Starting phenix.real_space_refine
on Thu Jun 12 18:19:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/3jcf_6551/06_2025/3jcf_6551.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/3jcf_6551/06_2025/3jcf_6551.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/3jcf_6551/06_2025/3jcf_6551.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/3jcf_6551/06_2025/3jcf_6551.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/3jcf_6551/06_2025/3jcf_6551.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/3jcf_6551/06_2025/3jcf_6551.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Mg     13      5.21       5
     S      40      5.16       5
     C    9250      2.51       5
     N    2305      2.21       5
     O    2620      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14228
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 2843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2843
          Classifications: {'peptide': 349}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 15, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "B"
      Number of atoms: 2843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2843
          Classifications: {'peptide': 349}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 15, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "C"
      Number of atoms: 2843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2843
          Classifications: {'peptide': 349}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 15, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "D"
      Number of atoms: 2843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2843
          Classifications: {'peptide': 349}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 15, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "E"
      Number of atoms: 2843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2843
          Classifications: {'peptide': 349}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 15, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {' MG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 9.93, per 1000 atoms: 0.70
  Number of scatterers: 14228
  At special positions: 0
  Unit cell: (116.025, 113.475, 124.95, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     Mg     13     11.99
     O    2620      8.00
     N    2305      7.00
     C    9250      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: 3.18
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3360

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 5 sheets defined
      57.6% alpha, 12.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 56
      removed outlier: 3.576A  pdb=" N   PHE A  53 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ASP A  55 " --> pdb=" O   PRO A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 80
      removed outlier: 3.527A  pdb=" N   VAL A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 92
    Processing helix  chain 'A' and resid 147 through 156
    Processing helix  chain 'A' and resid 159 through 163
      removed outlier: 4.106A  pdb=" N   ARG A 162 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 201
      removed outlier: 3.596A  pdb=" N   TYR A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   PHE A 182 " --> pdb=" O   VAL A 178 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   VAL A 183 " --> pdb=" O   ASP A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 237
      Proline residue:  A 227  - end of helix
      removed outlier: 4.170A  pdb=" N   GLU A 230 " --> pdb=" O   TRP A 226 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU A 235 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ARG A 237 " --> pdb=" O   SER A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 299
      removed outlier: 3.929A  pdb=" N   TYR A 250 " --> pdb=" O   GLU A 246 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASP A 253 " --> pdb=" O   PRO A 249 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE A 259 " --> pdb=" O   TYR A 255 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLY A 274 " --> pdb=" O   ASP A 270 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU A 276 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   ASP A 277 " --> pdb=" O   SER A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 313
    Processing helix  chain 'A' and resid 325 through 345
      removed outlier: 3.566A  pdb=" N   VAL A 329 " --> pdb=" O   TRP A 325 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLY A 335 " --> pdb=" O   LEU A 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 56
      removed outlier: 3.575A  pdb=" N   PHE B  53 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ASP B  55 " --> pdb=" O   PRO B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 80
      removed outlier: 3.527A  pdb=" N   VAL B  73 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 92
    Processing helix  chain 'B' and resid 147 through 156
    Processing helix  chain 'B' and resid 159 through 163
      removed outlier: 4.105A  pdb=" N   ARG B 162 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 201
      removed outlier: 3.598A  pdb=" N   TYR B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   PHE B 182 " --> pdb=" O   VAL B 178 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   VAL B 183 " --> pdb=" O   ASP B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 237
      Proline residue:  B 227  - end of helix
      removed outlier: 4.169A  pdb=" N   GLU B 230 " --> pdb=" O   TRP B 226 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU B 235 " --> pdb=" O   VAL B 231 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ARG B 237 " --> pdb=" O   SER B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 299
      removed outlier: 3.928A  pdb=" N   TYR B 250 " --> pdb=" O   GLU B 246 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASP B 253 " --> pdb=" O   PRO B 249 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE B 259 " --> pdb=" O   TYR B 255 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLY B 274 " --> pdb=" O   ASP B 270 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU B 276 " --> pdb=" O   VAL B 272 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   ASP B 277 " --> pdb=" O   SER B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 313
    Processing helix  chain 'B' and resid 325 through 345
      removed outlier: 3.568A  pdb=" N   VAL B 329 " --> pdb=" O   TRP B 325 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLY B 335 " --> pdb=" O   LEU B 331 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 50 through 56
      removed outlier: 3.576A  pdb=" N   PHE C  53 " --> pdb=" O   VAL C  50 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ASP C  55 " --> pdb=" O   PRO C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 80
      removed outlier: 3.527A  pdb=" N   VAL C  73 " --> pdb=" O   ARG C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 92
    Processing helix  chain 'C' and resid 147 through 156
    Processing helix  chain 'C' and resid 159 through 163
      removed outlier: 4.104A  pdb=" N   ARG C 162 " --> pdb=" O   GLY C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 201
      removed outlier: 3.596A  pdb=" N   TYR C 181 " --> pdb=" O   LEU C 177 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   PHE C 182 " --> pdb=" O   VAL C 178 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   VAL C 183 " --> pdb=" O   ASP C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 237
      Proline residue:  C 227  - end of helix
      removed outlier: 4.170A  pdb=" N   GLU C 230 " --> pdb=" O   TRP C 226 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU C 235 " --> pdb=" O   VAL C 231 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ARG C 237 " --> pdb=" O   SER C 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 246 through 299
      removed outlier: 3.928A  pdb=" N   TYR C 250 " --> pdb=" O   GLU C 246 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ASP C 253 " --> pdb=" O   PRO C 249 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE C 259 " --> pdb=" O   TYR C 255 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLY C 274 " --> pdb=" O   ASP C 270 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU C 276 " --> pdb=" O   VAL C 272 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   ASP C 277 " --> pdb=" O   SER C 273 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 313
    Processing helix  chain 'C' and resid 325 through 345
      removed outlier: 3.563A  pdb=" N   VAL C 329 " --> pdb=" O   TRP C 325 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLY C 335 " --> pdb=" O   LEU C 331 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 56
      removed outlier: 3.575A  pdb=" N   PHE D  53 " --> pdb=" O   VAL D  50 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ASP D  55 " --> pdb=" O   PRO D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 69 through 80
      removed outlier: 3.526A  pdb=" N   VAL D  73 " --> pdb=" O   ARG D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 92
    Processing helix  chain 'D' and resid 147 through 156
    Processing helix  chain 'D' and resid 159 through 163
      removed outlier: 4.106A  pdb=" N   ARG D 162 " --> pdb=" O   GLY D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 165 through 201
      removed outlier: 3.597A  pdb=" N   TYR D 181 " --> pdb=" O   LEU D 177 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   PHE D 182 " --> pdb=" O   VAL D 178 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   VAL D 183 " --> pdb=" O   ASP D 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 206 through 237
      Proline residue:  D 227  - end of helix
      removed outlier: 4.169A  pdb=" N   GLU D 230 " --> pdb=" O   TRP D 226 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU D 235 " --> pdb=" O   VAL D 231 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ARG D 237 " --> pdb=" O   SER D 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 246 through 299
      removed outlier: 3.928A  pdb=" N   TYR D 250 " --> pdb=" O   GLU D 246 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASP D 253 " --> pdb=" O   PRO D 249 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE D 259 " --> pdb=" O   TYR D 255 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLY D 274 " --> pdb=" O   ASP D 270 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU D 276 " --> pdb=" O   VAL D 272 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   ASP D 277 " --> pdb=" O   SER D 273 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 301 through 313
    Processing helix  chain 'D' and resid 325 through 345
      removed outlier: 3.567A  pdb=" N   VAL D 329 " --> pdb=" O   TRP D 325 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLY D 335 " --> pdb=" O   LEU D 331 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 50 through 56
      removed outlier: 3.574A  pdb=" N   PHE E  53 " --> pdb=" O   VAL E  50 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ASP E  55 " --> pdb=" O   PRO E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 69 through 80
      removed outlier: 3.526A  pdb=" N   VAL E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 83 through 92
    Processing helix  chain 'E' and resid 147 through 156
    Processing helix  chain 'E' and resid 159 through 163
      removed outlier: 4.105A  pdb=" N   ARG E 162 " --> pdb=" O   GLY E 159 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 165 through 201
      removed outlier: 3.597A  pdb=" N   TYR E 181 " --> pdb=" O   LEU E 177 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   PHE E 182 " --> pdb=" O   VAL E 178 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   VAL E 183 " --> pdb=" O   ASP E 179 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 206 through 237
      Proline residue:  E 227  - end of helix
      removed outlier: 4.170A  pdb=" N   GLU E 230 " --> pdb=" O   TRP E 226 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU E 235 " --> pdb=" O   VAL E 231 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ARG E 237 " --> pdb=" O   SER E 233 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 246 through 299
      removed outlier: 3.927A  pdb=" N   TYR E 250 " --> pdb=" O   GLU E 246 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ASP E 253 " --> pdb=" O   PRO E 249 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE E 259 " --> pdb=" O   TYR E 255 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLY E 274 " --> pdb=" O   ASP E 270 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU E 276 " --> pdb=" O   VAL E 272 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   ASP E 277 " --> pdb=" O   SER E 273 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 301 through 313
    Processing helix  chain 'E' and resid 325 through 345
      removed outlier: 3.566A  pdb=" N   VAL E 329 " --> pdb=" O   TRP E 325 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLY E 335 " --> pdb=" O   LEU E 331 " (cutoff:3.500A)
    Processing sheet with id=A, first strand: chain 'A' and resid 39 through 44
    Processing sheet with id=B, first strand: chain 'B' and resid 39 through 44
    Processing sheet with id=C, first strand: chain 'C' and resid 39 through 44
    Processing sheet with id=D, first strand: chain 'D' and resid 39 through 44
    Processing sheet with id=E, first strand: chain 'E' and resid 39 through 44

    880 hydrogen bonds defined for protein.
    2565 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: 3.94

  Time building geometry restraints manager: 3.83 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4471
        1.34 -     1.46: 1966
        1.46 -     1.57: 8013
        1.57 -     1.69: 0
        1.69 -     1.80: 75
  Bond restraints: 14525
  Sorted by residual:
  bond pdb=" CA  PRO C 240 "
       pdb=" C   PRO C 240 "
    ideal  model  delta    sigma   weight residual
    1.517  1.546 -0.028 9.30e-03 1.16e+04 9.35e+00
  bond pdb=" CA  PRO E 240 "
       pdb=" C   PRO E 240 "
    ideal  model  delta    sigma   weight residual
    1.517  1.545 -0.028 9.30e-03 1.16e+04 9.11e+00
  bond pdb=" CA  PRO A 240 "
       pdb=" C   PRO A 240 "
    ideal  model  delta    sigma   weight residual
    1.517  1.545 -0.028 9.30e-03 1.16e+04 8.95e+00
  bond pdb=" CA  PRO B 240 "
       pdb=" C   PRO B 240 "
    ideal  model  delta    sigma   weight residual
    1.517  1.545 -0.028 9.30e-03 1.16e+04 8.92e+00
  bond pdb=" CA  PRO D 240 "
       pdb=" C   PRO D 240 "
    ideal  model  delta    sigma   weight residual
    1.517  1.545 -0.028 9.30e-03 1.16e+04 8.78e+00
  ... (remaining 14520 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 18688
        2.03 -     4.06: 941
        4.06 -     6.08: 55
        6.08 -     8.11: 41
        8.11 -    10.14: 5
  Bond angle restraints: 19730
  Sorted by residual:
  angle pdb=" C   PRO C 240 "
        pdb=" N   PRO C 241 "
        pdb=" CA  PRO C 241 "
      ideal   model   delta    sigma   weight residual
     119.84  113.54    6.30 1.25e+00 6.40e-01 2.54e+01
  angle pdb=" C   PRO B 240 "
        pdb=" N   PRO B 241 "
        pdb=" CA  PRO B 241 "
      ideal   model   delta    sigma   weight residual
     119.84  113.59    6.25 1.25e+00 6.40e-01 2.50e+01
  angle pdb=" C   PRO D 240 "
        pdb=" N   PRO D 241 "
        pdb=" CA  PRO D 241 "
      ideal   model   delta    sigma   weight residual
     119.84  113.59    6.25 1.25e+00 6.40e-01 2.50e+01
  angle pdb=" C   PRO E 240 "
        pdb=" N   PRO E 241 "
        pdb=" CA  PRO E 241 "
      ideal   model   delta    sigma   weight residual
     119.84  113.60    6.24 1.25e+00 6.40e-01 2.49e+01
  angle pdb=" C   PRO A 240 "
        pdb=" N   PRO A 241 "
        pdb=" CA  PRO A 241 "
      ideal   model   delta    sigma   weight residual
     119.84  113.62    6.22 1.25e+00 6.40e-01 2.48e+01
  ... (remaining 19725 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     7.97: 7974
        7.97 -    15.93: 576
       15.93 -    23.90: 118
       23.90 -    31.86: 59
       31.86 -    39.83: 28
  Dihedral angle restraints: 8755
    sinusoidal: 3570
      harmonic: 5185
  Sorted by residual:
  dihedral pdb=" CA  LEU C 131 "
           pdb=" CB  LEU C 131 "
           pdb=" CG  LEU C 131 "
           pdb=" CD1 LEU C 131 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  140.17   39.83     3      1.50e+01 4.44e-03 7.07e+00
  dihedral pdb=" CA  LEU A 131 "
           pdb=" CB  LEU A 131 "
           pdb=" CG  LEU A 131 "
           pdb=" CD1 LEU A 131 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  140.19   39.81     3      1.50e+01 4.44e-03 7.07e+00
  dihedral pdb=" CA  LEU B 131 "
           pdb=" CB  LEU B 131 "
           pdb=" CG  LEU B 131 "
           pdb=" CD1 LEU B 131 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  140.22   39.78     3      1.50e+01 4.44e-03 7.06e+00
  ... (remaining 8752 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 1630
       0.024 -    0.047: 245
       0.047 -    0.071: 109
       0.071 -    0.095: 178
       0.095 -    0.119: 128
  Chirality restraints: 2290
  Sorted by residual:
  chirality pdb=" CA  ILE C 160 "
            pdb=" N   ILE C 160 "
            pdb=" C   ILE C 160 "
            pdb=" CB  ILE C 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.51e-01
  chirality pdb=" CA  ILE B 160 "
            pdb=" N   ILE B 160 "
            pdb=" C   ILE B 160 "
            pdb=" CB  ILE B 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.38e-01
  chirality pdb=" CA  ILE B 143 "
            pdb=" N   ILE B 143 "
            pdb=" C   ILE B 143 "
            pdb=" CB  ILE B 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.37e-01
  ... (remaining 2287 not shown)

  Planarity restraints: 2490
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E 239 "   -0.024 5.00e-02 4.00e+02   3.65e-02 2.13e+00
        pdb=" N   PRO E 240 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO E 240 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO E 240 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 239 "    0.024 5.00e-02 4.00e+02   3.63e-02 2.11e+00
        pdb=" N   PRO C 240 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO C 240 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C 240 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 239 "    0.024 5.00e-02 4.00e+02   3.62e-02 2.10e+00
        pdb=" N   PRO B 240 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B 240 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 240 "    0.021 5.00e-02 4.00e+02
  ... (remaining 2487 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 181
        2.63 -     3.19: 13699
        3.19 -     3.76: 22099
        3.76 -     4.33: 30360
        4.33 -     4.90: 49384
  Nonbonded interactions: 115723
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 253 "
            pdb="MG    MG D 402 "
     model   vdw
     2.057 2.170
  nonbonded pdb=" OD1 ASP B 253 "
            pdb="MG    MG C 402 "
     model   vdw
     2.058 2.170
  nonbonded pdb=" OD1 ASP D 253 "
            pdb="MG    MG E 402 "
     model   vdw
     2.059 2.170
  nonbonded pdb=" OD1 ASP A 253 "
            pdb="MG    MG B 402 "
     model   vdw
     2.059 2.170
  nonbonded pdb=" OD1 ASP E 253 "
            pdb="MG    MG A 402 "
     model   vdw
     2.062 2.170
  ... (remaining 115718 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = (chain 'E' and (resid 3 through 351 or resid 402 through 501))
}

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 group one per residue
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:             1.390
  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:             0.030
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     33.390
  Find NCS groups from input model:        0.540
  Set up NCS constraints:                  0.060
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
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   0.028  14525  Z= 0.289
  Angle     :  1.028  10.141  19730  Z= 0.718
  Chirality :  0.039   0.119   2290
  Planarity :  0.003   0.036   2490
  Dihedral  :  6.812  39.830   5395
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  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: -1.63 (0.18), residues: 1735
  helix: -0.43 (0.14), residues: 910
  sheet: -1.06 (0.32), residues: 240
  loop : -1.96 (0.24), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  61 
 HIS   0.001   0.000   HIS A  83 
 PHE   0.005   0.001   PHE A 345 
 TYR   0.007   0.001   TYR D 317 
 ARG   0.001   0.000   ARG C  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25335 (  880)
  hydrogen bonds       : angle       8.02725 ( 2565)
  covalent geometry    : bond        0.00377 (14525)
  covalent geometry    : angle       1.02768 (19730)

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

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

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 335
  time to evaluate  : 1.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 MET cc_start: 0.8092 (mtp) cc_final: 0.7527 (mtm)
REVERT: A   74 GLN cc_start: 0.8920 (tt0) cc_final: 0.8652 (tp-100)
REVERT: A  140 GLN cc_start: 0.8565 (mt0) cc_final: 0.8356 (mt0)
REVERT: A  152 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8752 (mt-10)
REVERT: A  209 GLN cc_start: 0.9136 (tt0) cc_final: 0.8909 (tm-30)
REVERT: A  288 ASN cc_start: 0.8986 (t0) cc_final: 0.8757 (t0)
REVERT: B   28 GLU cc_start: 0.7954 (tt0) cc_final: 0.7633 (tm-30)
REVERT: B   32 MET cc_start: 0.8429 (mtp) cc_final: 0.7998 (mtt)
REVERT: B   74 GLN cc_start: 0.9130 (tt0) cc_final: 0.8741 (tp-100)
REVERT: B  138 MET cc_start: 0.8479 (ttp) cc_final: 0.8007 (tmm)
REVERT: B  140 GLN cc_start: 0.8738 (mt0) cc_final: 0.8530 (mt0)
REVERT: B  152 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8755 (mt-10)
REVERT: B  213 GLN cc_start: 0.9103 (mm-40) cc_final: 0.8648 (tp40)
REVERT: C   32 MET cc_start: 0.8150 (mtp) cc_final: 0.7678 (mtt)
REVERT: C   74 GLN cc_start: 0.9003 (tt0) cc_final: 0.8561 (tp-100)
REVERT: D   32 MET cc_start: 0.8199 (mtp) cc_final: 0.7330 (mtm)
REVERT: D   61 TRP cc_start: 0.8533 (t60) cc_final: 0.8278 (t60)
REVERT: D   74 GLN cc_start: 0.9032 (tt0) cc_final: 0.8549 (tp-100)
REVERT: D  112 MET cc_start: 0.8932 (mtm) cc_final: 0.8599 (mtt)
REVERT: D  209 GLN cc_start: 0.9249 (tt0) cc_final: 0.9044 (tm-30)
REVERT: D  213 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8537 (tp40)
REVERT: D  217 ASN cc_start: 0.8839 (m-40) cc_final: 0.8573 (m110)
REVERT: D  296 ILE cc_start: 0.7743 (pt) cc_final: 0.7499 (pt)
REVERT: E   32 MET cc_start: 0.7933 (mtp) cc_final: 0.7266 (mtt)
REVERT: E   61 TRP cc_start: 0.8523 (t60) cc_final: 0.8143 (t60)
REVERT: E   74 GLN cc_start: 0.8885 (tt0) cc_final: 0.8505 (tp-100)
REVERT: E  152 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8655 (mt-10)
REVERT: E  209 GLN cc_start: 0.9252 (tt0) cc_final: 0.8987 (tm-30)
REVERT: E  213 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8635 (tp40)
REVERT: E  277 ASP cc_start: 0.9019 (m-30) cc_final: 0.8755 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 335
  average time/residue: 0.2946
  time to fit residues: 142.8467
Evaluate side-chains
  164 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 2.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 143 optimal weight:    2.9990
   chunk 128 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   chunk 44 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 68 optimal weight:   20.0000
   chunk 133 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 99 optimal weight:    5.9990
   chunk 154 optimal weight:    5.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  94 HIS
A 140 GLN
A 314 ASN
B  94 HIS
B  95 GLN
B 140 GLN
B 260 GLN
B 314 ASN
C  95 GLN
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 140 GLN
C 314 ASN
D  94 HIS
D 126 GLN
D 314 ASN
** E  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  94 HIS
E  95 GLN
E 140 GLN
E 314 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.071584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.059232 restraints weight = 45686.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.061432 restraints weight = 25831.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.062949 restraints weight = 17474.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14525  Z= 0.198
  Angle     :  0.679   7.511  19730  Z= 0.357
  Chirality :  0.043   0.185   2290
  Planarity :  0.004   0.047   2490
  Dihedral  :  4.084  14.334   1925
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  6.82 %
    Favored  : 91.02 %
  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:  0.36 (0.20), residues: 1735
  helix:  1.67 (0.17), residues: 940
  sheet: -0.85 (0.28), residues: 285
  loop : -1.83 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  61 
 HIS   0.005   0.001   HIS D  83 
 PHE   0.014   0.002   PHE D 306 
 TYR   0.016   0.002   TYR A 327 
 ARG   0.007   0.001   ARG C 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05776 (  880)
  hydrogen bonds       : angle       5.26326 ( 2565)
  covalent geometry    : bond        0.00442 (14525)
  covalent geometry    : angle       0.67901 (19730)

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

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

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 189
  time to evaluate  : 1.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLN cc_start: 0.8913 (tt0) cc_final: 0.8614 (tp-100)
REVERT: A  138 MET cc_start: 0.8077 (tmm) cc_final: 0.6699 (tmm)
REVERT: B   74 GLN cc_start: 0.8949 (tt0) cc_final: 0.8691 (tp-100)
REVERT: B  134 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8057 (m-40)
REVERT: B  138 MET cc_start: 0.8171 (ttp) cc_final: 0.7628 (tmm)
REVERT: B  140 GLN cc_start: 0.8587 (mt0) cc_final: 0.8225 (mt0)
REVERT: B  291 MET cc_start: 0.9080 (tpp) cc_final: 0.8804 (mmp)
REVERT: B  296 ILE cc_start: 0.9195 (pt) cc_final: 0.8929 (mt)
REVERT: C   74 GLN cc_start: 0.8945 (tt0) cc_final: 0.8373 (tp-100)
REVERT: C  138 MET cc_start: 0.8047 (ttp) cc_final: 0.7729 (tmm)
REVERT: C  296 ILE cc_start: 0.9202 (pt) cc_final: 0.8935 (mt)
REVERT: D   32 MET cc_start: 0.7833 (mtp) cc_final: 0.7541 (mtm)
REVERT: D   74 GLN cc_start: 0.8879 (tt0) cc_final: 0.8489 (tp-100)
REVERT: D  112 MET cc_start: 0.8336 (mtm) cc_final: 0.7986 (mtp)
REVERT: D  173 LEU cc_start: 0.9438 (mt) cc_final: 0.9104 (mp)
REVERT: D  213 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8501 (tp40)
REVERT: D  296 ILE cc_start: 0.9081 (pt) cc_final: 0.8711 (mt)
REVERT: E   32 MET cc_start: 0.7727 (mtp) cc_final: 0.7318 (mtt)
REVERT: E   61 TRP cc_start: 0.8783 (t60) cc_final: 0.8416 (t60)
REVERT: E   74 GLN cc_start: 0.8915 (tt0) cc_final: 0.8678 (tp-100)
  outliers start: 34
  outliers final: 24
  residues processed: 210
  average time/residue: 0.1902
  time to fit residues: 65.9215
Evaluate side-chains
  163 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 138
  time to evaluate  : 1.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  135 CYS
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue  135 CYS
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  334 MET
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue  135 CYS
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  331 LEU
Chi-restraints excluded: chain D residue  343 VAL
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  135 CYS
Chi-restraints excluded: chain E residue  343 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 139 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0970
   chunk 72 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 136 optimal weight:   20.0000
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 314 ASN
** B  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 314 ASN
C  95 GLN
C 126 GLN
C 314 ASN
D 314 ASN
** E  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 126 GLN
E 213 GLN
E 314 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.071637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.059187 restraints weight = 46059.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.061371 restraints weight = 26082.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.062918 restraints weight = 17666.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14525  Z= 0.148
  Angle     :  0.610   7.463  19730  Z= 0.316
  Chirality :  0.042   0.142   2290
  Planarity :  0.004   0.049   2490
  Dihedral  :  3.977  14.557   1925
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  8.79 %
    Favored  : 89.04 %
  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:  0.90 (0.21), residues: 1735
  helix:  2.12 (0.17), residues: 940
  sheet: -0.50 (0.29), residues: 285
  loop : -1.69 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  61 
 HIS   0.002   0.001   HIS C 120 
 PHE   0.021   0.001   PHE D 306 
 TYR   0.017   0.001   TYR A 327 
 ARG   0.004   0.000   ARG C 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04808 (  880)
  hydrogen bonds       : angle       4.88734 ( 2565)
  covalent geometry    : bond        0.00322 (14525)
  covalent geometry    : angle       0.61018 (19730)

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

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

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 145
  time to evaluate  : 1.926 
Fit side-chains
REVERT: A  138 MET cc_start: 0.7966 (tmm) cc_final: 0.6677 (tmm)
REVERT: A  300 ILE cc_start: 0.9207 (pt) cc_final: 0.8999 (pt)
REVERT: B   74 GLN cc_start: 0.8948 (tt0) cc_final: 0.8687 (tp-100)
REVERT: B  134 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8058 (m-40)
REVERT: B  138 MET cc_start: 0.8097 (ttp) cc_final: 0.7623 (tmm)
REVERT: B  140 GLN cc_start: 0.8529 (mt0) cc_final: 0.8128 (mt0)
REVERT: B  295 THR cc_start: 0.9525 (t) cc_final: 0.9306 (t)
REVERT: B  296 ILE cc_start: 0.9233 (pt) cc_final: 0.8957 (mt)
REVERT: C   74 GLN cc_start: 0.8964 (tt0) cc_final: 0.8526 (tp-100)
REVERT: D   32 MET cc_start: 0.7868 (mtp) cc_final: 0.7512 (mtm)
REVERT: D   74 GLN cc_start: 0.8831 (tt0) cc_final: 0.8432 (tp-100)
REVERT: D  112 MET cc_start: 0.8335 (mtm) cc_final: 0.8091 (mtt)
REVERT: E   61 TRP cc_start: 0.8799 (t60) cc_final: 0.8561 (t60)
REVERT: E   74 GLN cc_start: 0.8910 (tt0) cc_final: 0.8643 (tp-100)
REVERT: E  138 MET cc_start: 0.8116 (ttp) cc_final: 0.6401 (tmm)
  outliers start: 34
  outliers final: 18
  residues processed: 168
  average time/residue: 0.2033
  time to fit residues: 58.6691
Evaluate side-chains
  136 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 1.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   95 GLN
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  334 MET
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  299 THR
Chi-restraints excluded: chain D residue  331 LEU
Chi-restraints excluded: chain D residue  343 VAL
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain E residue  299 THR
Chi-restraints excluded: chain E residue  334 MET
Chi-restraints excluded: chain E residue  343 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 125 optimal weight:    0.0770
   chunk 128 optimal weight:    1.9990
   chunk 38 optimal weight:    0.1980
   chunk 96 optimal weight:    0.8980
   chunk 130 optimal weight:    0.7980
   chunk 156 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 59 optimal weight:    1.9990
   chunk 145 optimal weight:    6.9990
   chunk 101 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.7940

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

Flipped N/Q/H residues before XYZ refinement:
A 314 ASN
** B  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 260 GLN
B 314 ASN
** C  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  95 GLN
C 213 GLN
C 314 ASN
** D  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 314 ASN
E 314 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.071678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.059410 restraints weight = 46009.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.061609 restraints weight = 25440.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.063180 restraints weight = 17069.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  14525  Z= 0.133
  Angle     :  0.594   7.573  19730  Z= 0.305
  Chirality :  0.042   0.163   2290
  Planarity :  0.004   0.047   2490
  Dihedral  :  3.868  14.774   1925
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 10.45 %
    Favored  : 87.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.18 (0.21), residues: 1735
  helix:  2.30 (0.17), residues: 935
  sheet: -0.16 (0.30), residues: 270
  loop : -1.54 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  61 
 HIS   0.003   0.000   HIS C  94 
 PHE   0.016   0.001   PHE B 306 
 TYR   0.016   0.001   TYR A 327 
 ARG   0.004   0.000   ARG C  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04322 (  880)
  hydrogen bonds       : angle       4.53102 ( 2565)
  covalent geometry    : bond        0.00285 (14525)
  covalent geometry    : angle       0.59425 (19730)

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

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

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 131
  time to evaluate  : 1.682 
Fit side-chains
REVERT: A  138 MET cc_start: 0.7815 (tmm) cc_final: 0.6418 (tmm)
REVERT: A  300 ILE cc_start: 0.9239 (pt) cc_final: 0.9036 (pt)
REVERT: B   74 GLN cc_start: 0.8986 (tt0) cc_final: 0.8664 (tp-100)
REVERT: B  134 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8113 (m-40)
REVERT: B  138 MET cc_start: 0.8126 (ttp) cc_final: 0.7586 (tmm)
REVERT: B  140 GLN cc_start: 0.8589 (mt0) cc_final: 0.8166 (mt0)
REVERT: B  295 THR cc_start: 0.9541 (t) cc_final: 0.9294 (t)
REVERT: B  296 ILE cc_start: 0.9255 (pt) cc_final: 0.8992 (mt)
REVERT: C   74 GLN cc_start: 0.9051 (tt0) cc_final: 0.8547 (tp-100)
REVERT: D   32 MET cc_start: 0.7959 (mtp) cc_final: 0.7570 (mtm)
REVERT: D   74 GLN cc_start: 0.8967 (tt0) cc_final: 0.8512 (tp-100)
REVERT: D  112 MET cc_start: 0.8419 (mtm) cc_final: 0.8173 (mtt)
REVERT: D  295 THR cc_start: 0.9509 (t) cc_final: 0.9274 (t)
REVERT: E   74 GLN cc_start: 0.9001 (tt0) cc_final: 0.8699 (tp-100)
REVERT: E  209 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8573 (tm-30)
REVERT: E  300 ILE cc_start: 0.9273 (pt) cc_final: 0.9056 (pt)
  outliers start: 28
  outliers final: 16
  residues processed: 151
  average time/residue: 0.1876
  time to fit residues: 47.9715
Evaluate side-chains
  132 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 1.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  135 CYS
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain B residue  135 CYS
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  334 MET
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue  299 THR
Chi-restraints excluded: chain D residue  331 LEU
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  334 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 98 optimal weight:    4.9990
   chunk 156 optimal weight:    0.8980
   chunk 133 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   chunk 153 optimal weight:    0.9980
   chunk 164 optimal weight:    3.9990
   chunk 132 optimal weight:    0.9980
   chunk 63 optimal weight:    5.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
A  74 GLN
A 314 ASN
** B  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 314 ASN
C  83 HIS
C  95 GLN
C 314 ASN
** D  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 314 ASN
E 314 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.071302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.058668 restraints weight = 46273.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.060850 restraints weight = 26409.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.062397 restraints weight = 17898.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.3330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  14525  Z= 0.140
  Angle     :  0.600   7.736  19730  Z= 0.304
  Chirality :  0.042   0.184   2290
  Planarity :  0.004   0.046   2490
  Dihedral  :  3.832  15.444   1925
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 10.00 %
    Favored  : 87.07 %
  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:  1.33 (0.21), residues: 1735
  helix:  2.36 (0.17), residues: 940
  sheet: -0.01 (0.30), residues: 280
  loop : -1.47 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  61 
 HIS   0.002   0.000   HIS C  83 
 PHE   0.021   0.001   PHE B 306 
 TYR   0.015   0.001   TYR A 327 
 ARG   0.002   0.000   ARG D 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04158 (  880)
  hydrogen bonds       : angle       4.22414 ( 2565)
  covalent geometry    : bond        0.00309 (14525)
  covalent geometry    : angle       0.60049 (19730)

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

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

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 131
  time to evaluate  : 1.769 
Fit side-chains
REVERT: A   61 TRP cc_start: 0.8864 (t60) cc_final: 0.8396 (t60)
REVERT: A  134 ASN cc_start: 0.8744 (m-40) cc_final: 0.8497 (m-40)
REVERT: A  138 MET cc_start: 0.7790 (tmm) cc_final: 0.6543 (tmm)
REVERT: B   74 GLN cc_start: 0.8921 (tt0) cc_final: 0.8613 (tp-100)
REVERT: B  134 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8125 (m-40)
REVERT: B  138 MET cc_start: 0.8074 (ttp) cc_final: 0.7637 (tmm)
REVERT: B  140 GLN cc_start: 0.8568 (mt0) cc_final: 0.8170 (mt0)
REVERT: B  296 ILE cc_start: 0.9242 (pt) cc_final: 0.8967 (mt)
REVERT: B  304 LEU cc_start: 0.8958 (mp) cc_final: 0.8687 (mp)
REVERT: C   32 MET cc_start: 0.7244 (mtt) cc_final: 0.6873 (mtt)
REVERT: C   74 GLN cc_start: 0.9002 (tt0) cc_final: 0.8593 (tp-100)
REVERT: C  138 MET cc_start: 0.8140 (tmm) cc_final: 0.7573 (tmm)
REVERT: D   32 MET cc_start: 0.7916 (mtp) cc_final: 0.7561 (mtm)
REVERT: D   74 GLN cc_start: 0.8914 (tt0) cc_final: 0.8525 (tp-100)
REVERT: D  112 MET cc_start: 0.8358 (mtm) cc_final: 0.8132 (mtt)
REVERT: D  295 THR cc_start: 0.9458 (OUTLIER) cc_final: 0.9224 (t)
REVERT: E   74 GLN cc_start: 0.8957 (tt0) cc_final: 0.8744 (tp-100)
REVERT: E  138 MET cc_start: 0.8052 (ttp) cc_final: 0.6599 (tmm)
REVERT: E  291 MET cc_start: 0.9075 (mmm) cc_final: 0.8572 (mmt)
  outliers start: 46
  outliers final: 30
  residues processed: 163
  average time/residue: 0.1806
  time to fit residues: 50.0569
Evaluate side-chains
  150 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 118
  time to evaluate  : 1.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  135 CYS
Chi-restraints excluded: chain A residue  225 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain B residue  135 CYS
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  334 MET
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  135 CYS
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  265 VAL
Chi-restraints excluded: chain D residue  295 THR
Chi-restraints excluded: chain D residue  299 THR
Chi-restraints excluded: chain D residue  331 LEU
Chi-restraints excluded: chain D residue  334 MET
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  299 THR
Chi-restraints excluded: chain E residue  334 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 105 optimal weight:    6.9990
   chunk 168 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 141 optimal weight:    0.0980
   chunk 11 optimal weight:    1.9990
   chunk 137 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0040
   chunk 42 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.7994

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

Flipped N/Q/H residues before XYZ refinement:
A 314 ASN
** B  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 314 ASN
C  95 GLN
C 314 ASN
** D  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 314 ASN
E  83 HIS
E 314 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.071774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.059122 restraints weight = 46410.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.061307 restraints weight = 26384.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.062878 restraints weight = 17914.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.3498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14525  Z= 0.126
  Angle     :  0.598  10.100  19730  Z= 0.300
  Chirality :  0.041   0.177   2290
  Planarity :  0.003   0.046   2490
  Dihedral  :  3.761  15.380   1925
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 11.46 %
    Favored  : 86.31 %
  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:  1.56 (0.21), residues: 1735
  helix:  2.46 (0.17), residues: 950
  sheet:  0.29 (0.31), residues: 270
  loop : -1.35 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  61 
 HIS   0.003   0.000   HIS C  83 
 PHE   0.017   0.001   PHE B 306 
 TYR   0.015   0.001   TYR A 327 
 ARG   0.002   0.000   ARG D 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03979 (  880)
  hydrogen bonds       : angle       4.08082 ( 2565)
  covalent geometry    : bond        0.00271 (14525)
  covalent geometry    : angle       0.59772 (19730)

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

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

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 132
  time to evaluate  : 1.668 
Fit side-chains
REVERT: A  134 ASN cc_start: 0.8732 (m-40) cc_final: 0.8520 (m-40)
REVERT: A  138 MET cc_start: 0.7712 (tmm) cc_final: 0.6475 (tmm)
REVERT: B   74 GLN cc_start: 0.8916 (tt0) cc_final: 0.8613 (tp-100)
REVERT: B  134 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8115 (m-40)
REVERT: B  138 MET cc_start: 0.8031 (ttp) cc_final: 0.7313 (tmm)
REVERT: C   74 GLN cc_start: 0.8984 (tt0) cc_final: 0.8620 (tp-100)
REVERT: C  138 MET cc_start: 0.8172 (tmm) cc_final: 0.7525 (tmm)
REVERT: D   32 MET cc_start: 0.7910 (mtp) cc_final: 0.7558 (mtm)
REVERT: D   74 GLN cc_start: 0.8917 (tt0) cc_final: 0.8524 (tp-100)
REVERT: D  112 MET cc_start: 0.8329 (mtm) cc_final: 0.8125 (mtt)
REVERT: E   74 GLN cc_start: 0.8961 (tt0) cc_final: 0.8742 (tp-100)
REVERT: E  209 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8582 (tm-30)
  outliers start: 35
  outliers final: 24
  residues processed: 158
  average time/residue: 0.1797
  time to fit residues: 48.7488
Evaluate side-chains
  144 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 1.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain B residue  135 CYS
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  295 THR
Chi-restraints excluded: chain D residue  299 THR
Chi-restraints excluded: chain D residue  331 LEU
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  299 THR
Chi-restraints excluded: chain E residue  334 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 159 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   chunk 122 optimal weight:    3.9990
   chunk 164 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 114 optimal weight:    7.9990
   chunk 152 optimal weight:    6.9990
   chunk 2 optimal weight:    7.9990
   chunk 137 optimal weight:    4.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 314 ASN
** B  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 314 ASN
** C  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 314 ASN
** D  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 314 ASN
E 314 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.068648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.055968 restraints weight = 47276.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.058050 restraints weight = 27133.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.059507 restraints weight = 18610.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  14525  Z= 0.243
  Angle     :  0.677   7.831  19730  Z= 0.340
  Chirality :  0.044   0.182   2290
  Planarity :  0.004   0.050   2490
  Dihedral  :  3.959  17.601   1925
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 11.72 %
    Favored  : 85.41 %
  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:  1.51 (0.21), residues: 1735
  helix:  2.40 (0.17), residues: 950
  sheet:  0.03 (0.32), residues: 265
  loop : -1.17 (0.28), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E  61 
 HIS   0.003   0.001   HIS B  83 
 PHE   0.019   0.002   PHE B 306 
 TYR   0.013   0.002   TYR E 168 
 ARG   0.002   0.000   ARG C 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04374 (  880)
  hydrogen bonds       : angle       4.33018 ( 2565)
  covalent geometry    : bond        0.00552 (14525)
  covalent geometry    : angle       0.67724 (19730)

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

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

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 117
  time to evaluate  : 2.161 
Fit side-chains
REVERT: A   61 TRP cc_start: 0.8981 (t60) cc_final: 0.8663 (t60)
REVERT: A  112 MET cc_start: 0.8342 (mtm) cc_final: 0.8119 (mtt)
REVERT: A  138 MET cc_start: 0.8066 (tmm) cc_final: 0.6746 (tmm)
REVERT: A  291 MET cc_start: 0.9183 (mmp) cc_final: 0.8463 (mmp)
REVERT: B   74 GLN cc_start: 0.8924 (tt0) cc_final: 0.8651 (tp-100)
REVERT: B  138 MET cc_start: 0.8212 (ttp) cc_final: 0.7838 (tmm)
REVERT: C   74 GLN cc_start: 0.9017 (tt0) cc_final: 0.8666 (tp-100)
REVERT: C  138 MET cc_start: 0.8375 (tmm) cc_final: 0.8075 (tmm)
REVERT: C  291 MET cc_start: 0.9159 (tpp) cc_final: 0.8704 (mmp)
REVERT: D   32 MET cc_start: 0.8051 (mtp) cc_final: 0.7658 (mtm)
REVERT: D   74 GLN cc_start: 0.8941 (tt0) cc_final: 0.8638 (tp-100)
REVERT: D  112 MET cc_start: 0.8364 (mtm) cc_final: 0.8150 (mtt)
REVERT: E  291 MET cc_start: 0.8882 (mmt) cc_final: 0.8348 (mmt)
  outliers start: 45
  outliers final: 32
  residues processed: 149
  average time/residue: 0.2147
  time to fit residues: 55.1893
Evaluate side-chains
  146 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 1.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  135 CYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain B residue  135 CYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  334 MET
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  104 ASN
Chi-restraints excluded: chain D residue  129 LEU
Chi-restraints excluded: chain D residue  135 CYS
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  295 THR
Chi-restraints excluded: chain D residue  299 THR
Chi-restraints excluded: chain D residue  331 LEU
Chi-restraints excluded: chain D residue  334 MET
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  247 THR
Chi-restraints excluded: chain E residue  299 THR
Chi-restraints excluded: chain E residue  334 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 132 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 151 optimal weight:    3.9990
   chunk 156 optimal weight:    2.9990
   chunk 41 optimal weight:    7.9990
   chunk 120 optimal weight:    3.9990
   chunk 148 optimal weight:    8.9990
   chunk 166 optimal weight:    0.8980
   chunk 131 optimal weight:    0.7980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
A 314 ASN
B 314 ASN
C  83 HIS
C  95 GLN
C 314 ASN
** D  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 314 ASN
E 314 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.069868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.057214 restraints weight = 46458.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.059332 restraints weight = 26696.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.060836 restraints weight = 18180.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.3811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  14525  Z= 0.155
  Angle     :  0.620   8.927  19730  Z= 0.312
  Chirality :  0.043   0.208   2290
  Planarity :  0.004   0.048   2490
  Dihedral  :  3.910  17.808   1925
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 12.61 %
    Favored  : 85.29 %
  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:  1.61 (0.21), residues: 1735
  helix:  2.48 (0.17), residues: 945
  sheet:  0.18 (0.32), residues: 265
  loop : -1.17 (0.28), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  61 
 HIS   0.002   0.001   HIS D 120 
 PHE   0.022   0.001   PHE B 306 
 TYR   0.017   0.001   TYR C 327 
 ARG   0.002   0.000   ARG E  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04082 (  880)
  hydrogen bonds       : angle       4.17449 ( 2565)
  covalent geometry    : bond        0.00355 (14525)
  covalent geometry    : angle       0.62003 (19730)

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

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

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 118
  time to evaluate  : 1.698 
Fit side-chains
REVERT: A  138 MET cc_start: 0.7973 (tmm) cc_final: 0.6637 (tmm)
REVERT: A  291 MET cc_start: 0.9239 (mmp) cc_final: 0.8674 (mmm)
REVERT: B   74 GLN cc_start: 0.8911 (tt0) cc_final: 0.8628 (tp-100)
REVERT: B  134 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.8136 (m-40)
REVERT: B  138 MET cc_start: 0.8081 (ttp) cc_final: 0.7784 (tmm)
REVERT: B  334 MET cc_start: 0.8155 (ppp) cc_final: 0.7946 (ppp)
REVERT: C   74 GLN cc_start: 0.8994 (tt0) cc_final: 0.8663 (tp-100)
REVERT: C  138 MET cc_start: 0.8283 (tmm) cc_final: 0.7964 (tmm)
REVERT: D   32 MET cc_start: 0.7951 (mtp) cc_final: 0.7590 (mtm)
REVERT: D   74 GLN cc_start: 0.8924 (tt0) cc_final: 0.8634 (tp-100)
REVERT: E  291 MET cc_start: 0.8579 (mmt) cc_final: 0.8321 (mmt)
  outliers start: 33
  outliers final: 27
  residues processed: 143
  average time/residue: 0.2390
  time to fit residues: 58.5455
Evaluate side-chains
  141 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 2.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  135 CYS
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain B residue  135 CYS
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  334 MET
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  129 LEU
Chi-restraints excluded: chain D residue  135 CYS
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  299 THR
Chi-restraints excluded: chain E residue  135 CYS
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  299 THR
Chi-restraints excluded: chain E residue  334 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 144 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0010
   chunk 156 optimal weight:    0.8980
   chunk 169 optimal weight:    6.9990
   chunk 92 optimal weight:    3.9990
   chunk 96 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 128 optimal weight:    2.9990
   chunk 68 optimal weight:   10.0000
   chunk 100 optimal weight:    6.9990
   overall best weight:    1.0788

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

Flipped N/Q/H residues before XYZ refinement:
A 314 ASN
B 314 ASN
C  83 HIS
C  95 GLN
C 314 ASN
** D  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 314 ASN
E 314 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.070451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.057845 restraints weight = 46294.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.059958 restraints weight = 26469.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.061486 restraints weight = 18103.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.3871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  14525  Z= 0.141
  Angle     :  0.619   8.596  19730  Z= 0.312
  Chirality :  0.043   0.193   2290
  Planarity :  0.003   0.048   2490
  Dihedral  :  3.876  17.663   1925
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.74 %
    Favored  : 85.29 %
  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:  1.63 (0.21), residues: 1735
  helix:  2.48 (0.17), residues: 945
  sheet:  0.43 (0.33), residues: 255
  loop : -1.24 (0.28), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  61 
 HIS   0.002   0.001   HIS D 257 
 PHE   0.027   0.001   PHE D 306 
 TYR   0.016   0.001   TYR C 327 
 ARG   0.002   0.000   ARG E 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04007 (  880)
  hydrogen bonds       : angle       4.11965 ( 2565)
  covalent geometry    : bond        0.00319 (14525)
  covalent geometry    : angle       0.61935 (19730)

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

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

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 120
  time to evaluate  : 1.817 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 MET cc_start: 0.7964 (tmm) cc_final: 0.6610 (tmm)
REVERT: B   74 GLN cc_start: 0.8929 (tt0) cc_final: 0.8643 (tp-100)
REVERT: B  134 ASN cc_start: 0.8583 (m110) cc_final: 0.8220 (m-40)
REVERT: B  138 MET cc_start: 0.8042 (ttp) cc_final: 0.7775 (tmm)
REVERT: C   74 GLN cc_start: 0.8988 (tt0) cc_final: 0.8656 (tp-100)
REVERT: C  138 MET cc_start: 0.8223 (tmm) cc_final: 0.7928 (tmm)
REVERT: D   32 MET cc_start: 0.7956 (mtp) cc_final: 0.7580 (mtm)
REVERT: D   74 GLN cc_start: 0.8912 (tt0) cc_final: 0.8614 (tp-100)
REVERT: D  126 GLN cc_start: 0.9064 (tt0) cc_final: 0.8849 (tt0)
REVERT: E  138 MET cc_start: 0.8202 (ttp) cc_final: 0.7612 (tmm)
REVERT: E  209 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8602 (tm-30)
  outliers start: 31
  outliers final: 29
  residues processed: 142
  average time/residue: 0.2280
  time to fit residues: 55.9306
Evaluate side-chains
  146 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 117
  time to evaluate  : 1.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  135 CYS
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  135 CYS
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  334 MET
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  129 LEU
Chi-restraints excluded: chain D residue  135 CYS
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  299 THR
Chi-restraints excluded: chain D residue  331 LEU
Chi-restraints excluded: chain D residue  334 MET
Chi-restraints excluded: chain E residue  135 CYS
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  299 THR
Chi-restraints excluded: chain E residue  334 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 163 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 155 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9990
   chunk 149 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 91 optimal weight:    0.3980
   chunk 126 optimal weight:    5.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 314 ASN
B 314 ASN
C  83 HIS
C 314 ASN
** D  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 314 ASN
** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 314 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.070360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.057834 restraints weight = 46155.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.059957 restraints weight = 26303.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.061461 restraints weight = 17977.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  14525  Z= 0.146
  Angle     :  0.624   8.403  19730  Z= 0.314
  Chirality :  0.043   0.188   2290
  Planarity :  0.003   0.048   2490
  Dihedral  :  3.866  17.733   1925
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.68 %
    Favored  : 85.35 %
  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:  1.62 (0.21), residues: 1735
  helix:  2.47 (0.17), residues: 945
  sheet:  0.48 (0.33), residues: 255
  loop : -1.26 (0.28), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  61 
 HIS   0.002   0.000   HIS D 120 
 PHE   0.023   0.001   PHE B 306 
 TYR   0.015   0.001   TYR C 327 
 ARG   0.002   0.000   ARG D 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03982 (  880)
  hydrogen bonds       : angle       4.10329 ( 2565)
  covalent geometry    : bond        0.00336 (14525)
  covalent geometry    : angle       0.62363 (19730)

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

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

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3470 Ramachandran restraints generated.
    1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 114
  time to evaluate  : 2.069 
Fit side-chains
REVERT: A  138 MET cc_start: 0.8026 (tmm) cc_final: 0.6712 (tmm)
REVERT: B   74 GLN cc_start: 0.8925 (tt0) cc_final: 0.8644 (tp-100)
REVERT: B  138 MET cc_start: 0.8059 (ttp) cc_final: 0.7762 (tmm)
REVERT: C   74 GLN cc_start: 0.8952 (tt0) cc_final: 0.8680 (tp-100)
REVERT: C  138 MET cc_start: 0.8204 (tmm) cc_final: 0.7904 (tmm)
REVERT: D   32 MET cc_start: 0.7962 (mtp) cc_final: 0.7590 (mtm)
REVERT: D   74 GLN cc_start: 0.8847 (tt0) cc_final: 0.8513 (tp-100)
REVERT: D  306 PHE cc_start: 0.8605 (t80) cc_final: 0.8372 (t80)
REVERT: E  138 MET cc_start: 0.8202 (ttp) cc_final: 0.7618 (tmm)
REVERT: E  209 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8601 (tm-30)
  outliers start: 31
  outliers final: 29
  residues processed: 137
  average time/residue: 0.2132
  time to fit residues: 51.0225
Evaluate side-chains
  142 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 113
  time to evaluate  : 1.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  135 CYS
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  135 CYS
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  334 MET
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  129 LEU
Chi-restraints excluded: chain D residue  135 CYS
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  299 THR
Chi-restraints excluded: chain D residue  331 LEU
Chi-restraints excluded: chain D residue  334 MET
Chi-restraints excluded: chain E residue  135 CYS
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  299 THR
Chi-restraints excluded: chain E residue  334 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 159 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 122 optimal weight:    6.9990
   chunk 88 optimal weight:    0.0020
   chunk 25 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 87 optimal weight:    4.9990
   chunk 153 optimal weight:    2.9990
   chunk 155 optimal weight:    5.9990
   chunk 135 optimal weight:    3.9990
   overall best weight:    0.6388

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

Flipped N/Q/H residues before XYZ refinement:
A 314 ASN
B 314 ASN
C  83 HIS
C 314 ASN
D  83 HIS
** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 314 ASN
** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 314 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.071228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.058680 restraints weight = 46712.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.060861 restraints weight = 26631.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.062407 restraints weight = 17967.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.3997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  14525  Z= 0.127
  Angle     :  0.627  13.173  19730  Z= 0.313
  Chirality :  0.042   0.188   2290
  Planarity :  0.003   0.047   2490
  Dihedral  :  3.824  17.356   1925
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.06 %
    Favored  : 85.29 %
  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:  1.65 (0.21), residues: 1735
  helix:  2.52 (0.17), residues: 940
  sheet:  0.73 (0.33), residues: 260
  loop : -1.42 (0.28), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  61 
 HIS   0.003   0.000   HIS B  83 
 PHE   0.022   0.001   PHE B 306 
 TYR   0.015   0.001   TYR C 327 
 ARG   0.002   0.000   ARG D 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03899 (  880)
  hydrogen bonds       : angle       4.02389 ( 2565)
  covalent geometry    : bond        0.00280 (14525)
  covalent geometry    : angle       0.62687 (19730)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4350.29 seconds
wall clock time: 80 minutes 7.43 seconds (4807.43 seconds total)