" O   GLY C 271 " (cutoff:3.500A)
      Proline residue:  C 289  - end of helix
    Processing helix  chain 'C' and resid 306 through 312
      removed outlier: 3.823A  pdb=" N   GLU C 310 " --> pdb=" O   LYS C 307 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ILE C 311 " --> pdb=" O   VAL C 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 326 through 335
      removed outlier: 3.596A  pdb=" N   LEU C 330 " --> pdb=" O   ASN C 326 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU C 333 " --> pdb=" O   SER C 329 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 336 through 339
      removed outlier: 4.197A  pdb=" N   ILE C 339 " --> pdb=" O   GLU C 336 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 336 through 339'
    Processing helix  chain 'C' and resid 342 through 350
      removed outlier: 3.799A  pdb=" N   LYS C 346 " --> pdb=" O   VAL C 342 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   VAL C 350 " --> pdb=" O   LYS C 346 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 32 through 60
      removed outlier: 3.732A  pdb=" N   LYS D  36 " --> pdb=" O   LEU D  32 " (cutoff:3.500A)
      Proline residue:  D  46  - end of helix
    Processing helix  chain 'D' and resid 73 through 87
      removed outlier: 3.554A  pdb=" N   ALA D  77 " --> pdb=" O   SER D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 96 through 98
      No H-bonds generated for 'chain 'D' and resid 96 through 98'
    Processing helix  chain 'D' and resid 99 through 120
      removed outlier: 3.961A  pdb=" N   LYS D 107 " --> pdb=" O   LEU D 103 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   PHE D 108 " --> pdb=" O   TRP D 104 " (cutoff:3.500A)
      Proline residue:  D 110  - end of helix
    Processing helix  chain 'D' and resid 121 through 131
    Processing helix  chain 'D' and resid 131 through 157
      removed outlier: 3.844A  pdb=" N   ILE D 135 " --> pdb=" O   ALA D 131 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ASN D 151 " --> pdb=" O   ASP D 147 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ARG D 152 " --> pdb=" O   LYS D 148 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ALA D 153 " --> pdb=" O   VAL D 149 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ILE D 154 " --> pdb=" O   TYR D 150 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   LYS D 155 " --> pdb=" O   ASN D 151 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA D 156 " --> pdb=" O   ARG D 152 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA D 157 " --> pdb=" O   ALA D 153 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 195 through 203
      removed outlier: 3.888A  pdb=" N   LYS D 201 " --> pdb=" O   GLU D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 206
      No H-bonds generated for 'chain 'D' and resid 204 through 206'
    Processing helix  chain 'D' and resid 209 through 238
      removed outlier: 4.462A  pdb=" N   SER D 238 " --> pdb=" O   TYR D 234 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 294
      removed outlier: 3.503A  pdb=" N   PHE D 273 " --> pdb=" O   ALA D 269 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LEU D 275 " --> pdb=" O   GLY D 271 " (cutoff:3.500A)
      Proline residue:  D 289  - end of helix
    Processing helix  chain 'D' and resid 306 through 312
      removed outlier: 3.823A  pdb=" N   GLU D 310 " --> pdb=" O   LYS D 307 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ILE D 311 " --> pdb=" O   VAL D 308 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 326 through 335
      removed outlier: 3.596A  pdb=" N   LEU D 330 " --> pdb=" O   ASN D 326 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU D 333 " --> pdb=" O   SER D 329 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 336 through 339
      removed outlier: 4.198A  pdb=" N   ILE D 339 " --> pdb=" O   GLU D 336 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 336 through 339'
    Processing helix  chain 'D' and resid 342 through 350
      removed outlier: 3.799A  pdb=" N   LYS D 346 " --> pdb=" O   VAL D 342 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   VAL D 350 " --> pdb=" O   LYS D 346 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 32 through 60
      removed outlier: 3.732A  pdb=" N   LYS E  36 " --> pdb=" O   LEU E  32 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   MET E  37 " --> pdb=" O   ALA E  33 " (cutoff:3.500A)
      Proline residue:  E  46  - end of helix
    Processing helix  chain 'E' and resid 73 through 87
      removed outlier: 3.554A  pdb=" N   ALA E  77 " --> pdb=" O   SER E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 96 through 98
      No H-bonds generated for 'chain 'E' and resid 96 through 98'
    Processing helix  chain 'E' and resid 99 through 120
      removed outlier: 3.961A  pdb=" N   LYS E 107 " --> pdb=" O   LEU E 103 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   PHE E 108 " --> pdb=" O   TRP E 104 " (cutoff:3.500A)
      Proline residue:  E 110  - end of helix
    Processing helix  chain 'E' and resid 121 through 131
    Processing helix  chain 'E' and resid 131 through 157
      removed outlier: 3.844A  pdb=" N   ILE E 135 " --> pdb=" O   ALA E 131 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ASN E 151 " --> pdb=" O   ASP E 147 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ARG E 152 " --> pdb=" O   LYS E 148 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   ALA E 153 " --> pdb=" O   VAL E 149 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ILE E 154 " --> pdb=" O   TYR E 150 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   LYS E 155 " --> pdb=" O   ASN E 151 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA E 156 " --> pdb=" O   ARG E 152 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA E 157 " --> pdb=" O   ALA E 153 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 195 through 203
      removed outlier: 3.888A  pdb=" N   LYS E 201 " --> pdb=" O   GLU E 197 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 204 through 206
      No H-bonds generated for 'chain 'E' and resid 204 through 206'
    Processing helix  chain 'E' and resid 209 through 238
      removed outlier: 4.462A  pdb=" N   SER E 238 " --> pdb=" O   TYR E 234 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 294
      removed outlier: 3.502A  pdb=" N   PHE E 273 " --> pdb=" O   ALA E 269 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   LEU E 275 " --> pdb=" O   GLY E 271 " (cutoff:3.500A)
      Proline residue:  E 289  - end of helix
    Processing helix  chain 'E' and resid 306 through 312
      removed outlier: 3.823A  pdb=" N   GLU E 310 " --> pdb=" O   LYS E 307 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ILE E 311 " --> pdb=" O   VAL E 308 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 326 through 335
      removed outlier: 3.595A  pdb=" N   LEU E 330 " --> pdb=" O   ASN E 326 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU E 333 " --> pdb=" O   SER E 329 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 336 through 339
      removed outlier: 4.198A  pdb=" N   ILE E 339 " --> pdb=" O   GLU E 336 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 336 through 339'
    Processing helix  chain 'E' and resid 342 through 350
      removed outlier: 3.800A  pdb=" N   LYS E 346 " --> pdb=" O   VAL E 342 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   VAL E 350 " --> pdb=" O   LYS E 346 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 32 through 60
      removed outlier: 3.732A  pdb=" N   LYS F  36 " --> pdb=" O   LEU F  32 " (cutoff:3.500A)
      Proline residue:  F  46  - end of helix
    Processing helix  chain 'F' and resid 73 through 87
      removed outlier: 3.553A  pdb=" N   ALA F  77 " --> pdb=" O   SER F  73 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 96 through 98
      No H-bonds generated for 'chain 'F' and resid 96 through 98'
    Processing helix  chain 'F' and resid 99 through 120
      removed outlier: 3.961A  pdb=" N   LYS F 107 " --> pdb=" O   LEU F 103 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   PHE F 108 " --> pdb=" O   TRP F 104 " (cutoff:3.500A)
      Proline residue:  F 110  - end of helix
    Processing helix  chain 'F' and resid 121 through 131
    Processing helix  chain 'F' and resid 131 through 157
      removed outlier: 3.844A  pdb=" N   ILE F 135 " --> pdb=" O   ALA F 131 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ASN F 151 " --> pdb=" O   ASP F 147 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ARG F 152 " --> pdb=" O   LYS F 148 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ALA F 153 " --> pdb=" O   VAL F 149 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ILE F 154 " --> pdb=" O   TYR F 150 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   LYS F 155 " --> pdb=" O   ASN F 151 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA F 156 " --> pdb=" O   ARG F 152 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA F 157 " --> pdb=" O   ALA F 153 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 195 through 203
      removed outlier: 3.888A  pdb=" N   LYS F 201 " --> pdb=" O   GLU F 197 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 204 through 206
      No H-bonds generated for 'chain 'F' and resid 204 through 206'
    Processing helix  chain 'F' and resid 209 through 238
      removed outlier: 4.461A  pdb=" N   SER F 238 " --> pdb=" O   TYR F 234 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 269 through 294
      removed outlier: 3.502A  pdb=" N   PHE F 273 " --> pdb=" O   ALA F 269 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LEU F 275 " --> pdb=" O   GLY F 271 " (cutoff:3.500A)
      Proline residue:  F 289  - end of helix
    Processing helix  chain 'F' and resid 306 through 312
      removed outlier: 3.823A  pdb=" N   GLU F 310 " --> pdb=" O   LYS F 307 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ILE F 311 " --> pdb=" O   VAL F 308 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 326 through 335
      removed outlier: 3.596A  pdb=" N   LEU F 330 " --> pdb=" O   ASN F 326 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU F 333 " --> pdb=" O   SER F 329 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 336 through 339
      removed outlier: 4.198A  pdb=" N   ILE F 339 " --> pdb=" O   GLU F 336 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 336 through 339'
    Processing helix  chain 'F' and resid 342 through 350
      removed outlier: 3.800A  pdb=" N   LYS F 346 " --> pdb=" O   VAL F 342 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   VAL F 350 " --> pdb=" O   LYS F 346 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 32 through 60
      removed outlier: 3.732A  pdb=" N   LYS G  36 " --> pdb=" O   LEU G  32 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   MET G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
      Proline residue:  G  46  - end of helix
    Processing helix  chain 'G' and resid 73 through 87
      removed outlier: 3.554A  pdb=" N   ALA G  77 " --> pdb=" O   SER G  73 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 96 through 98
      No H-bonds generated for 'chain 'G' and resid 96 through 98'
    Processing helix  chain 'G' and resid 99 through 120
      removed outlier: 3.962A  pdb=" N   LYS G 107 " --> pdb=" O   LEU G 103 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   PHE G 108 " --> pdb=" O   TRP G 104 " (cutoff:3.500A)
      Proline residue:  G 110  - end of helix
    Processing helix  chain 'G' and resid 121 through 131
    Processing helix  chain 'G' and resid 131 through 157
      removed outlier: 3.843A  pdb=" N   ILE G 135 " --> pdb=" O   ALA G 131 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ASN G 151 " --> pdb=" O   ASP G 147 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ARG G 152 " --> pdb=" O   LYS G 148 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   ALA G 153 " --> pdb=" O   VAL G 149 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ILE G 154 " --> pdb=" O   TYR G 150 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   LYS G 155 " --> pdb=" O   ASN G 151 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA G 156 " --> pdb=" O   ARG G 152 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA G 157 " --> pdb=" O   ALA G 153 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 195 through 203
      removed outlier: 3.889A  pdb=" N   LYS G 201 " --> pdb=" O   GLU G 197 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 204 through 206
      No H-bonds generated for 'chain 'G' and resid 204 through 206'
    Processing helix  chain 'G' and resid 209 through 238
      removed outlier: 4.462A  pdb=" N   SER G 238 " --> pdb=" O   TYR G 234 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 269 through 294
      removed outlier: 3.503A  pdb=" N   PHE G 273 " --> pdb=" O   ALA G 269 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LEU G 275 " --> pdb=" O   GLY G 271 " (cutoff:3.500A)
      Proline residue:  G 289  - end of helix
    Processing helix  chain 'G' and resid 306 through 312
      removed outlier: 3.823A  pdb=" N   GLU G 310 " --> pdb=" O   LYS G 307 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ILE G 311 " --> pdb=" O   VAL G 308 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 326 through 335
      removed outlier: 3.596A  pdb=" N   LEU G 330 " --> pdb=" O   ASN G 326 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU G 333 " --> pdb=" O   SER G 329 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 336 through 339
      removed outlier: 4.198A  pdb=" N   ILE G 339 " --> pdb=" O   GLU G 336 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 336 through 339'
    Processing helix  chain 'G' and resid 342 through 350
      removed outlier: 3.800A  pdb=" N   LYS G 346 " --> pdb=" O   VAL G 342 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   VAL G 350 " --> pdb=" O   LYS G 346 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66
    Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66
    Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66
    Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66
    Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66
    Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66
    Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66

    885 hydrogen bonds defined for protein.
    2592 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: 2.18

  Time building geometry restraints manager: 1.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4991
        1.34 -     1.46: 3005
        1.46 -     1.57: 9595
        1.57 -     1.69: 0
        1.69 -     1.81: 77
  Bond restraints: 17668
  Sorted by residual:
  bond pdb=" C   GLU B  22 "
       pdb=" N   PRO B  23 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.050 2.34e-02 1.83e+03 4.49e+00
  bond pdb=" C   GLU F  22 "
       pdb=" N   PRO F  23 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.049 2.34e-02 1.83e+03 4.47e+00
  bond pdb=" C   GLU C  22 "
       pdb=" N   PRO C  23 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.049 2.34e-02 1.83e+03 4.47e+00
  bond pdb=" C   GLU G  22 "
       pdb=" N   PRO G  23 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.049 2.34e-02 1.83e+03 4.46e+00
  bond pdb=" C   GLU D  22 "
       pdb=" N   PRO D  23 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.049 2.34e-02 1.83e+03 4.44e+00
  ... (remaining 17663 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.90: 23479
        2.90 -     5.80: 440
        5.80 -     8.71: 70
        8.71 -    11.61: 7
       11.61 -    14.51: 14
  Bond angle restraints: 24010
  Sorted by residual:
  angle pdb=" CA  LEU A 237 "
        pdb=" CB  LEU A 237 "
        pdb=" CG  LEU A 237 "
      ideal   model   delta    sigma   weight residual
     116.30  130.81  -14.51 3.50e+00 8.16e-02 1.72e+01
  angle pdb=" CA  LEU F 237 "
        pdb=" CB  LEU F 237 "
        pdb=" CG  LEU F 237 "
      ideal   model   delta    sigma   weight residual
     116.30  130.80  -14.50 3.50e+00 8.16e-02 1.72e+01
  angle pdb=" CA  LEU B 237 "
        pdb=" CB  LEU B 237 "
        pdb=" CG  LEU B 237 "
      ideal   model   delta    sigma   weight residual
     116.30  130.79  -14.49 3.50e+00 8.16e-02 1.71e+01
  angle pdb=" CA  LEU E 237 "
        pdb=" CB  LEU E 237 "
        pdb=" CG  LEU E 237 "
      ideal   model   delta    sigma   weight residual
     116.30  130.79  -14.49 3.50e+00 8.16e-02 1.71e+01
  angle pdb=" CA  LEU G 237 "
        pdb=" CB  LEU G 237 "
        pdb=" CG  LEU G 237 "
      ideal   model   delta    sigma   weight residual
     116.30  130.77  -14.47 3.50e+00 8.16e-02 1.71e+01
  ... (remaining 24005 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.80: 9471
       16.80 -    33.60: 924
       33.60 -    50.41: 147
       50.41 -    67.21: 28
       67.21 -    84.01: 42
  Dihedral angle restraints: 10612
    sinusoidal: 4165
      harmonic: 6447
  Sorted by residual:
  dihedral pdb=" CA  LEU A 237 "
           pdb=" C   LEU A 237 "
           pdb=" N   SER A 238 "
           pdb=" CA  SER A 238 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.06   18.94     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  LEU D 237 "
           pdb=" C   LEU D 237 "
           pdb=" N   SER D 238 "
           pdb=" CA  SER D 238 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.08   18.92     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  LEU C 237 "
           pdb=" C   LEU C 237 "
           pdb=" N   SER C 238 "
           pdb=" CA  SER C 238 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.12   18.88     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 10609 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1756
       0.042 -    0.084: 780
       0.084 -    0.126: 247
       0.126 -    0.168: 52
       0.168 -    0.211: 21
  Chirality restraints: 2856
  Sorted by residual:
  chirality pdb=" CB  VAL A 317 "
            pdb=" CA  VAL A 317 "
            pdb=" CG1 VAL A 317 "
            pdb=" CG2 VAL A 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CB  VAL C 317 "
            pdb=" CA  VAL C 317 "
            pdb=" CG1 VAL C 317 "
            pdb=" CG2 VAL C 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CB  VAL F 317 "
            pdb=" CA  VAL F 317 "
            pdb=" CG1 VAL F 317 "
            pdb=" CG2 VAL F 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 2853 not shown)

  Planarity restraints: 2912
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 101 "   -0.042 5.00e-02 4.00e+02   6.34e-02 6.44e+00
        pdb=" N   PRO B 102 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO B 102 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 102 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 101 "   -0.042 5.00e-02 4.00e+02   6.34e-02 6.43e+00
        pdb=" N   PRO A 102 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 102 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 102 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 101 "   -0.042 5.00e-02 4.00e+02   6.32e-02 6.40e+00
        pdb=" N   PRO D 102 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO D 102 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D 102 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 2909 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 5414
        2.83 -     3.35: 16176
        3.35 -     3.87: 26278
        3.87 -     4.38: 28971
        4.38 -     4.90: 51825
  Nonbonded interactions: 128664
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A  56 "
            pdb=" OH  TYR F 111 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" O   SER E 238 "
            pdb=" OG  SER E 238 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OH  TYR E 111 "
            pdb=" OE1 GLN G  56 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" O   SER F 238 "
            pdb=" OG  SER F 238 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" O   SER G 238 "
            pdb=" OG  SER G 238 "
     model   vdw
     2.323 3.040
  ... (remaining 128659 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

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:             0.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     12.590
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
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      :  0.007   0.077  17682  Z= 0.283
  Angle     :  0.996  14.509  24038  Z= 0.516
  Chirality :  0.054   0.211   2856
  Planarity :  0.008   0.063   2912
  Dihedral  : 14.553  84.010   6370
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 2.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  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 are not related in a simple way.
  whole: -4.14 (0.14), residues: 2128
  helix: -2.17 (0.11), residues: 1295
  sheet: -1.42 (0.37), residues: 126
  loop : -3.91 (0.18), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 300 
 TYR   0.017   0.002   TYR C 213 
 PHE   0.017   0.002   PHE G 244 
 TRP   0.013   0.003   TRP G 127 
 HIS   0.004   0.002   HIS C 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00681 (17668)
  covalent geometry    : angle       0.99598 (24010)
  SS BOND              : bond        0.00190 (   14)
  SS BOND              : angle       0.94240 (   28)
  hydrogen bonds       : bond        0.13576 (  885)
  hydrogen bonds       : angle       5.03065 ( 2592)

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

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

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A   90 GLN cc_start: 0.8649 (pm20) cc_final: 0.8348 (pm20)
REVERT: A  104 TRP cc_start: 0.7793 (t60) cc_final: 0.7411 (t60)
REVERT: A  347 CYS cc_start: 0.8199 (m) cc_final: 0.7963 (m)
REVERT: B  104 TRP cc_start: 0.7832 (t60) cc_final: 0.7454 (t60)
REVERT: B  208 ASN cc_start: 0.8466 (t0) cc_final: 0.8182 (t0)
REVERT: B  347 CYS cc_start: 0.8321 (m) cc_final: 0.8108 (m)
REVERT: C   37 MET cc_start: 0.7561 (ttp) cc_final: 0.7195 (tmm)
REVERT: C  208 ASN cc_start: 0.8683 (t0) cc_final: 0.8369 (t0)
REVERT: D   37 MET cc_start: 0.7492 (ttp) cc_final: 0.7203 (tmm)
REVERT: D  208 ASN cc_start: 0.8646 (t0) cc_final: 0.8305 (t0)
REVERT: F   37 MET cc_start: 0.7362 (ttp) cc_final: 0.7028 (tmm)
REVERT: F  104 TRP cc_start: 0.7933 (t60) cc_final: 0.7527 (t60)
REVERT: F  208 ASN cc_start: 0.8597 (t0) cc_final: 0.8157 (t0)
REVERT: F  307 LYS cc_start: 0.9389 (tptt) cc_final: 0.8986 (tppt)
REVERT: G   90 GLN cc_start: 0.8550 (pm20) cc_final: 0.8236 (pm20)
REVERT: G  104 TRP cc_start: 0.7665 (t60) cc_final: 0.7355 (t60)
REVERT: G  299 PHE cc_start: 0.8528 (t80) cc_final: 0.8307 (t80)
REVERT: G  334 PHE cc_start: 0.7409 (t80) cc_final: 0.6875 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 226
  average time/residue: 0.1118
  time to fit residues: 40.0493
Evaluate side-chains
  159 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 194 optimal weight:    0.0980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    8.9990
   chunk 200 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.8980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
A 205 ASN
A 274 GLN
A 280 ASN
A 319 HIS
B  76 GLN
B 100 ASN
B 205 ASN
B 274 GLN
B 280 ASN
B 319 HIS
C  76 GLN
C 205 ASN
C 274 GLN
C 280 ASN
C 319 HIS
D  76 GLN
D 100 ASN
D 205 ASN
D 274 GLN
D 280 ASN
D 319 HIS
E  76 GLN
E 205 ASN
E 274 GLN
E 280 ASN
E 319 HIS
F  76 GLN
F 100 ASN
F 205 ASN
F 274 GLN
F 280 ASN
F 319 HIS
G  76 GLN
G 205 ASN
G 274 GLN
G 280 ASN
G 319 HIS

Total number of N/Q/H flips: 38

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.171593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.114089 restraints weight = 22962.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.69
r_work: 0.3167 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  17682  Z= 0.111
  Angle     :  0.587   9.849  24038  Z= 0.290
  Chirality :  0.037   0.115   2856
  Planarity :  0.006   0.049   2912
  Dihedral  :  4.433  19.248   2296
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 11.76 %
    Favored  : 86.59 %
  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 are not related in a simple way.
  whole: -1.81 (0.18), residues: 2128
  helix: -0.02 (0.14), residues: 1302
  sheet: -0.89 (0.42), residues: 126
  loop : -3.58 (0.20), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  29 
 TYR   0.013   0.001   TYR A 345 
 PHE   0.008   0.001   PHE E 244 
 TRP   0.003   0.001   TRP G 127 
 HIS   0.001   0.000   HIS G 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (17668)
  covalent geometry    : angle       0.58685 (24010)
  SS BOND              : bond        0.00058 (   14)
  SS BOND              : angle       0.61447 (   28)
  hydrogen bonds       : bond        0.04364 (  885)
  hydrogen bonds       : angle       3.56894 ( 2592)

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

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

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 233
  time to evaluate  : 0.458 
Fit side-chains
REVERT: A   31 GLU cc_start: 0.7203 (mp0) cc_final: 0.6841 (mp0)
REVERT: A  104 TRP cc_start: 0.8145 (t60) cc_final: 0.7651 (t60)
REVERT: A  347 CYS cc_start: 0.8296 (m) cc_final: 0.8040 (m)
REVERT: B  104 TRP cc_start: 0.8132 (t60) cc_final: 0.7923 (t60)
REVERT: B  208 ASN cc_start: 0.8531 (t0) cc_final: 0.8173 (t0)
REVERT: B  280 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8233 (t0)
REVERT: B  347 CYS cc_start: 0.8145 (m) cc_final: 0.7751 (m)
REVERT: C   31 GLU cc_start: 0.6921 (mp0) cc_final: 0.6695 (mp0)
REVERT: C   37 MET cc_start: 0.7528 (ttp) cc_final: 0.6990 (tmm)
REVERT: C  208 ASN cc_start: 0.8726 (t0) cc_final: 0.8319 (t0)
REVERT: D   31 GLU cc_start: 0.6996 (mp0) cc_final: 0.6698 (mp0)
REVERT: D   37 MET cc_start: 0.7553 (ttp) cc_final: 0.7167 (tmm)
REVERT: D  208 ASN cc_start: 0.8702 (t0) cc_final: 0.8211 (t0)
REVERT: E   30 LEU cc_start: 0.7518 (mt) cc_final: 0.7276 (mp)
REVERT: E   31 GLU cc_start: 0.7103 (mp0) cc_final: 0.6889 (mp0)
REVERT: E   37 MET cc_start: 0.7585 (ttp) cc_final: 0.7238 (tmm)
REVERT: E  208 ASN cc_start: 0.8518 (t0) cc_final: 0.8177 (t0)
REVERT: E  345 TYR cc_start: 0.7759 (t80) cc_final: 0.7520 (t80)
REVERT: F   37 MET cc_start: 0.7413 (ttp) cc_final: 0.7029 (tmm)
REVERT: F  208 ASN cc_start: 0.8684 (t0) cc_final: 0.8126 (t0)
REVERT: G   90 GLN cc_start: 0.8568 (pm20) cc_final: 0.8178 (pm20)
REVERT: G  299 PHE cc_start: 0.8695 (t80) cc_final: 0.8476 (t80)
  outliers start: 32
  outliers final: 16
  residues processed: 249
  average time/residue: 0.1126
  time to fit residues: 44.1972
Evaluate side-chains
  195 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 178
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue  280 ASN
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  353 ASN
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  343 LYS
Chi-restraints excluded: chain D residue  353 ASN
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain F residue  225 LEU
Chi-restraints excluded: chain F residue  343 LYS
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain G residue   62 THR
Chi-restraints excluded: chain G residue  343 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 74 optimal weight:   20.0000
   chunk 145 optimal weight:    5.9990
   chunk 126 optimal weight:    4.9990
   chunk 123 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0070
   chunk 128 optimal weight:    4.9990
   chunk 204 optimal weight:   10.0000
   chunk 139 optimal weight:    6.9990
   chunk 159 optimal weight:    6.9990
   chunk 148 optimal weight:    5.9990
   overall best weight:    4.4006

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
A 205 ASN
A 280 ASN
B  89 GLN
B 205 ASN
B 280 ASN
C  89 GLN
C 205 ASN
D  89 GLN
D 205 ASN
D 280 ASN
E  89 GLN
E 205 ASN
F  89 GLN
F 205 ASN
F 280 ASN
G  89 GLN
G 205 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.163528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.107215 restraints weight = 23548.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.65
r_work: 0.3072 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068  17682  Z= 0.255
  Angle     :  0.705  11.088  24038  Z= 0.356
  Chirality :  0.042   0.168   2856
  Planarity :  0.006   0.055   2912
  Dihedral  :  4.666  18.839   2296
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 13.77 %
    Favored  : 83.08 %
  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 are not related in a simple way.
  whole: -1.12 (0.19), residues: 2128
  helix:  0.59 (0.15), residues: 1309
  sheet: -0.72 (0.44), residues: 126
  loop : -3.46 (0.21), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  29 
 TYR   0.021   0.002   TYR C 213 
 PHE   0.015   0.002   PHE B 244 
 TRP   0.014   0.003   TRP D  85 
 HIS   0.003   0.001   HIS G 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00636 (17668)
  covalent geometry    : angle       0.70536 (24010)
  SS BOND              : bond        0.00287 (   14)
  SS BOND              : angle       0.63949 (   28)
  hydrogen bonds       : bond        0.06234 (  885)
  hydrogen bonds       : angle       3.96230 ( 2592)

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

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

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 187
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A   31 GLU cc_start: 0.7128 (mp0) cc_final: 0.6698 (mp0)
REVERT: A   37 MET cc_start: 0.7386 (tmm) cc_final: 0.7092 (tmm)
REVERT: A   89 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7378 (mm110)
REVERT: A  347 CYS cc_start: 0.8329 (m) cc_final: 0.8102 (m)
REVERT: B  104 TRP cc_start: 0.8203 (t60) cc_final: 0.7991 (t60)
REVERT: B  208 ASN cc_start: 0.8483 (t0) cc_final: 0.8139 (t0)
REVERT: B  280 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8407 (t0)
REVERT: B  347 CYS cc_start: 0.8346 (m) cc_final: 0.8003 (m)
REVERT: C   31 GLU cc_start: 0.7010 (mp0) cc_final: 0.6753 (mp0)
REVERT: C   37 MET cc_start: 0.7680 (ttp) cc_final: 0.7044 (tmm)
REVERT: C   89 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7376 (mm110)
REVERT: C  208 ASN cc_start: 0.8744 (t0) cc_final: 0.8340 (t0)
REVERT: D   31 GLU cc_start: 0.7206 (mp0) cc_final: 0.6879 (mp0)
REVERT: D   37 MET cc_start: 0.7565 (ttp) cc_final: 0.6899 (tmm)
REVERT: D   89 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7426 (mm110)
REVERT: D  120 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8059 (mm)
REVERT: D  208 ASN cc_start: 0.8655 (t0) cc_final: 0.8200 (t0)
REVERT: E   30 LEU cc_start: 0.7514 (mt) cc_final: 0.7234 (mp)
REVERT: E   31 GLU cc_start: 0.7098 (mp0) cc_final: 0.6838 (mp0)
REVERT: E  208 ASN cc_start: 0.8628 (t0) cc_final: 0.8284 (t0)
REVERT: F   37 MET cc_start: 0.7463 (ttp) cc_final: 0.6752 (tmm)
REVERT: F   89 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7468 (mm110)
REVERT: F  208 ASN cc_start: 0.8471 (t0) cc_final: 0.8013 (t0)
REVERT: G   89 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7427 (mm110)
  outliers start: 61
  outliers final: 45
  residues processed: 228
  average time/residue: 0.1155
  time to fit residues: 41.9445
Evaluate side-chains
  223 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 171
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 CYS
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  280 ASN
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue  118 ILE
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  258 THR
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  353 ASN
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   89 GLN
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  240 LEU
Chi-restraints excluded: chain D residue  258 THR
Chi-restraints excluded: chain D residue  343 LYS
Chi-restraints excluded: chain D residue  353 ASN
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain E residue  258 THR
Chi-restraints excluded: chain E residue  304 ASP
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain E residue  353 ASN
Chi-restraints excluded: chain F residue   40 CYS
Chi-restraints excluded: chain F residue   89 GLN
Chi-restraints excluded: chain F residue  118 ILE
Chi-restraints excluded: chain F residue  225 LEU
Chi-restraints excluded: chain F residue  254 ARG
Chi-restraints excluded: chain F residue  258 THR
Chi-restraints excluded: chain F residue  279 ILE
Chi-restraints excluded: chain F residue  285 VAL
Chi-restraints excluded: chain F residue  343 LYS
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain G residue   62 THR
Chi-restraints excluded: chain G residue   89 GLN
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain G residue  258 THR
Chi-restraints excluded: chain G residue  285 VAL
Chi-restraints excluded: chain G residue  343 LYS
Chi-restraints excluded: chain G residue  353 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 109 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9980
   chunk 1 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   chunk 205 optimal weight:   10.0000
   chunk 165 optimal weight:    6.9990
   chunk 170 optimal weight:    3.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
A 205 ASN
B 205 ASN
B 280 ASN
C 205 ASN
C 280 ASN
D 205 ASN
E 205 ASN
F 205 ASN
G 205 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.164957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.115699 restraints weight = 23312.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.94
r_work: 0.3090 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  17682  Z= 0.127
  Angle     :  0.583  10.389  24038  Z= 0.289
  Chirality :  0.038   0.120   2856
  Planarity :  0.005   0.044   2912
  Dihedral  :  4.259  18.205   2296
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.45 %
    Favored  : 81.12 %
  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 are not related in a simple way.
  whole: -0.55 (0.19), residues: 2128
  helix:  1.05 (0.15), residues: 1302
  sheet: -0.39 (0.48), residues: 126
  loop : -3.23 (0.21), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  29 
 TYR   0.013   0.001   TYR G 213 
 PHE   0.020   0.001   PHE A 299 
 TRP   0.004   0.001   TRP D 127 
 HIS   0.001   0.000   HIS A 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (17668)
  covalent geometry    : angle       0.58281 (24010)
  SS BOND              : bond        0.00082 (   14)
  SS BOND              : angle       0.53500 (   28)
  hydrogen bonds       : bond        0.04540 (  885)
  hydrogen bonds       : angle       3.62320 ( 2592)

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

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

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 200
  time to evaluate  : 0.609 
Fit side-chains
REVERT: A   31 GLU cc_start: 0.7206 (mp0) cc_final: 0.6680 (mp0)
REVERT: A  104 TRP cc_start: 0.8204 (t60) cc_final: 0.7979 (t60)
REVERT: A  347 CYS cc_start: 0.8133 (m) cc_final: 0.7903 (m)
REVERT: B  104 TRP cc_start: 0.8049 (t60) cc_final: 0.7846 (t60)
REVERT: B  208 ASN cc_start: 0.8446 (t0) cc_final: 0.8068 (t0)
REVERT: B  347 CYS cc_start: 0.8251 (m) cc_final: 0.7863 (m)
REVERT: C   31 GLU cc_start: 0.6978 (mp0) cc_final: 0.6673 (mp0)
REVERT: C   37 MET cc_start: 0.7671 (ttp) cc_final: 0.7332 (tmm)
REVERT: C  208 ASN cc_start: 0.8672 (t0) cc_final: 0.8273 (t0)
REVERT: D   31 GLU cc_start: 0.7001 (mp0) cc_final: 0.6663 (mp0)
REVERT: D   37 MET cc_start: 0.7570 (ttp) cc_final: 0.6999 (tmm)
REVERT: D  120 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7921 (mm)
REVERT: D  208 ASN cc_start: 0.8678 (t0) cc_final: 0.8227 (t0)
REVERT: E   30 LEU cc_start: 0.7500 (mt) cc_final: 0.7221 (mp)
REVERT: E   31 GLU cc_start: 0.7106 (mp0) cc_final: 0.6830 (mp0)
REVERT: E  208 ASN cc_start: 0.8536 (t0) cc_final: 0.8200 (t0)
REVERT: F   31 GLU cc_start: 0.6819 (mp0) cc_final: 0.6540 (mp0)
REVERT: F   37 MET cc_start: 0.7391 (ttp) cc_final: 0.7011 (tmm)
REVERT: F  208 ASN cc_start: 0.8524 (t0) cc_final: 0.8016 (t0)
  outliers start: 47
  outliers final: 35
  residues processed: 228
  average time/residue: 0.1074
  time to fit residues: 39.6508
Evaluate side-chains
  213 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 177
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain C residue  118 ILE
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  258 THR
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  353 ASN
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  258 THR
Chi-restraints excluded: chain D residue  343 LYS
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain E residue  258 THR
Chi-restraints excluded: chain E residue  304 ASP
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain E residue  353 ASN
Chi-restraints excluded: chain F residue  118 ILE
Chi-restraints excluded: chain F residue  225 LEU
Chi-restraints excluded: chain F residue  258 THR
Chi-restraints excluded: chain F residue  343 LYS
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain G residue   62 THR
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain G residue  258 THR
Chi-restraints excluded: chain G residue  343 LYS
Chi-restraints excluded: chain G residue  353 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 64 optimal weight:    8.9990
   chunk 166 optimal weight:    2.9990
   chunk 195 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 105 optimal weight:   10.0000
   chunk 200 optimal weight:    3.9990
   chunk 180 optimal weight:    7.9990
   chunk 89 optimal weight:   20.0000
   chunk 209 optimal weight:    3.9990
   chunk 44 optimal weight:   20.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
A 134 HIS
A 205 ASN
B 205 ASN
C  89 GLN
C 205 ASN
D  89 GLN
D 205 ASN
E 205 ASN
F  89 GLN
F 205 ASN
G  89 GLN
G 205 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.163987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.107968 restraints weight = 23386.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.65
r_work: 0.3123 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.1885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066  17682  Z= 0.224
  Angle     :  0.662  10.883  24038  Z= 0.333
  Chirality :  0.041   0.157   2856
  Planarity :  0.005   0.051   2912
  Dihedral  :  4.447  19.054   2296
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 18.00 %
    Favored  : 78.44 %
  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 are not related in a simple way.
  whole: -0.49 (0.19), residues: 2128
  helix:  1.07 (0.16), residues: 1309
  sheet: -0.40 (0.47), residues: 126
  loop : -3.18 (0.22), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  29 
 TYR   0.018   0.002   TYR G 213 
 PHE   0.016   0.001   PHE E 299 
 TRP   0.011   0.002   TRP D 127 
 HIS   0.003   0.001   HIS D 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00561 (17668)
  covalent geometry    : angle       0.66203 (24010)
  SS BOND              : bond        0.00215 (   14)
  SS BOND              : angle       0.59803 (   28)
  hydrogen bonds       : bond        0.05777 (  885)
  hydrogen bonds       : angle       3.91543 ( 2592)

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

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

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 178
  time to evaluate  : 0.655 
Fit side-chains
REVERT: A   31 GLU cc_start: 0.7359 (mp0) cc_final: 0.7096 (mp0)
REVERT: A   89 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7411 (mm110)
REVERT: A  347 CYS cc_start: 0.8264 (m) cc_final: 0.8034 (m)
REVERT: B  208 ASN cc_start: 0.8515 (t0) cc_final: 0.8162 (t0)
REVERT: B  347 CYS cc_start: 0.8325 (m) cc_final: 0.7921 (m)
REVERT: C   37 MET cc_start: 0.7637 (ttp) cc_final: 0.6989 (tmm)
REVERT: C  208 ASN cc_start: 0.8779 (t0) cc_final: 0.8367 (t0)
REVERT: D   16 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6611 (pp)
REVERT: D   31 GLU cc_start: 0.7131 (mp0) cc_final: 0.6800 (mp0)
REVERT: D   37 MET cc_start: 0.7577 (ttp) cc_final: 0.6919 (tmm)
REVERT: D   89 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7433 (mm110)
REVERT: D  120 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8161 (mm)
REVERT: D  208 ASN cc_start: 0.8739 (t0) cc_final: 0.8286 (t0)
REVERT: E   31 GLU cc_start: 0.7271 (mp0) cc_final: 0.6970 (mp0)
REVERT: E  208 ASN cc_start: 0.8671 (t0) cc_final: 0.8325 (t0)
REVERT: F   16 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6438 (pp)
REVERT: F   31 GLU cc_start: 0.6957 (mp0) cc_final: 0.6716 (mp0)
REVERT: F   37 MET cc_start: 0.7546 (ttp) cc_final: 0.7158 (tmm)
REVERT: F  208 ASN cc_start: 0.8528 (t0) cc_final: 0.8065 (t0)
REVERT: G   16 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6501 (pp)
REVERT: G   89 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7676 (mm110)
  outliers start: 69
  outliers final: 52
  residues processed: 228
  average time/residue: 0.1082
  time to fit residues: 39.8874
Evaluate side-chains
  231 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 172
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 CYS
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain C residue  118 ILE
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  258 THR
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  353 ASN
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   89 GLN
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  258 THR
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  343 LYS
Chi-restraints excluded: chain D residue  353 ASN
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain E residue  258 THR
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  304 ASP
Chi-restraints excluded: chain E residue  318 LEU
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain E residue  353 ASN
Chi-restraints excluded: chain F residue   16 LEU
Chi-restraints excluded: chain F residue   40 CYS
Chi-restraints excluded: chain F residue  118 ILE
Chi-restraints excluded: chain F residue  225 LEU
Chi-restraints excluded: chain F residue  258 THR
Chi-restraints excluded: chain F residue  285 VAL
Chi-restraints excluded: chain F residue  292 VAL
Chi-restraints excluded: chain F residue  318 LEU
Chi-restraints excluded: chain F residue  343 LYS
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain G residue   62 THR
Chi-restraints excluded: chain G residue   89 GLN
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain G residue  258 THR
Chi-restraints excluded: chain G residue  278 VAL
Chi-restraints excluded: chain G residue  285 VAL
Chi-restraints excluded: chain G residue  318 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 103 optimal weight:    8.9990
   chunk 149 optimal weight:    5.9990
   chunk 107 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 15 optimal weight:   10.0000
   chunk 208 optimal weight:    5.9990
   chunk 207 optimal weight:   20.0000
   chunk 6 optimal weight:    0.8980
   chunk 87 optimal weight:    0.0270
   chunk 126 optimal weight:    1.9990
   overall best weight:    1.9844

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
A 205 ASN
A 280 ASN
B 205 ASN
C 205 ASN
C 280 ASN
D  89 GLN
D 205 ASN
E 205 ASN
F 205 ASN
F 280 ASN
G  89 GLN
G 205 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.166593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.116868 restraints weight = 23239.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 2.92
r_work: 0.3126 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  17682  Z= 0.141
  Angle     :  0.590  10.597  24038  Z= 0.293
  Chirality :  0.038   0.127   2856
  Planarity :  0.005   0.043   2912
  Dihedral  :  4.214  17.747   2296
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 18.00 %
    Favored  : 78.39 %
  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 are not related in a simple way.
  whole: -0.31 (0.20), residues: 2128
  helix:  1.22 (0.16), residues: 1309
  sheet: -0.39 (0.47), residues: 126
  loop : -3.10 (0.22), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  29 
 TYR   0.015   0.001   TYR G 213 
 PHE   0.017   0.001   PHE C 299 
 TRP   0.005   0.001   TRP D 127 
 HIS   0.002   0.001   HIS E 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (17668)
  covalent geometry    : angle       0.59002 (24010)
  SS BOND              : bond        0.00079 (   14)
  SS BOND              : angle       0.52282 (   28)
  hydrogen bonds       : bond        0.04763 (  885)
  hydrogen bonds       : angle       3.68953 ( 2592)

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

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

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 182
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A   31 GLU cc_start: 0.7255 (mp0) cc_final: 0.6820 (mp0)
REVERT: A  104 TRP cc_start: 0.8240 (t60) cc_final: 0.8035 (t60)
REVERT: A  280 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8345 (t0)
REVERT: A  347 CYS cc_start: 0.8093 (m) cc_final: 0.7845 (m)
REVERT: B   16 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6406 (pp)
REVERT: B  208 ASN cc_start: 0.8432 (t0) cc_final: 0.8077 (t0)
REVERT: B  347 CYS cc_start: 0.8257 (m) cc_final: 0.7821 (m)
REVERT: C   16 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6332 (pp)
REVERT: C  208 ASN cc_start: 0.8700 (t0) cc_final: 0.8313 (t0)
REVERT: D   31 GLU cc_start: 0.7031 (mp0) cc_final: 0.6682 (mp0)
REVERT: D   37 MET cc_start: 0.7532 (ttp) cc_final: 0.6911 (tmm)
REVERT: D   89 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7324 (mm110)
REVERT: D  120 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7994 (mm)
REVERT: D  208 ASN cc_start: 0.8717 (t0) cc_final: 0.8264 (t0)
REVERT: E   16 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6743 (pp)
REVERT: E  208 ASN cc_start: 0.8539 (t0) cc_final: 0.8185 (t0)
REVERT: F   31 GLU cc_start: 0.6834 (mp0) cc_final: 0.6559 (mp0)
REVERT: F   37 MET cc_start: 0.7453 (ttp) cc_final: 0.7101 (tmm)
REVERT: F  208 ASN cc_start: 0.8573 (t0) cc_final: 0.8119 (t0)
REVERT: F  292 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8194 (p)
  outliers start: 70
  outliers final: 52
  residues processed: 230
  average time/residue: 0.1125
  time to fit residues: 41.0018
Evaluate side-chains
  233 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 174
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 CYS
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain C residue  118 ILE
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  258 THR
Chi-restraints excluded: chain C residue  280 ASN
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  353 ASN
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   89 GLN
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  258 THR
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  334 PHE
Chi-restraints excluded: chain D residue  343 LYS
Chi-restraints excluded: chain D residue  353 ASN
Chi-restraints excluded: chain E residue   16 LEU
Chi-restraints excluded: chain E residue   37 MET
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain E residue  258 THR
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  282 VAL
Chi-restraints excluded: chain E residue  304 ASP
Chi-restraints excluded: chain E residue  318 LEU
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain F residue   40 CYS
Chi-restraints excluded: chain F residue  118 ILE
Chi-restraints excluded: chain F residue  225 LEU
Chi-restraints excluded: chain F residue  254 ARG
Chi-restraints excluded: chain F residue  258 THR
Chi-restraints excluded: chain F residue  280 ASN
Chi-restraints excluded: chain F residue  285 VAL
Chi-restraints excluded: chain F residue  292 VAL
Chi-restraints excluded: chain F residue  318 LEU
Chi-restraints excluded: chain F residue  343 LYS
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain G residue   62 THR
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain G residue  258 THR
Chi-restraints excluded: chain G residue  278 VAL
Chi-restraints excluded: chain G residue  318 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 132 optimal weight:    4.9990
   chunk 64 optimal weight:    8.9990
   chunk 57 optimal weight:   30.0000
   chunk 87 optimal weight:   30.0000
   chunk 7 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 27 optimal weight:   30.0000
   chunk 199 optimal weight:    6.9990
   chunk 80 optimal weight:    0.0050
   chunk 167 optimal weight:    3.9990
   chunk 147 optimal weight:   20.0000
   overall best weight:    3.0002

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
A 205 ASN
A 280 ASN
B 205 ASN
C 205 ASN
C 280 ASN
D  89 GLN
D 205 ASN
E 205 ASN
F  89 GLN
F 205 ASN
F 280 ASN
G 205 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.164687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.109050 restraints weight = 23280.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 2.66
r_work: 0.3138 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  17682  Z= 0.184
  Angle     :  0.620  10.660  24038  Z= 0.310
  Chirality :  0.040   0.142   2856
  Planarity :  0.005   0.045   2912
  Dihedral  :  4.244  17.500   2296
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.99 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 17.90 %
    Favored  : 78.18 %
  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 are not related in a simple way.
  whole: -0.27 (0.20), residues: 2128
  helix:  1.26 (0.15), residues: 1309
  sheet: -0.40 (0.47), residues: 126
  loop : -3.10 (0.22), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  29 
 TYR   0.017   0.001   TYR G 213 
 PHE   0.019   0.001   PHE E 299 
 TRP   0.009   0.002   TRP D 127 
 HIS   0.002   0.001   HIS E 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (17668)
  covalent geometry    : angle       0.62044 (24010)
  SS BOND              : bond        0.00150 (   14)
  SS BOND              : angle       0.57009 (   28)
  hydrogen bonds       : bond        0.05217 (  885)
  hydrogen bonds       : angle       3.79233 ( 2592)

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

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

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 177
  time to evaluate  : 0.655 
Fit side-chains
REVERT: A   16 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6602 (pp)
REVERT: A   31 GLU cc_start: 0.7409 (mp0) cc_final: 0.6982 (mp0)
REVERT: A  280 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8396 (t0)
REVERT: A  347 CYS cc_start: 0.8144 (m) cc_final: 0.7896 (m)
REVERT: B   16 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6319 (pp)
REVERT: B  208 ASN cc_start: 0.8432 (t0) cc_final: 0.8097 (t0)
REVERT: B  343 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8087 (mttm)
REVERT: B  347 CYS cc_start: 0.8293 (m) cc_final: 0.7832 (m)
REVERT: C   16 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6320 (pp)
REVERT: C   37 MET cc_start: 0.7617 (ttp) cc_final: 0.7037 (tmm)
REVERT: C  208 ASN cc_start: 0.8772 (t0) cc_final: 0.8376 (t0)
REVERT: D   31 GLU cc_start: 0.7153 (mp0) cc_final: 0.6808 (mp0)
REVERT: D   37 MET cc_start: 0.7552 (ttp) cc_final: 0.6908 (tmm)
REVERT: D   89 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7393 (mm110)
REVERT: D  120 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8176 (mm)
REVERT: D  208 ASN cc_start: 0.8764 (t0) cc_final: 0.8303 (t0)
REVERT: E   16 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6737 (pp)
REVERT: E  208 ASN cc_start: 0.8656 (t0) cc_final: 0.8276 (t0)
REVERT: F   31 GLU cc_start: 0.6999 (mp0) cc_final: 0.6731 (mp0)
REVERT: F   37 MET cc_start: 0.7524 (ttp) cc_final: 0.7145 (tmm)
REVERT: F  208 ASN cc_start: 0.8647 (t0) cc_final: 0.8196 (t0)
REVERT: F  292 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8192 (p)
REVERT: G   16 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6465 (pp)
  outliers start: 76
  outliers final: 57
  residues processed: 229
  average time/residue: 0.1106
  time to fit residues: 40.7282
Evaluate side-chains
  238 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 171
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   40 CYS
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  343 LYS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain C residue  118 ILE
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  258 THR
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  353 ASN
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   89 GLN
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  258 THR
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  334 PHE
Chi-restraints excluded: chain D residue  343 LYS
Chi-restraints excluded: chain D residue  353 ASN
Chi-restraints excluded: chain E residue   16 LEU
Chi-restraints excluded: chain E residue   37 MET
Chi-restraints excluded: chain E residue   40 CYS
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain E residue  258 THR
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  282 VAL
Chi-restraints excluded: chain E residue  304 ASP
Chi-restraints excluded: chain E residue  318 LEU
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain F residue   40 CYS
Chi-restraints excluded: chain F residue  118 ILE
Chi-restraints excluded: chain F residue  225 LEU
Chi-restraints excluded: chain F residue  254 ARG
Chi-restraints excluded: chain F residue  258 THR
Chi-restraints excluded: chain F residue  282 VAL
Chi-restraints excluded: chain F residue  285 VAL
Chi-restraints excluded: chain F residue  292 VAL
Chi-restraints excluded: chain F residue  318 LEU
Chi-restraints excluded: chain F residue  343 LYS
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain G residue   40 CYS
Chi-restraints excluded: chain G residue   62 THR
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain G residue  258 THR
Chi-restraints excluded: chain G residue  278 VAL
Chi-restraints excluded: chain G residue  318 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 21 optimal weight:    0.2980
   chunk 67 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 187 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 175 optimal weight:    9.9990
   chunk 88 optimal weight:    7.9990
   chunk 50 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0970
   chunk 94 optimal weight:    7.9990
   chunk 154 optimal weight:    4.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 205 ASN
A 280 ASN
B 205 ASN
C 205 ASN
D  89 GLN
D 205 ASN
D 280 ASN
E 205 ASN
F 205 ASN
F 280 ASN
G 205 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.164627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.108008 restraints weight = 23398.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 2.65
r_work: 0.3119 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  17682  Z= 0.129
  Angle     :  0.577  10.538  24038  Z= 0.286
  Chirality :  0.038   0.124   2856
  Planarity :  0.005   0.043   2912
  Dihedral  :  4.069  17.372   2296
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 18.10 %
    Favored  : 78.18 %
  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 are not related in a simple way.
  whole: -0.09 (0.20), residues: 2128
  helix:  1.41 (0.15), residues: 1309
  sheet: -0.37 (0.47), residues: 126
  loop : -3.03 (0.22), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  29 
 TYR   0.016   0.001   TYR A 345 
 PHE   0.021   0.001   PHE E 299 
 TRP   0.005   0.001   TRP G  85 
 HIS   0.001   0.001   HIS A 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (17668)
  covalent geometry    : angle       0.57721 (24010)
  SS BOND              : bond        0.00056 (   14)
  SS BOND              : angle       0.50164 (   28)
  hydrogen bonds       : bond        0.04497 (  885)
  hydrogen bonds       : angle       3.64023 ( 2592)

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

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

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 193
  time to evaluate  : 0.698 
Fit side-chains
REVERT: A   16 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6559 (pp)
REVERT: A   31 GLU cc_start: 0.7341 (mp0) cc_final: 0.6899 (mp0)
REVERT: A  104 TRP cc_start: 0.8286 (t60) cc_final: 0.8079 (t60)
REVERT: A  347 CYS cc_start: 0.8181 (m) cc_final: 0.7932 (m)
REVERT: B   16 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6368 (pp)
REVERT: B  111 TYR cc_start: 0.8192 (m-80) cc_final: 0.7973 (m-10)
REVERT: B  208 ASN cc_start: 0.8397 (t0) cc_final: 0.8010 (t0)
REVERT: B  347 CYS cc_start: 0.8229 (m) cc_final: 0.7782 (m)
REVERT: C   16 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6242 (pp)
REVERT: C   37 MET cc_start: 0.7654 (ttp) cc_final: 0.6969 (tmm)
REVERT: C  208 ASN cc_start: 0.8683 (t0) cc_final: 0.8269 (t0)
REVERT: D   16 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6583 (pp)
REVERT: D   31 GLU cc_start: 0.7125 (mp0) cc_final: 0.6774 (mp0)
REVERT: D   37 MET cc_start: 0.7691 (ttp) cc_final: 0.7028 (tmm)
REVERT: D   89 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7164 (mm110)
REVERT: D  120 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7938 (mm)
REVERT: D  208 ASN cc_start: 0.8682 (t0) cc_final: 0.8216 (t0)
REVERT: E  208 ASN cc_start: 0.8530 (t0) cc_final: 0.8164 (t0)
REVERT: F   16 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6205 (pp)
REVERT: F   31 GLU cc_start: 0.6913 (mp0) cc_final: 0.6662 (mp0)
REVERT: F   37 MET cc_start: 0.7418 (ttp) cc_final: 0.7067 (tmm)
REVERT: F  208 ASN cc_start: 0.8578 (t0) cc_final: 0.8076 (t0)
  outliers start: 72
  outliers final: 51
  residues processed: 246
  average time/residue: 0.1111
  time to fit residues: 43.9941
Evaluate side-chains
  236 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 178
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   40 CYS
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain C residue  118 ILE
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  258 THR
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  353 ASN
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   89 GLN
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  258 THR
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  334 PHE
Chi-restraints excluded: chain D residue  353 ASN
Chi-restraints excluded: chain E residue   37 MET
Chi-restraints excluded: chain E residue   40 CYS
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  258 THR
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  282 VAL
Chi-restraints excluded: chain E residue  304 ASP
Chi-restraints excluded: chain E residue  318 LEU
Chi-restraints excluded: chain F residue   16 LEU
Chi-restraints excluded: chain F residue   40 CYS
Chi-restraints excluded: chain F residue  118 ILE
Chi-restraints excluded: chain F residue  225 LEU
Chi-restraints excluded: chain F residue  254 ARG
Chi-restraints excluded: chain F residue  258 THR
Chi-restraints excluded: chain F residue  285 VAL
Chi-restraints excluded: chain F residue  318 LEU
Chi-restraints excluded: chain F residue  343 LYS
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain G residue   40 CYS
Chi-restraints excluded: chain G residue   62 THR
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain G residue  258 THR
Chi-restraints excluded: chain G residue  278 VAL
Chi-restraints excluded: chain G residue  285 VAL
Chi-restraints excluded: chain G residue  318 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 138 optimal weight:    0.8980
   chunk 199 optimal weight:    3.9990
   chunk 146 optimal weight:    8.9990
   chunk 79 optimal weight:    0.5980
   chunk 116 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 209 optimal weight:   20.0000
   chunk 154 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 153 optimal weight:    0.9990
   chunk 195 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 205 ASN
B 205 ASN
C 205 ASN
D  89 GLN
D 205 ASN
E 205 ASN
F 205 ASN
F 280 ASN
G 205 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.165672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.109199 restraints weight = 23285.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.65
r_work: 0.3137 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  17682  Z= 0.118
  Angle     :  0.568  10.319  24038  Z= 0.281
  Chirality :  0.038   0.125   2856
  Planarity :  0.004   0.043   2912
  Dihedral  :  3.913  16.929   2296
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 19.24 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.20), residues: 2128
  helix:  1.53 (0.15), residues: 1309
  sheet: -0.30 (0.46), residues: 126
  loop : -2.94 (0.22), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  29 
 TYR   0.017   0.001   TYR C 345 
 PHE   0.022   0.001   PHE E 299 
 TRP   0.004   0.001   TRP F  74 
 HIS   0.001   0.001   HIS A 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (17668)
  covalent geometry    : angle       0.56774 (24010)
  SS BOND              : bond        0.00037 (   14)
  SS BOND              : angle       0.48117 (   28)
  hydrogen bonds       : bond        0.04179 (  885)
  hydrogen bonds       : angle       3.58814 ( 2592)

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

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

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 194
  time to evaluate  : 0.545 
Fit side-chains
REVERT: A   16 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6637 (pp)
REVERT: A   31 GLU cc_start: 0.7324 (mp0) cc_final: 0.6901 (mp0)
REVERT: A  104 TRP cc_start: 0.8228 (t60) cc_final: 0.8004 (t60)
REVERT: A  347 CYS cc_start: 0.8143 (m) cc_final: 0.7904 (m)
REVERT: B   16 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6313 (pp)
REVERT: B  111 TYR cc_start: 0.8153 (m-80) cc_final: 0.7952 (m-10)
REVERT: B  208 ASN cc_start: 0.8423 (t0) cc_final: 0.8026 (t0)
REVERT: B  347 CYS cc_start: 0.8207 (m) cc_final: 0.7765 (m)
REVERT: C   16 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6232 (pp)
REVERT: C   37 MET cc_start: 0.7515 (ttp) cc_final: 0.6938 (tmm)
REVERT: C  208 ASN cc_start: 0.8688 (t0) cc_final: 0.8285 (t0)
REVERT: D   16 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6566 (pp)
REVERT: D   31 GLU cc_start: 0.7117 (mp0) cc_final: 0.6763 (mp0)
REVERT: D   37 MET cc_start: 0.7671 (ttp) cc_final: 0.6969 (tmm)
REVERT: D   89 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7197 (mm110)
REVERT: D  208 ASN cc_start: 0.8673 (t0) cc_final: 0.8189 (t0)
REVERT: E  208 ASN cc_start: 0.8492 (t0) cc_final: 0.8116 (t0)
REVERT: F   16 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6252 (pp)
REVERT: F   31 GLU cc_start: 0.6865 (mp0) cc_final: 0.6604 (mp0)
REVERT: F   37 MET cc_start: 0.7393 (ttp) cc_final: 0.7062 (tmm)
REVERT: F   97 GLU cc_start: 0.4270 (mm-30) cc_final: 0.4033 (mp0)
REVERT: F  208 ASN cc_start: 0.8562 (t0) cc_final: 0.8042 (t0)
  outliers start: 51
  outliers final: 40
  residues processed: 232
  average time/residue: 0.1153
  time to fit residues: 42.7284
Evaluate side-chains
  227 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 181
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue   40 CYS
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain C residue  118 ILE
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  353 ASN
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   89 GLN
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  334 PHE
Chi-restraints excluded: chain D residue  353 ASN
Chi-restraints excluded: chain E residue   37 MET
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  118 ILE
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain E residue  258 THR
Chi-restraints excluded: chain E residue  304 ASP
Chi-restraints excluded: chain E residue  318 LEU
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain F residue   16 LEU
Chi-restraints excluded: chain F residue   40 CYS
Chi-restraints excluded: chain F residue  118 ILE
Chi-restraints excluded: chain F residue  225 LEU
Chi-restraints excluded: chain F residue  254 ARG
Chi-restraints excluded: chain F residue  258 THR
Chi-restraints excluded: chain F residue  318 LEU
Chi-restraints excluded: chain F residue  343 LYS
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain G residue   40 CYS
Chi-restraints excluded: chain G residue   62 THR
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain G residue  278 VAL
Chi-restraints excluded: chain G residue  318 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 201 optimal weight:    3.9990
   chunk 128 optimal weight:    0.0000
   chunk 46 optimal weight:    0.8980
   chunk 111 optimal weight:    0.6980
   chunk 58 optimal weight:    9.9990
   chunk 175 optimal weight:    9.9990
   chunk 44 optimal weight:    5.9990
   chunk 122 optimal weight:    0.2980
   chunk 37 optimal weight:    6.9990
   chunk 82 optimal weight:    4.9990
   chunk 180 optimal weight:    0.0370
   overall best weight:    0.3862

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
A 205 ASN
B  89 GLN
B 205 ASN
C 205 ASN
D 205 ASN
E  89 GLN
E 205 ASN
F 205 ASN
G 205 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.172778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.117124 restraints weight = 22966.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 2.69
r_work: 0.3211 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3050 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  17682  Z= 0.104
  Angle     :  0.548   9.692  24038  Z= 0.269
  Chirality :  0.038   0.128   2856
  Planarity :  0.004   0.042   2912
  Dihedral  :  3.603  16.970   2296
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 20.68 %
    Favored  : 77.77 %
  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 are not related in a simple way.
  whole:  0.40 (0.20), residues: 2128
  helix:  1.79 (0.16), residues: 1295
  sheet: -0.81 (0.50), residues: 84
  loop : -2.50 (0.23), residues: 749

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  29 
 TYR   0.019   0.001   TYR B 345 
 PHE   0.024   0.001   PHE C 299 
 TRP   0.008   0.001   TRP B 104 
 HIS   0.002   0.001   HIS B 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 (17668)
  covalent geometry    : angle       0.54811 (24010)
  SS BOND              : bond        0.00056 (   14)
  SS BOND              : angle       0.45209 (   28)
  hydrogen bonds       : bond        0.03195 (  885)
  hydrogen bonds       : angle       3.44250 ( 2592)

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

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

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4256 Ramachandran restraints generated.
    2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 215
  time to evaluate  : 0.578 
Fit side-chains
REVERT: A   16 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6668 (pp)
REVERT: A   31 GLU cc_start: 0.7133 (mp0) cc_final: 0.6720 (mp0)
REVERT: B   29 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7508 (mtm-85)
REVERT: B  208 ASN cc_start: 0.8433 (t0) cc_final: 0.8046 (t0)
REVERT: B  347 CYS cc_start: 0.8049 (m) cc_final: 0.7630 (m)
REVERT: C  208 ASN cc_start: 0.8709 (t0) cc_final: 0.8256 (t0)
REVERT: C  280 ASN cc_start: 0.8469 (t0) cc_final: 0.7933 (t0)
REVERT: D   16 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6565 (pp)
REVERT: D   37 MET cc_start: 0.7617 (ttp) cc_final: 0.6936 (tmm)
REVERT: D  208 ASN cc_start: 0.8639 (t0) cc_final: 0.8128 (t0)
REVERT: E  208 ASN cc_start: 0.8359 (t0) cc_final: 0.7945 (t0)
REVERT: F   16 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6375 (pp)
REVERT: F   37 MET cc_start: 0.7373 (ttp) cc_final: 0.6984 (tmm)
REVERT: F  104 TRP cc_start: 0.7891 (t60) cc_final: 0.7318 (t60)
REVERT: F  208 ASN cc_start: 0.8514 (t0) cc_final: 0.7968 (t0)
REVERT: F  280 ASN cc_start: 0.8434 (t0) cc_final: 0.8100 (t0)
REVERT: G   90 GLN cc_start: 0.8554 (pm20) cc_final: 0.8160 (pm20)
  outliers start: 30
  outliers final: 18
  residues processed: 236
  average time/residue: 0.1131
  time to fit residues: 43.1252
Evaluate side-chains
  217 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 196
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  353 ASN
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  353 ASN
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  334 PHE
Chi-restraints excluded: chain E residue   37 MET
Chi-restraints excluded: chain E residue  304 ASP
Chi-restraints excluded: chain E residue  318 LEU
Chi-restraints excluded: chain F residue   16 LEU
Chi-restraints excluded: chain F residue  318 LEU
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain G residue   62 THR
Chi-restraints excluded: chain G residue  318 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   chunk 138 optimal weight:    7.9990
   chunk 186 optimal weight:    4.9990
   chunk 187 optimal weight:    1.9990
   chunk 177 optimal weight:    7.9990
   chunk 118 optimal weight:    4.9990
   chunk 120 optimal weight:   10.0000
   chunk 197 optimal weight:    8.9990
   chunk 160 optimal weight:    0.9990
   chunk 130 optimal weight:    2.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
A 205 ASN
A 280 ASN
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 205 ASN
C 205 ASN
D 205 ASN
E 205 ASN
F 205 ASN
G  89 GLN
G 205 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.163643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.113603 restraints weight = 23271.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 2.86
r_work: 0.3075 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  17682  Z= 0.177
  Angle     :  0.620  10.395  24038  Z= 0.311
  Chirality :  0.040   0.140   2856
  Planarity :  0.005   0.050   2912
  Dihedral  :  3.912  15.633   2296
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 20.84 %
    Favored  : 77.15 %
  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 are not related in a simple way.
  whole:  0.32 (0.20), residues: 2128
  helix:  1.71 (0.15), residues: 1302
  sheet: -0.11 (0.47), residues: 126
  loop : -2.79 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  29 
 TYR   0.017   0.001   TYR C 213 
 PHE   0.024   0.001   PHE E 299 
 TRP   0.010   0.002   TRP B 104 
 HIS   0.003   0.001   HIS C 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (17668)
  covalent geometry    : angle       0.62055 (24010)
  SS BOND              : bond        0.00109 (   14)
  SS BOND              : angle       0.52925 (   28)
  hydrogen bonds       : bond        0.05034 (  885)
  hydrogen bonds       : angle       3.73632 ( 2592)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4763.97 seconds
wall clock time: 82 minutes 2.93 seconds (4922.93 seconds total)