Starting phenix.real_space_refine
on Sat Jan 18 16:37:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8twv_41672/01_2025/8twv_41672.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8twv_41672/01_2025/8twv_41672.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8twv_41672/01_2025/8twv_41672.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8twv_41672/01_2025/8twv_41672.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8twv_41672/01_2025/8twv_41672.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8twv_41672/01_2025/8twv_41672.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.009 sd=   0.220
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      25      5.16       5
     C    8305      2.51       5
     N    2115      2.21       5
     O    2275      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 12720
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2540
          Classifications: {'peptide': 310}
          Link IDs: {'PTRANS': 13, 'TRANS': 296}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'3CN': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 4.77, per 1000 atoms: 0.38
  Number of scatterers: 12720
  At special positions: 0
  Unit cell: (92.352, 91.168, 124.32, 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      25     16.00
     O    2275      8.00
     N    2115      7.00
     C    8305      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.92
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2930

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 15 sheets defined
      34.2% alpha, 35.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 70
      removed outlier: 3.678A  pdb=" N   TRP A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 208
    Processing helix  chain 'A' and resid 208 through 221
    Processing helix  chain 'A' and resid 227 through 245
      removed outlier: 3.961A  pdb=" N   THR A 234 " --> pdb=" O   GLU A 230 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER A 235 " --> pdb=" O   ARG A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 253
      removed outlier: 3.718A  pdb=" N   ILE A 252 " --> pdb=" O   TYR A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 287
    Processing helix  chain 'A' and resid 299 through 320
      removed outlier: 3.618A  pdb=" N   ALA A 303 " --> pdb=" O   ARG A 299 " (cutoff:3.500A)
      Proline residue:  A 305  - end of helix
      removed outlier: 3.505A  pdb=" N   GLY A 312 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU A 315 " --> pdb=" O   ILE A 311 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 70
      removed outlier: 3.678A  pdb=" N   TRP E  66 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 201 through 208
    Processing helix  chain 'E' and resid 208 through 221
    Processing helix  chain 'E' and resid 227 through 245
      removed outlier: 3.961A  pdb=" N   THR E 234 " --> pdb=" O   GLU E 230 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER E 235 " --> pdb=" O   ARG E 231 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 248 through 253
      removed outlier: 3.718A  pdb=" N   ILE E 252 " --> pdb=" O   TYR E 248 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 260 through 287
    Processing helix  chain 'E' and resid 299 through 320
      removed outlier: 3.617A  pdb=" N   ALA E 303 " --> pdb=" O   ARG E 299 " (cutoff:3.500A)
      Proline residue:  E 305  - end of helix
      removed outlier: 3.506A  pdb=" N   GLY E 312 " --> pdb=" O   PHE E 308 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU E 315 " --> pdb=" O   ILE E 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 70
      removed outlier: 3.678A  pdb=" N   TRP B  66 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 208
    Processing helix  chain 'B' and resid 208 through 221
    Processing helix  chain 'B' and resid 227 through 245
      removed outlier: 3.961A  pdb=" N   THR B 234 " --> pdb=" O   GLU B 230 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER B 235 " --> pdb=" O   ARG B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 253
      removed outlier: 3.718A  pdb=" N   ILE B 252 " --> pdb=" O   TYR B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 287
    Processing helix  chain 'B' and resid 299 through 320
      removed outlier: 3.618A  pdb=" N   ALA B 303 " --> pdb=" O   ARG B 299 " (cutoff:3.500A)
      Proline residue:  B 305  - end of helix
      removed outlier: 3.505A  pdb=" N   GLY B 312 " --> pdb=" O   PHE B 308 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU B 315 " --> pdb=" O   ILE B 311 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 70
      removed outlier: 3.679A  pdb=" N   TRP D  66 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 201 through 208
    Processing helix  chain 'D' and resid 208 through 221
    Processing helix  chain 'D' and resid 227 through 245
      removed outlier: 3.960A  pdb=" N   THR D 234 " --> pdb=" O   GLU D 230 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER D 235 " --> pdb=" O   ARG D 231 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 253
      removed outlier: 3.717A  pdb=" N   ILE D 252 " --> pdb=" O   TYR D 248 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 260 through 287
    Processing helix  chain 'D' and resid 299 through 320
      removed outlier: 3.618A  pdb=" N   ALA D 303 " --> pdb=" O   ARG D 299 " (cutoff:3.500A)
      Proline residue:  D 305  - end of helix
      removed outlier: 3.505A  pdb=" N   GLY D 312 " --> pdb=" O   PHE D 308 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU D 315 " --> pdb=" O   ILE D 311 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 70
      removed outlier: 3.679A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 208 through 221
    Processing helix  chain 'C' and resid 227 through 245
      removed outlier: 3.961A  pdb=" N   THR C 234 " --> pdb=" O   GLU C 230 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER C 235 " --> pdb=" O   ARG C 231 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 248 through 253
      removed outlier: 3.717A  pdb=" N   ILE C 252 " --> pdb=" O   TYR C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 287
    Processing helix  chain 'C' and resid 299 through 320
      removed outlier: 3.618A  pdb=" N   ALA C 303 " --> pdb=" O   ARG C 299 " (cutoff:3.500A)
      Proline residue:  C 305  - end of helix
      removed outlier: 3.505A  pdb=" N   GLY C 312 " --> pdb=" O   PHE C 308 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU C 315 " --> pdb=" O   ILE C 311 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58
      removed outlier: 4.475A  pdb=" N   SER A 109 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58
      removed outlier: 4.056A  pdb=" N   LYS A  34 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   GLY A  25 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   ASP A  36 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   ILE A  23 " --> pdb=" O   ASP A  36 " (cutoff:3.500A)
      removed outlier: 8.360A  pdb=" N   TYR A  38 " --> pdb=" O   ASN A  21 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   ASN A  21 " --> pdb=" O   TYR A  38 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   VAL A  40 " --> pdb=" O   PHE A  19 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   PHE A  19 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   GLN A  42 " --> pdb=" O   SER A  17 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   SER A  17 " --> pdb=" O   GLN A  42 " (cutoff:3.500A)
      removed outlier: 8.794A  pdb=" N   THR A  44 " --> pdb=" O   SER A  15 " (cutoff:3.500A)
      removed outlier: 9.609A  pdb=" N   SER A  15 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   VAL A  16 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ILE A 145 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ILE A  18 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   VAL A 147 " --> pdb=" O   ILE A  18 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   ILE A  20 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.511A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   PHE A 188 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   SER A 171 " --> pdb=" O   PHE A 188 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ARG A 190 " --> pdb=" O   HIS A 169 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   HIS A 169 " --> pdb=" O   ARG A 190 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   THR A 192 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   SER A 167 " --> pdb=" O   THR A 192 " (cutoff:3.500A)
      removed outlier: 7.168A  pdb=" N   ARG A 194 " --> pdb=" O   LYS A 165 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   LYS A 165 " --> pdb=" O   ARG A 194 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   ASP A 196 " --> pdb=" O   ARG A 163 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 56 through 58
      removed outlier: 4.475A  pdb=" N   SER E 109 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 58
      removed outlier: 4.056A  pdb=" N   LYS E  34 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   GLY E  25 " --> pdb=" O   LYS E  34 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   ASP E  36 " --> pdb=" O   ILE E  23 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   ILE E  23 " --> pdb=" O   ASP E  36 " (cutoff:3.500A)
      removed outlier: 8.360A  pdb=" N   TYR E  38 " --> pdb=" O   ASN E  21 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   ASN E  21 " --> pdb=" O   TYR E  38 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   VAL E  40 " --> pdb=" O   PHE E  19 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   PHE E  19 " --> pdb=" O   VAL E  40 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   GLN E  42 " --> pdb=" O   SER E  17 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   SER E  17 " --> pdb=" O   GLN E  42 " (cutoff:3.500A)
      removed outlier: 8.794A  pdb=" N   THR E  44 " --> pdb=" O   SER E  15 " (cutoff:3.500A)
      removed outlier: 9.609A  pdb=" N   SER E  15 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 7.311A  pdb=" N   VAL E  16 " --> pdb=" O   SER E 143 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   ILE E 145 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   ILE E  18 " --> pdb=" O   ILE E 145 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   VAL E 147 " --> pdb=" O   ILE E  18 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   ILE E  20 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.512A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   PHE E 188 " --> pdb=" O   SER E 171 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   SER E 171 " --> pdb=" O   PHE E 188 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ARG E 190 " --> pdb=" O   HIS E 169 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   HIS E 169 " --> pdb=" O   ARG E 190 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   THR E 192 " --> pdb=" O   SER E 167 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   SER E 167 " --> pdb=" O   THR E 192 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   ARG E 194 " --> pdb=" O   LYS E 165 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   LYS E 165 " --> pdb=" O   ARG E 194 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   ASP E 196 " --> pdb=" O   ARG E 163 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 58
      removed outlier: 4.475A  pdb=" N   SER B 109 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 56 through 58
      removed outlier: 4.055A  pdb=" N   LYS B  34 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   GLY B  25 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   ASP B  36 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 5.438A  pdb=" N   ILE B  23 " --> pdb=" O   ASP B  36 " (cutoff:3.500A)
      removed outlier: 8.360A  pdb=" N   TYR B  38 " --> pdb=" O   ASN B  21 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   ASN B  21 " --> pdb=" O   TYR B  38 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   VAL B  40 " --> pdb=" O   PHE B  19 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   PHE B  19 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   GLN B  42 " --> pdb=" O   SER B  17 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   SER B  17 " --> pdb=" O   GLN B  42 " (cutoff:3.500A)
      removed outlier: 8.794A  pdb=" N   THR B  44 " --> pdb=" O   SER B  15 " (cutoff:3.500A)
      removed outlier: 9.609A  pdb=" N   SER B  15 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   VAL B  16 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ILE B 145 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ILE B  18 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   VAL B 147 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   ILE B  20 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.511A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   PHE B 188 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   SER B 171 " --> pdb=" O   PHE B 188 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ARG B 190 " --> pdb=" O   HIS B 169 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   HIS B 169 " --> pdb=" O   ARG B 190 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   THR B 192 " --> pdb=" O   SER B 167 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   SER B 167 " --> pdb=" O   THR B 192 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   ARG B 194 " --> pdb=" O   LYS B 165 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   LYS B 165 " --> pdb=" O   ARG B 194 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   ASP B 196 " --> pdb=" O   ARG B 163 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 58
      removed outlier: 4.475A  pdb=" N   SER D 109 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 56 through 58
      removed outlier: 4.056A  pdb=" N   LYS D  34 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   GLY D  25 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   ASP D  36 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   ILE D  23 " --> pdb=" O   ASP D  36 " (cutoff:3.500A)
      removed outlier: 8.359A  pdb=" N   TYR D  38 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   ASN D  21 " --> pdb=" O   TYR D  38 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   VAL D  40 " --> pdb=" O   PHE D  19 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   PHE D  19 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   GLN D  42 " --> pdb=" O   SER D  17 " (cutoff:3.500A)
      removed outlier: 8.095A  pdb=" N   SER D  17 " --> pdb=" O   GLN D  42 " (cutoff:3.500A)
      removed outlier: 8.793A  pdb=" N   THR D  44 " --> pdb=" O   SER D  15 " (cutoff:3.500A)
      removed outlier: 9.609A  pdb=" N   SER D  15 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   VAL D  16 " --> pdb=" O   SER D 143 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ILE D 145 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ILE D  18 " --> pdb=" O   ILE D 145 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   VAL D 147 " --> pdb=" O   ILE D  18 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   ILE D  20 " --> pdb=" O   VAL D 147 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.512A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   PHE D 188 " --> pdb=" O   SER D 171 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   SER D 171 " --> pdb=" O   PHE D 188 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ARG D 190 " --> pdb=" O   HIS D 169 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   HIS D 169 " --> pdb=" O   ARG D 190 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   THR D 192 " --> pdb=" O   SER D 167 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   SER D 167 " --> pdb=" O   THR D 192 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   ARG D 194 " --> pdb=" O   LYS D 165 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   LYS D 165 " --> pdb=" O   ARG D 194 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   ASP D 196 " --> pdb=" O   ARG D 163 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 56 through 58
      removed outlier: 4.476A  pdb=" N   SER C 109 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 56 through 58
      removed outlier: 4.056A  pdb=" N   LYS C  34 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   GLY C  25 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   ASP C  36 " --> pdb=" O   ILE C  23 " (cutoff:3.500A)
      removed outlier: 5.438A  pdb=" N   ILE C  23 " --> pdb=" O   ASP C  36 " (cutoff:3.500A)
      removed outlier: 8.360A  pdb=" N   TYR C  38 " --> pdb=" O   ASN C  21 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   ASN C  21 " --> pdb=" O   TYR C  38 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   VAL C  40 " --> pdb=" O   PHE C  19 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   PHE C  19 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   GLN C  42 " --> pdb=" O   SER C  17 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   SER C  17 " --> pdb=" O   GLN C  42 " (cutoff:3.500A)
      removed outlier: 8.793A  pdb=" N   THR C  44 " --> pdb=" O   SER C  15 " (cutoff:3.500A)
      removed outlier: 9.610A  pdb=" N   SER C  15 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   VAL C  16 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ILE C 145 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ILE C  18 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   VAL C 147 " --> pdb=" O   ILE C  18 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   ILE C  20 " --> pdb=" O   VAL C 147 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.512A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   PHE C 188 " --> pdb=" O   SER C 171 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   SER C 171 " --> pdb=" O   PHE C 188 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ARG C 190 " --> pdb=" O   HIS C 169 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   HIS C 169 " --> pdb=" O   ARG C 190 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   THR C 192 " --> pdb=" O   SER C 167 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   SER C 167 " --> pdb=" O   THR C 192 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   ARG C 194 " --> pdb=" O   LYS C 165 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   LYS C 165 " --> pdb=" O   ARG C 194 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   ASP C 196 " --> pdb=" O   ARG C 163 " (cutoff:3.500A)

    575 hydrogen bonds defined for protein.
    1680 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.46

  Time building geometry restraints manager: 3.37 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: 4020
        1.34 -     1.46: 2849
        1.46 -     1.57: 6146
        1.57 -     1.69: 5
        1.69 -     1.81: 45
  Bond restraints: 13065
  Sorted by residual:
  bond pdb=" CA  PHE B 208 "
       pdb=" CB  PHE B 208 "
    ideal  model  delta    sigma   weight residual
    1.530  1.560 -0.030 1.69e-02 3.50e+03 3.10e+00
  bond pdb=" CA  PHE A 208 "
       pdb=" CB  PHE A 208 "
    ideal  model  delta    sigma   weight residual
    1.530  1.560 -0.030 1.69e-02 3.50e+03 3.07e+00
  bond pdb=" CA  PHE E 208 "
       pdb=" CB  PHE E 208 "
    ideal  model  delta    sigma   weight residual
    1.530  1.560 -0.030 1.69e-02 3.50e+03 3.06e+00
  bond pdb=" CA  PHE C 208 "
       pdb=" CB  PHE C 208 "
    ideal  model  delta    sigma   weight residual
    1.530  1.560 -0.029 1.69e-02 3.50e+03 3.02e+00
  bond pdb=" CA  PHE D 208 "
       pdb=" CB  PHE D 208 "
    ideal  model  delta    sigma   weight residual
    1.530  1.560 -0.029 1.69e-02 3.50e+03 3.01e+00
  ... (remaining 13060 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 17116
        1.61 -     3.22: 494
        3.22 -     4.83: 115
        4.83 -     6.44: 40
        6.44 -     8.05: 15
  Bond angle restraints: 17780
  Sorted by residual:
  angle pdb=" N   ARG D 299 "
        pdb=" CA  ARG D 299 "
        pdb=" C   ARG D 299 "
      ideal   model   delta    sigma   weight residual
     113.20  107.78    5.42 1.21e+00 6.83e-01 2.01e+01
  angle pdb=" N   ARG B 299 "
        pdb=" CA  ARG B 299 "
        pdb=" C   ARG B 299 "
      ideal   model   delta    sigma   weight residual
     113.20  107.81    5.39 1.21e+00 6.83e-01 1.99e+01
  angle pdb=" N   ARG A 299 "
        pdb=" CA  ARG A 299 "
        pdb=" C   ARG A 299 "
      ideal   model   delta    sigma   weight residual
     113.20  107.82    5.38 1.21e+00 6.83e-01 1.98e+01
  angle pdb=" N   ARG C 299 "
        pdb=" CA  ARG C 299 "
        pdb=" C   ARG C 299 "
      ideal   model   delta    sigma   weight residual
     113.20  107.83    5.37 1.21e+00 6.83e-01 1.97e+01
  angle pdb=" N   ARG E 299 "
        pdb=" CA  ARG E 299 "
        pdb=" C   ARG E 299 "
      ideal   model   delta    sigma   weight residual
     113.20  107.86    5.34 1.21e+00 6.83e-01 1.95e+01
  ... (remaining 17775 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 6675
       17.64 -    35.27: 696
       35.27 -    52.91: 179
       52.91 -    70.55: 45
       70.55 -    88.19: 10
  Dihedral angle restraints: 7605
    sinusoidal: 3060
      harmonic: 4545
  Sorted by residual:
  dihedral pdb=" CA  ASP D 115 "
           pdb=" CB  ASP D 115 "
           pdb=" CG  ASP D 115 "
           pdb=" OD1 ASP D 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.59   58.59     1      2.00e+01 2.50e-03 1.15e+01
  dihedral pdb=" CA  ASP B 115 "
           pdb=" CB  ASP B 115 "
           pdb=" CG  ASP B 115 "
           pdb=" OD1 ASP B 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.58   58.58     1      2.00e+01 2.50e-03 1.15e+01
  dihedral pdb=" CA  ASP E 115 "
           pdb=" CB  ASP E 115 "
           pdb=" CG  ASP E 115 "
           pdb=" OD1 ASP E 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.56   58.56     1      2.00e+01 2.50e-03 1.15e+01
  ... (remaining 7602 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1255
       0.042 -    0.083: 446
       0.083 -    0.125: 201
       0.125 -    0.166: 38
       0.166 -    0.208: 15
  Chirality restraints: 1955
  Sorted by residual:
  chirality pdb=" CA  THR A  61 "
            pdb=" N   THR A  61 "
            pdb=" C   THR A  61 "
            pdb=" CB  THR A  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.32    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  THR C  61 "
            pdb=" N   THR C  61 "
            pdb=" C   THR C  61 "
            pdb=" CB  THR C  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.32    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  THR D  61 "
            pdb=" N   THR D  61 "
            pdb=" C   THR D  61 "
            pdb=" CB  THR D  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.32    0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 1952 not shown)

  Planarity restraints: 2265
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 208 "    0.011 2.00e-02 2.50e+03   1.79e-02 5.63e+00
        pdb=" CG  PHE C 208 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 208 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 208 "    0.017 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 208 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 208 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 208 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 208 "    0.011 2.00e-02 2.50e+03   1.79e-02 5.62e+00
        pdb=" CG  PHE B 208 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 208 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 208 "    0.017 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 208 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 208 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 208 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 208 "    0.011 2.00e-02 2.50e+03   1.79e-02 5.59e+00
        pdb=" CG  PHE E 208 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 208 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 208 "    0.017 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 208 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 208 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 208 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 2262 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 2493
        2.78 -     3.31: 11409
        3.31 -     3.84: 21313
        3.84 -     4.37: 25170
        4.37 -     4.90: 43579
  Nonbonded interactions: 103964
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU D  59 "
            pdb=" OG  SER C 134 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OE2 GLU E  59 "
            pdb=" OG  SER D 134 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   THR E  61 "
            pdb=" OG1 THR E  61 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" O   THR A  61 "
            pdb=" OG1 THR A  61 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   THR B  61 "
            pdb=" OG1 THR B  61 "
     model   vdw
     2.304 3.040
  ... (remaining 103959 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.360
  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:          0.410
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     25.350
  Find NCS groups from input model:        0.240
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  13065  Z= 0.266
  Angle     :  0.727   8.046  17780  Z= 0.437
  Chirality :  0.053   0.208   1955
  Planarity :  0.005   0.062   2265
  Dihedral  : 15.797  88.185   4675
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  : 19.13 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.21), residues: 1540
  helix: -1.61 (0.19), residues: 525
  sheet:  1.36 (0.27), residues: 430
  loop : -2.25 (0.24), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 206 
 HIS   0.006   0.001   HIS A 285 
 PHE   0.040   0.002   PHE B 208 
 TYR   0.009   0.001   TYR B  38 
 ARG   0.010   0.001   ARG B 231 

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 1.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 ARG cc_start: 0.6869 (mtm180) cc_final: 0.6411 (mpt-90)
REVERT: E   34 LYS cc_start: 0.8971 (mttp) cc_final: 0.8762 (mttm)
REVERT: E  208 PHE cc_start: 0.8704 (t80) cc_final: 0.8396 (t80)
REVERT: E  230 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6983 (mp0)
REVERT: E  231 ARG cc_start: 0.6850 (mtm180) cc_final: 0.6450 (mpt-90)
REVERT: B  225 LEU cc_start: 0.8615 (mp) cc_final: 0.8385 (mp)
REVERT: B  231 ARG cc_start: 0.6871 (mtm180) cc_final: 0.6335 (mpt-90)
REVERT: D   86 ASP cc_start: 0.8750 (t70) cc_final: 0.8482 (t70)
REVERT: D  230 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7121 (mp0)
REVERT: D  231 ARG cc_start: 0.6980 (mtm180) cc_final: 0.6661 (mpt-90)
REVERT: C  113 ASP cc_start: 0.8233 (m-30) cc_final: 0.7625 (p0)
REVERT: C  208 PHE cc_start: 0.8676 (t80) cc_final: 0.8473 (t80)
REVERT: C  231 ARG cc_start: 0.6807 (mtm180) cc_final: 0.6369 (mpt-90)
  outliers start: 1
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2683
  time to fit residues: 56.5384
Evaluate side-chains
  116 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 1.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 130 optimal weight:    4.9990
   chunk 117 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0270
   chunk 40 optimal weight:    7.9990
   chunk 79 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 121 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 73 optimal weight:    5.9990
   chunk 90 optimal weight:    6.9990
   chunk 140 optimal weight:    6.9990
   overall best weight:    1.7642

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.153938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.116755 restraints weight = 15397.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 1.95
r_work: 0.2852 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2699 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024  13065  Z= 0.260
  Angle     :  0.549   7.273  17780  Z= 0.280
  Chirality :  0.046   0.133   1955
  Planarity :  0.003   0.022   2265
  Dihedral  :  4.293  14.832   1715
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 18.84 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.22), residues: 1540
  helix:  0.54 (0.24), residues: 505
  sheet:  1.06 (0.25), residues: 480
  loop : -1.92 (0.25), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 206 
 HIS   0.004   0.001   HIS A 285 
 PHE   0.011   0.001   PHE A 208 
 TYR   0.011   0.001   TYR D  33 
 ARG   0.003   0.000   ARG A  65 

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 124
  time to evaluate  : 1.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   34 LYS cc_start: 0.8940 (mttp) cc_final: 0.8732 (mttm)
REVERT: E  185 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8515 (pt0)
REVERT: E  231 ARG cc_start: 0.7139 (mtm180) cc_final: 0.6896 (mtt-85)
REVERT: B   86 ASP cc_start: 0.8849 (t70) cc_final: 0.8360 (t70)
REVERT: B  151 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.7900 (m110)
REVERT: B  225 LEU cc_start: 0.8808 (mp) cc_final: 0.8524 (mp)
REVERT: B  231 ARG cc_start: 0.7055 (mtm180) cc_final: 0.6220 (mpt-90)
REVERT: D   30 GLU cc_start: 0.8922 (pm20) cc_final: 0.8273 (pm20)
REVERT: D  151 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.7574 (t0)
REVERT: D  231 ARG cc_start: 0.7160 (mtm180) cc_final: 0.6839 (mtt-85)
REVERT: D  264 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8277 (mt0)
REVERT: C  151 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8241 (t0)
REVERT: C  185 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8582 (pt0)
  outliers start: 34
  outliers final: 16
  residues processed: 158
  average time/residue: 0.2430
  time to fit residues: 56.7544
Evaluate side-chains
  137 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 1.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  151 ASN
Chi-restraints excluded: chain B residue  185 GLN
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue  151 ASN
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  264 GLN
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain C residue  185 GLN
Chi-restraints excluded: chain C residue  214 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 150 optimal weight:    0.6980
   chunk 106 optimal weight:    0.7980
   chunk 128 optimal weight:    0.9990
   chunk 91 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 100 optimal weight:    5.9990
   chunk 117 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
C 251 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.157595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.119581 restraints weight = 15477.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 2.02
r_work: 0.2883 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2731 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.1640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  13065  Z= 0.156
  Angle     :  0.475   6.311  17780  Z= 0.241
  Chirality :  0.044   0.129   1955
  Planarity :  0.003   0.021   2265
  Dihedral  :  4.054  17.280   1715
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 20.72 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.22), residues: 1540
  helix:  1.07 (0.24), residues: 505
  sheet:  1.04 (0.25), residues: 475
  loop : -1.84 (0.25), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 206 
 HIS   0.004   0.001   HIS A 285 
 PHE   0.008   0.001   PHE A 208 
 TYR   0.010   0.001   TYR D  38 
 ARG   0.003   0.000   ARG D 231 

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 1.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8124 (mt0)
REVERT: E   34 LYS cc_start: 0.8932 (mttp) cc_final: 0.8712 (mttm)
REVERT: E  129 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.7989 (mt-10)
REVERT: E  231 ARG cc_start: 0.7162 (mtm180) cc_final: 0.6955 (mtt180)
REVERT: E  264 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7658 (mt0)
REVERT: B   86 ASP cc_start: 0.8948 (t70) cc_final: 0.8573 (t70)
  outliers start: 19
  outliers final: 12
  residues processed: 136
  average time/residue: 0.2612
  time to fit residues: 51.9442
Evaluate side-chains
  126 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 1.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  264 GLN
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue  129 GLU
Chi-restraints excluded: chain E residue  222 VAL
Chi-restraints excluded: chain E residue  264 GLN
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain C residue  265 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 110 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 30 optimal weight:   10.0000
   chunk 100 optimal weight:    6.9990
   chunk 152 optimal weight:    8.9990
   chunk 81 optimal weight:    2.9990
   chunk 125 optimal weight:    0.8980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
C 251 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.132580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.099091 restraints weight = 15800.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 1.68
r_work: 0.2887 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2746 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019  13065  Z= 0.164
  Angle     :  0.469   7.314  17780  Z= 0.238
  Chirality :  0.044   0.126   1955
  Planarity :  0.002   0.020   2265
  Dihedral  :  3.992  17.144   1715
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 19.13 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.22), residues: 1540
  helix:  1.35 (0.24), residues: 505
  sheet:  1.07 (0.25), residues: 475
  loop : -1.71 (0.25), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 206 
 HIS   0.004   0.001   HIS A 285 
 PHE   0.006   0.001   PHE C 228 
 TYR   0.010   0.001   TYR D  38 
 ARG   0.002   0.000   ARG A  65 

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 127
  time to evaluate  : 1.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8803 (mm-30)
REVERT: A  264 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8266 (mt0)
REVERT: E  129 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8038 (mt-10)
REVERT: E  185 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8441 (pt0)
REVERT: E  264 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7790 (mt0)
REVERT: B   36 ASP cc_start: 0.8780 (t70) cc_final: 0.8522 (t0)
REVERT: B   86 ASP cc_start: 0.8864 (t70) cc_final: 0.8538 (t70)
REVERT: B  129 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8051 (mt-10)
REVERT: D  230 GLU cc_start: 0.7053 (mp0) cc_final: 0.6565 (pm20)
REVERT: D  231 ARG cc_start: 0.7274 (mtm180) cc_final: 0.7015 (mtm180)
REVERT: C  129 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8125 (mt-10)
REVERT: C  239 MET cc_start: 0.8528 (ttt) cc_final: 0.8319 (ttt)
  outliers start: 38
  outliers final: 22
  residues processed: 163
  average time/residue: 0.2458
  time to fit residues: 59.1710
Evaluate side-chains
  147 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 119
  time to evaluate  : 1.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  264 GLN
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue  129 GLU
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  222 VAL
Chi-restraints excluded: chain E residue  264 GLN
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  129 GLU
Chi-restraints excluded: chain B residue  185 GLN
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  265 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 83 optimal weight:    8.9990
   chunk 96 optimal weight:    3.9990
   chunk 138 optimal weight:    9.9990
   chunk 146 optimal weight:    6.9990
   chunk 64 optimal weight:    0.7980
   chunk 70 optimal weight:    5.9990
   chunk 113 optimal weight:    1.9990
   chunk 124 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 298 GLN
E 298 GLN
B 298 GLN
D 298 GLN
C 251 ASN
C 298 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.157355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.120791 restraints weight = 15607.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 2.05
r_work: 0.2791 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2639 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13065  Z= 0.295
  Angle     :  0.523   6.326  17780  Z= 0.268
  Chirality :  0.046   0.131   1955
  Planarity :  0.003   0.019   2265
  Dihedral  :  4.238  19.277   1715
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 18.27 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.22), residues: 1540
  helix:  1.40 (0.24), residues: 505
  sheet:  1.14 (0.25), residues: 470
  loop : -1.72 (0.25), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 206 
 HIS   0.003   0.001   HIS A 285 
 PHE   0.010   0.001   PHE E 142 
 TYR   0.012   0.002   TYR E 204 
 ARG   0.002   0.000   ARG A 105 

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 123
  time to evaluate  : 1.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ARG cc_start: 0.8190 (mmm-85) cc_final: 0.7954 (tpp80)
REVERT: A  129 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8351 (mt-10)
REVERT: A  151 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8004 (m110)
REVERT: A  264 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8457 (mt0)
REVERT: E   86 ASP cc_start: 0.8841 (t70) cc_final: 0.8421 (t70)
REVERT: E  185 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8468 (pt0)
REVERT: E  231 ARG cc_start: 0.7495 (mtm180) cc_final: 0.7119 (mtt180)
REVERT: E  264 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8419 (mt0)
REVERT: B   86 ASP cc_start: 0.8855 (t70) cc_final: 0.8437 (t70)
REVERT: B  129 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8308 (mt-10)
REVERT: D   30 GLU cc_start: 0.9044 (pm20) cc_final: 0.8719 (pm20)
REVERT: D  264 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8238 (mt0)
REVERT: C  151 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8339 (t0)
  outliers start: 46
  outliers final: 28
  residues processed: 165
  average time/residue: 0.2505
  time to fit residues: 60.3527
Evaluate side-chains
  159 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 123
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  151 ASN
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  221 SER
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  264 GLN
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain E residue  221 SER
Chi-restraints excluded: chain E residue  222 VAL
Chi-restraints excluded: chain E residue  264 GLN
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  129 GLU
Chi-restraints excluded: chain B residue  185 GLN
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  221 SER
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  264 GLN
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  265 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 61 optimal weight:    9.9990
   chunk 86 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 95 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 133 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
C 251 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.131324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.097537 restraints weight = 16227.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 1.76
r_work: 0.3144 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13065  Z= 0.166
  Angle     :  0.472   6.244  17780  Z= 0.238
  Chirality :  0.044   0.126   1955
  Planarity :  0.002   0.022   2265
  Dihedral  :  3.997  15.752   1715
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.35 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.22), residues: 1540
  helix:  1.48 (0.24), residues: 505
  sheet:  1.19 (0.25), residues: 465
  loop : -1.73 (0.25), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 161 
 HIS   0.004   0.001   HIS A 285 
 PHE   0.008   0.001   PHE A 142 
 TYR   0.009   0.001   TYR D  38 
 ARG   0.002   0.000   ARG D 231 

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 132
  time to evaluate  : 1.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8724 (mm-30)
REVERT: A   65 ARG cc_start: 0.8243 (mmm-85) cc_final: 0.8016 (tpp80)
REVERT: A  129 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8129 (mt-10)
REVERT: A  264 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8480 (mt0)
REVERT: E   86 ASP cc_start: 0.8736 (t70) cc_final: 0.8435 (t70)
REVERT: E  185 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8473 (pt0)
REVERT: B  129 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8069 (mt-10)
REVERT: B  231 ARG cc_start: 0.7492 (mtm180) cc_final: 0.7099 (mtt180)
REVERT: D   30 GLU cc_start: 0.8854 (pm20) cc_final: 0.8649 (pm20)
REVERT: D   36 ASP cc_start: 0.9070 (t0) cc_final: 0.8690 (t0)
REVERT: D  231 ARG cc_start: 0.7414 (mtm180) cc_final: 0.7139 (mtm-85)
REVERT: D  248 TYR cc_start: 0.8914 (t80) cc_final: 0.8694 (t80)
REVERT: C   30 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8523 (pm20)
  outliers start: 33
  outliers final: 21
  residues processed: 160
  average time/residue: 0.2438
  time to fit residues: 56.8646
Evaluate side-chains
  153 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 127
  time to evaluate  : 1.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  264 GLN
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  221 SER
Chi-restraints excluded: chain E residue  222 VAL
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  129 GLU
Chi-restraints excluded: chain B residue  185 GLN
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue  221 SER
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  265 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 34 optimal weight:    0.4980
   chunk 52 optimal weight:    0.8980
   chunk 76 optimal weight:    9.9990
   chunk 37 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 121 optimal weight:    0.9980
   chunk 88 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
C 251 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.130707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.097439 restraints weight = 15990.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 1.68
r_work: 0.2861 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2717 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13065  Z= 0.192
  Angle     :  0.484   7.435  17780  Z= 0.244
  Chirality :  0.045   0.126   1955
  Planarity :  0.002   0.021   2265
  Dihedral  :  3.959  15.765   1715
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 19.21 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.22), residues: 1540
  helix:  1.51 (0.24), residues: 505
  sheet:  1.18 (0.25), residues: 470
  loop : -1.79 (0.25), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 161 
 HIS   0.004   0.001   HIS A 285 
 PHE   0.009   0.001   PHE A 142 
 TYR   0.010   0.001   TYR D  38 
 ARG   0.002   0.000   ARG D 231 

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 126
  time to evaluate  : 1.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8761 (mm-30)
REVERT: A   65 ARG cc_start: 0.8161 (mmm-85) cc_final: 0.7943 (tpp80)
REVERT: A  113 ASP cc_start: 0.8264 (m-30) cc_final: 0.7741 (p0)
REVERT: A  129 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8175 (mt-10)
REVERT: A  264 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8441 (mt0)
REVERT: A  304 PHE cc_start: 0.4963 (OUTLIER) cc_final: 0.4132 (t80)
REVERT: E   86 ASP cc_start: 0.8770 (t70) cc_final: 0.8464 (t70)
REVERT: E  185 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8483 (pt0)
REVERT: E  304 PHE cc_start: 0.4926 (OUTLIER) cc_final: 0.3317 (t80)
REVERT: B   30 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8415 (mp0)
REVERT: B   82 VAL cc_start: 0.9198 (t) cc_final: 0.8963 (t)
REVERT: B  129 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8066 (mt-10)
REVERT: B  151 ASN cc_start: 0.8313 (OUTLIER) cc_final: 0.7972 (m110)
REVERT: D   30 GLU cc_start: 0.8881 (pm20) cc_final: 0.8630 (pm20)
REVERT: D   65 ARG cc_start: 0.7860 (mmm-85) cc_final: 0.7463 (ttm-80)
REVERT: D  129 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8167 (mt-10)
REVERT: D  231 ARG cc_start: 0.7337 (mtm180) cc_final: 0.7082 (mtm-85)
REVERT: D  248 TYR cc_start: 0.8955 (t80) cc_final: 0.8748 (t80)
REVERT: C   30 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8473 (pm20)
REVERT: C  304 PHE cc_start: 0.5267 (OUTLIER) cc_final: 0.4144 (t80)
  outliers start: 45
  outliers final: 29
  residues processed: 164
  average time/residue: 0.2477
  time to fit residues: 59.6771
Evaluate side-chains
  161 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 121
  time to evaluate  : 1.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  221 SER
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  264 GLN
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain E residue  221 SER
Chi-restraints excluded: chain E residue  222 VAL
Chi-restraints excluded: chain E residue  304 PHE
Chi-restraints excluded: chain B residue   30 GLU
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  129 GLU
Chi-restraints excluded: chain B residue  151 ASN
Chi-restraints excluded: chain B residue  185 GLN
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue  129 GLU
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  221 SER
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  265 MET
Chi-restraints excluded: chain C residue  304 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 35 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 76 optimal weight:    7.9990
   chunk 119 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 131 optimal weight:    6.9990
   chunk 122 optimal weight:    8.9990
   chunk 134 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
D 154 ASN
C 154 ASN
C 251 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.127019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.093261 restraints weight = 16382.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 1.72
r_work: 0.2962 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2807 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  13065  Z= 0.362
  Angle     :  0.554   7.538  17780  Z= 0.283
  Chirality :  0.047   0.131   1955
  Planarity :  0.003   0.020   2265
  Dihedral  :  4.301  20.413   1715
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 18.84 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.22), residues: 1540
  helix:  1.40 (0.24), residues: 505
  sheet:  1.17 (0.26), residues: 450
  loop : -1.84 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 206 
 HIS   0.003   0.001   HIS A 285 
 PHE   0.010   0.001   PHE A 142 
 TYR   0.013   0.002   TYR C 204 
 ARG   0.002   0.000   ARG B 190 

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 125
  time to evaluate  : 1.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ARG cc_start: 0.8286 (mmm-85) cc_final: 0.8080 (tpp80)
REVERT: A  129 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8296 (mt-10)
REVERT: A  151 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8056 (m110)
REVERT: A  264 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8593 (mt0)
REVERT: A  304 PHE cc_start: 0.5190 (OUTLIER) cc_final: 0.4359 (t80)
REVERT: E  185 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8435 (pt0)
REVERT: E  231 ARG cc_start: 0.7645 (mtm180) cc_final: 0.7376 (mtt180)
REVERT: E  264 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8640 (mt0)
REVERT: E  304 PHE cc_start: 0.5357 (OUTLIER) cc_final: 0.3836 (t80)
REVERT: B   30 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8604 (pm20)
REVERT: B  129 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8372 (mt-10)
REVERT: B  151 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.8065 (m110)
REVERT: B  304 PHE cc_start: 0.5449 (OUTLIER) cc_final: 0.4319 (t80)
REVERT: D  129 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8313 (mt-10)
REVERT: D  231 ARG cc_start: 0.7444 (mtm180) cc_final: 0.7201 (mtm-85)
REVERT: D  304 PHE cc_start: 0.5154 (OUTLIER) cc_final: 0.3869 (t80)
REVERT: C   30 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8545 (pm20)
REVERT: C  184 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8144 (m-40)
REVERT: C  304 PHE cc_start: 0.5535 (OUTLIER) cc_final: 0.4329 (t80)
  outliers start: 54
  outliers final: 31
  residues processed: 173
  average time/residue: 0.2369
  time to fit residues: 60.2535
Evaluate side-chains
  166 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 119
  time to evaluate  : 1.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  151 ASN
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  221 SER
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  264 GLN
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain E residue  221 SER
Chi-restraints excluded: chain E residue  222 VAL
Chi-restraints excluded: chain E residue  264 GLN
Chi-restraints excluded: chain E residue  304 PHE
Chi-restraints excluded: chain E residue  306 LEU
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   30 GLU
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  129 GLU
Chi-restraints excluded: chain B residue  151 ASN
Chi-restraints excluded: chain B residue  185 GLN
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue  129 GLU
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  221 SER
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue  184 ASN
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  265 MET
Chi-restraints excluded: chain C residue  304 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 124 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 145 optimal weight:    6.9990
   chunk 106 optimal weight:    2.9990
   chunk 99 optimal weight:    0.0770
   chunk 128 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 139 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   overall best weight:    1.1540

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

Flipped N/Q/H residues before XYZ refinement:
E 154 ASN
B 154 ASN
D 154 ASN
C 154 ASN
C 251 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.129888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.096729 restraints weight = 16122.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 1.67
r_work: 0.2844 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2704 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13065  Z= 0.191
  Angle     :  0.493   7.653  17780  Z= 0.249
  Chirality :  0.045   0.126   1955
  Planarity :  0.002   0.023   2265
  Dihedral  :  4.042  15.726   1715
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 19.42 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.22), residues: 1540
  helix:  1.47 (0.24), residues: 505
  sheet:  1.16 (0.26), residues: 450
  loop : -1.89 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP E 161 
 HIS   0.004   0.001   HIS A 285 
 PHE   0.009   0.001   PHE B 208 
 TYR   0.010   0.001   TYR D  38 
 ARG   0.002   0.000   ARG D 231 

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 126
  time to evaluate  : 1.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8786 (mm-30)
REVERT: A   65 ARG cc_start: 0.8194 (mmm-85) cc_final: 0.7968 (tpp80)
REVERT: A  113 ASP cc_start: 0.8285 (m-30) cc_final: 0.7892 (p0)
REVERT: A  129 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8172 (mt-10)
REVERT: A  264 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8353 (mt0)
REVERT: A  304 PHE cc_start: 0.5092 (OUTLIER) cc_final: 0.4265 (t80)
REVERT: E  185 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8501 (pt0)
REVERT: E  264 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8559 (mt0)
REVERT: E  304 PHE cc_start: 0.5206 (OUTLIER) cc_final: 0.3607 (t80)
REVERT: B   30 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8633 (pm20)
REVERT: B   82 VAL cc_start: 0.9192 (t) cc_final: 0.8966 (t)
REVERT: B  129 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8111 (mt-10)
REVERT: B  304 PHE cc_start: 0.5316 (OUTLIER) cc_final: 0.4208 (t80)
REVERT: D   65 ARG cc_start: 0.7918 (mmm-85) cc_final: 0.7554 (ttm-80)
REVERT: D  129 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8192 (mt-10)
REVERT: D  151 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.8160 (m110)
REVERT: D  231 ARG cc_start: 0.7400 (mtm180) cc_final: 0.7161 (mtm-85)
REVERT: D  248 TYR cc_start: 0.8979 (t80) cc_final: 0.8759 (t80)
REVERT: D  264 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8426 (mt0)
REVERT: D  304 PHE cc_start: 0.5043 (OUTLIER) cc_final: 0.3751 (t80)
REVERT: C   30 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8541 (pm20)
REVERT: C  304 PHE cc_start: 0.5386 (OUTLIER) cc_final: 0.4225 (t80)
  outliers start: 51
  outliers final: 27
  residues processed: 169
  average time/residue: 0.2415
  time to fit residues: 59.6646
Evaluate side-chains
  165 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 123
  time to evaluate  : 1.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  264 GLN
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain E residue  221 SER
Chi-restraints excluded: chain E residue  222 VAL
Chi-restraints excluded: chain E residue  264 GLN
Chi-restraints excluded: chain E residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   30 GLU
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  129 GLU
Chi-restraints excluded: chain B residue  185 GLN
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue  129 GLU
Chi-restraints excluded: chain D residue  151 ASN
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  221 SER
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  264 GLN
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  265 MET
Chi-restraints excluded: chain C residue  304 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 81 optimal weight:    1.9990
   chunk 119 optimal weight:    0.7980
   chunk 114 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 127 optimal weight:    4.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
E 154 ASN
B 154 ASN
D 154 ASN
C 251 ASN
C 264 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.126047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.092555 restraints weight = 16288.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 1.70
r_work: 0.2950 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2795 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  13065  Z= 0.397
  Angle     :  0.572   7.740  17780  Z= 0.292
  Chirality :  0.047   0.135   1955
  Planarity :  0.003   0.020   2265
  Dihedral  :  4.357  21.545   1715
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 19.21 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.22), residues: 1540
  helix:  1.34 (0.24), residues: 505
  sheet:  1.05 (0.26), residues: 450
  loop : -1.90 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E 161 
 HIS   0.003   0.001   HIS A 177 
 PHE   0.013   0.001   PHE B 208 
 TYR   0.014   0.002   TYR D 245 
 ARG   0.002   0.000   ARG E 105 

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 121
  time to evaluate  : 1.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.8043 (tpp80)
REVERT: A  113 ASP cc_start: 0.8397 (m-30) cc_final: 0.8032 (p0)
REVERT: A  129 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8296 (mt-10)
REVERT: A  151 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8119 (m110)
REVERT: A  264 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8580 (mt0)
REVERT: A  304 PHE cc_start: 0.5129 (OUTLIER) cc_final: 0.4301 (t80)
REVERT: E   30 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8627 (pm20)
REVERT: E  185 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8494 (pt0)
REVERT: E  231 ARG cc_start: 0.7663 (mtm180) cc_final: 0.7392 (mtt180)
REVERT: E  264 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8645 (mt0)
REVERT: E  304 PHE cc_start: 0.5451 (OUTLIER) cc_final: 0.3961 (t80)
REVERT: B   30 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8654 (pm20)
REVERT: B  129 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8413 (mt-10)
REVERT: B  151 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.8150 (m110)
REVERT: B  169 HIS cc_start: 0.7748 (t70) cc_final: 0.7527 (t70)
REVERT: B  304 PHE cc_start: 0.5505 (OUTLIER) cc_final: 0.4376 (t80)
REVERT: D  129 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8344 (mt-10)
REVERT: D  231 ARG cc_start: 0.7471 (mtm180) cc_final: 0.7234 (mtm-85)
REVERT: D  264 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8505 (mt0)
REVERT: D  304 PHE cc_start: 0.5232 (OUTLIER) cc_final: 0.3911 (t80)
REVERT: C   30 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8562 (pm20)
REVERT: C  151 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8300 (m-40)
REVERT: C  184 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8168 (m-40)
REVERT: C  304 PHE cc_start: 0.5604 (OUTLIER) cc_final: 0.4416 (t80)
  outliers start: 54
  outliers final: 27
  residues processed: 167
  average time/residue: 0.2529
  time to fit residues: 61.7354
Evaluate side-chains
  162 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 116
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  129 GLU
Chi-restraints excluded: chain A residue  151 ASN
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  264 GLN
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   30 GLU
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain E residue  221 SER
Chi-restraints excluded: chain E residue  222 VAL
Chi-restraints excluded: chain E residue  264 GLN
Chi-restraints excluded: chain E residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   30 GLU
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  129 GLU
Chi-restraints excluded: chain B residue  151 ASN
Chi-restraints excluded: chain B residue  185 GLN
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue  129 GLU
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  221 SER
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  264 GLN
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue  151 ASN
Chi-restraints excluded: chain C residue  184 ASN
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  265 MET
Chi-restraints excluded: chain C residue  304 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 58.2403 > 50:
  distance: 47 - 152:  15.817
  distance: 50 - 149:  21.048
  distance: 62 - 136:  24.075
  distance: 65 - 133:  15.358
  distance: 109 - 113:  10.370
  distance: 113 - 114:  13.524
  distance: 114 - 115:  21.955
  distance: 114 - 117:  17.039
  distance: 115 - 116:  35.973
  distance: 115 - 122:  22.553
  distance: 117 - 118:  11.726
  distance: 118 - 119:   6.109
  distance: 119 - 120:  17.389
  distance: 120 - 121:  12.090
  distance: 122 - 123:  11.740
  distance: 122 - 226:  17.926
  distance: 123 - 124:   9.990
  distance: 123 - 126:   8.575
  distance: 124 - 125:  13.184
  distance: 124 - 133:  10.183
  distance: 125 - 223:  24.798
  distance: 126 - 127:  20.559
  distance: 127 - 128:   3.996
  distance: 128 - 129:  16.347
  distance: 129 - 130:  15.567
  distance: 130 - 131:  25.475
  distance: 130 - 132:  20.159
  distance: 133 - 134:   9.854
  distance: 134 - 135:  27.183
  distance: 134 - 137:  21.809
  distance: 135 - 136:  19.421
  distance: 135 - 141:  22.615
  distance: 137 - 138:  22.107
  distance: 138 - 139:  22.521
  distance: 138 - 140:  11.888
  distance: 141 - 142:  14.927
  distance: 141 - 208:  32.480
  distance: 142 - 143:  15.149
  distance: 142 - 145:  33.770
  distance: 143 - 144:   9.070
  distance: 143 - 149:  20.212
  distance: 144 - 205:  35.270
  distance: 145 - 146:  43.978
  distance: 146 - 147:  17.649
  distance: 147 - 148:  22.238
  distance: 149 - 150:  10.868
  distance: 150 - 151:   9.079
  distance: 150 - 153:  20.945
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  distance: 168 - 174:  25.015
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  distance: 194 - 195:  16.113
  distance: 195 - 196:  15.480