Starting phenix.real_space_refine
on Thu Sep 18 04:59:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/3jcf_6551/09_2025/3jcf_6551.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/3jcf_6551/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/3jcf_6551/09_2025/3jcf_6551.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/3jcf_6551/09_2025/3jcf_6551.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/3jcf_6551/09_2025/3jcf_6551.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/3jcf_6551/09_2025/3jcf_6551.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.67, per 1000 atoms: 0.26
  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: 1.21
  Conformation dependent library (CDL) restraints added in 553.0 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  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: 0.31
  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: 2.11

  Time building geometry restraints manager: 1.60 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 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:             1.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.720
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.100
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.63 (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
 ARG   0.001   0.000   ARG C  69 
 TYR   0.007   0.001   TYR D 317 
 PHE   0.005   0.001   PHE A 345 
 TRP   0.003   0.001   TRP A  61 
 HIS   0.001   0.000   HIS A  83 

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

*********************** 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  : 0.550 
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: 0.1225
  time to fit residues: 59.8617
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  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:   20.0000
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    0.0070
   chunk 149 optimal weight:    7.9990
   overall best weight:    1.3402

-------------------------------------------------------------------------------
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 = 0.3368 r_free = 0.3368 target = 0.072438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.060086 restraints weight = 45843.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.062328 restraints weight = 25789.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.063889 restraints weight = 17331.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.065021 restraints weight = 12993.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.065839 restraints weight = 10429.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  14525  Z= 0.171
  Angle     :  0.672   8.061  19730  Z= 0.353
  Chirality :  0.042   0.165   2290
  Planarity :  0.004   0.046   2490
  Dihedral  :  4.056  14.106   1925
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  6.37 %
    Favored  : 91.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.20), residues: 1735
  helix:  1.68 (0.17), residues: 940
  sheet: -0.74 (0.30), residues: 250
  loop : -1.67 (0.26), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 153 
 TYR   0.016   0.001   TYR A 327 
 PHE   0.014   0.001   PHE D 306 
 TRP   0.006   0.001   TRP A 226 
 HIS   0.002   0.001   HIS B  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (14525)
  covalent geometry    : angle       0.67157 (19730)
  hydrogen bonds       : bond        0.05647 (  880)
  hydrogen bonds       : angle       5.25930 ( 2565)

*********************** 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
  225 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 191
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLN cc_start: 0.8832 (tt0) cc_final: 0.8630 (tp-100)
REVERT: A  138 MET cc_start: 0.8020 (tmm) cc_final: 0.6614 (tmm)
REVERT: B   74 GLN cc_start: 0.8883 (tt0) cc_final: 0.8620 (tp-100)
REVERT: B  100 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7640 (mm-30)
REVERT: B  134 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.7964 (m-40)
REVERT: B  138 MET cc_start: 0.8208 (ttp) cc_final: 0.7542 (tmm)
REVERT: B  140 GLN cc_start: 0.8548 (mt0) cc_final: 0.8162 (mt0)
REVERT: B  291 MET cc_start: 0.9058 (tpp) cc_final: 0.8787 (mmp)
REVERT: B  296 ILE cc_start: 0.9205 (pt) cc_final: 0.8960 (mt)
REVERT: C   74 GLN cc_start: 0.8855 (tt0) cc_final: 0.8337 (tp-100)
REVERT: C  138 MET cc_start: 0.8087 (ttp) cc_final: 0.7661 (tmm)
REVERT: C  296 ILE cc_start: 0.9204 (pt) cc_final: 0.8958 (mt)
REVERT: D   32 MET cc_start: 0.7820 (mtp) cc_final: 0.7533 (mtt)
REVERT: D   74 GLN cc_start: 0.8787 (tt0) cc_final: 0.8430 (tp-100)
REVERT: D   91 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8864 (mt)
REVERT: D  112 MET cc_start: 0.8326 (mtm) cc_final: 0.7995 (mtp)
REVERT: D  173 LEU cc_start: 0.9456 (mt) cc_final: 0.9138 (mp)
REVERT: D  213 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8481 (tp40)
REVERT: D  296 ILE cc_start: 0.9077 (pt) cc_final: 0.8770 (mt)
REVERT: E   32 MET cc_start: 0.7726 (mtp) cc_final: 0.7275 (mtt)
REVERT: E   61 TRP cc_start: 0.8781 (t60) cc_final: 0.8400 (t60)
  outliers start: 34
  outliers final: 23
  residues processed: 212
  average time/residue: 0.0915
  time to fit residues: 32.0275
Evaluate side-chains
  168 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 142
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
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  100 GLU
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   91 LEU
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  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 96 optimal weight:    2.9990
   chunk 107 optimal weight:    0.6980
   chunk 100 optimal weight:    6.9990
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.9980
   chunk 111 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 115 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 68 optimal weight:   20.0000
   chunk 41 optimal weight:    7.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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  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: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.071348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.058868 restraints weight = 46472.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.061051 restraints weight = 26298.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.062593 restraints weight = 17795.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.063695 restraints weight = 13403.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.064503 restraints weight = 10828.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.2814

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= 0.162
  Angle     :  0.615   7.487  19730  Z= 0.317
  Chirality :  0.042   0.140   2290
  Planarity :  0.004   0.049   2490
  Dihedral  :  3.972  14.730   1925
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  8.60 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.21), residues: 1735
  helix:  2.14 (0.17), residues: 940
  sheet: -0.47 (0.29), residues: 285
  loop : -1.69 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 202 
 TYR   0.016   0.001   TYR A 327 
 PHE   0.020   0.001   PHE D 306 
 TRP   0.008   0.001   TRP D  61 
 HIS   0.003   0.001   HIS E  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (14525)
  covalent geometry    : angle       0.61547 (19730)
  hydrogen bonds       : bond        0.04812 (  880)
  hydrogen bonds       : angle       4.91936 ( 2565)

*********************** 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
  184 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 147
  time to evaluate  : 0.535 
Fit side-chains
REVERT: A  138 MET cc_start: 0.7962 (tmm) cc_final: 0.6620 (tmm)
REVERT: A  300 ILE cc_start: 0.9237 (pt) cc_final: 0.9028 (pt)
REVERT: B   74 GLN cc_start: 0.8878 (tt0) cc_final: 0.8666 (tp-100)
REVERT: B  134 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8039 (m-40)
REVERT: B  138 MET cc_start: 0.8188 (ttp) cc_final: 0.7159 (tmm)
REVERT: B  296 ILE cc_start: 0.9224 (pt) cc_final: 0.8970 (mt)
REVERT: C   74 GLN cc_start: 0.8887 (tt0) cc_final: 0.8353 (tp-100)
REVERT: C  138 MET cc_start: 0.8034 (ttp) cc_final: 0.7674 (tmm)
REVERT: D   32 MET cc_start: 0.7902 (mtp) cc_final: 0.7551 (mtm)
REVERT: D   74 GLN cc_start: 0.8764 (tt0) cc_final: 0.8401 (tp-100)
REVERT: D   91 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.8919 (mt)
REVERT: D  112 MET cc_start: 0.8337 (mtm) cc_final: 0.8112 (mtt)
REVERT: D  295 THR cc_start: 0.9529 (t) cc_final: 0.9312 (t)
REVERT: D  296 ILE cc_start: 0.9150 (pt) cc_final: 0.8859 (mt)
REVERT: E   61 TRP cc_start: 0.8816 (t60) cc_final: 0.8593 (t60)
REVERT: E  138 MET cc_start: 0.8213 (ttp) cc_final: 0.6315 (tmm)
REVERT: E  291 MET cc_start: 0.8823 (mmt) cc_final: 0.8599 (mmm)
  outliers start: 37
  outliers final: 19
  residues processed: 174
  average time/residue: 0.0855
  time to fit residues: 25.4754
Evaluate side-chains
  138 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
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  343 VAL
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain C residue   47 VAL
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   91 LEU
Chi-restraints excluded: chain D residue  135 CYS
Chi-restraints excluded: chain D residue  137 LEU
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  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 68 optimal weight:   20.0000
   chunk 45 optimal weight:    7.9990
   chunk 148 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   chunk 117 optimal weight:    5.9990
   chunk 70 optimal weight:    5.9990
   chunk 155 optimal weight:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0980
   chunk 121 optimal weight:    2.9990
   chunk 129 optimal weight:    0.9980
   overall best weight:    2.8186

-------------------------------------------------------------------------------
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  83 HIS
** 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 = 0.3294 r_free = 0.3294 target = 0.069159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.056626 restraints weight = 47015.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.058707 restraints weight = 26937.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.060179 restraints weight = 18370.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.061256 restraints weight = 13973.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.062024 restraints weight = 11370.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  14525  Z= 0.236
  Angle     :  0.664   7.450  19730  Z= 0.340
  Chirality :  0.044   0.164   2290
  Planarity :  0.004   0.050   2490
  Dihedral  :  4.070  16.368   1925
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  :  9.62 %
    Favored  : 87.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.21), residues: 1735
  helix:  2.18 (0.17), residues: 940
  sheet: -0.48 (0.30), residues: 285
  loop : -1.62 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 252 
 TYR   0.016   0.002   TYR A 327 
 PHE   0.017   0.002   PHE D 306 
 TRP   0.008   0.001   TRP E  61 
 HIS   0.006   0.001   HIS E  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 (14525)
  covalent geometry    : angle       0.66381 (19730)
  hydrogen bonds       : bond        0.04645 (  880)
  hydrogen bonds       : angle       4.66376 ( 2565)

*********************** 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
  171 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 124
  time to evaluate  : 0.622 
Fit side-chains
REVERT: A   61 TRP cc_start: 0.9030 (t60) cc_final: 0.8566 (t60)
REVERT: A  112 MET cc_start: 0.8385 (mtm) cc_final: 0.8146 (mtt)
REVERT: A  138 MET cc_start: 0.8127 (tmm) cc_final: 0.6734 (tmm)
REVERT: A  300 ILE cc_start: 0.9265 (pt) cc_final: 0.9062 (pt)
REVERT: B   74 GLN cc_start: 0.8874 (tt0) cc_final: 0.8669 (tp-100)
REVERT: B  134 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8124 (m-40)
REVERT: B  138 MET cc_start: 0.8296 (ttp) cc_final: 0.7800 (tmm)
REVERT: B  296 ILE cc_start: 0.9222 (pt) cc_final: 0.8902 (mt)
REVERT: C   74 GLN cc_start: 0.8933 (tt0) cc_final: 0.8393 (tp-100)
REVERT: C  138 MET cc_start: 0.8118 (ttp) cc_final: 0.7704 (tmm)
REVERT: D   32 MET cc_start: 0.8032 (mtp) cc_final: 0.7717 (mtm)
REVERT: D   74 GLN cc_start: 0.8836 (tt0) cc_final: 0.8496 (tp-100)
REVERT: D  296 ILE cc_start: 0.9234 (pt) cc_final: 0.8895 (mt)
REVERT: E  138 MET cc_start: 0.8274 (ttp) cc_final: 0.7628 (tmm)
  outliers start: 47
  outliers final: 26
  residues processed: 158
  average time/residue: 0.0857
  time to fit residues: 23.2149
Evaluate side-chains
  133 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
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  232 LEU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain B residue  231 VAL
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   95 GLN
Chi-restraints excluded: chain C residue  132 THR
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  137 LEU
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  247 THR
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  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 45 optimal weight:    0.0870
   chunk 55 optimal weight:    3.9990
   chunk 115 optimal weight:    2.9990
   chunk 144 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 145 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 117 optimal weight:    4.9990
   chunk 85 optimal weight:    0.8980
   chunk 133 optimal weight:    7.9990
   chunk 101 optimal weight:    7.9990
   overall best weight:    1.3962

-------------------------------------------------------------------------------
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  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.069743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.057477 restraints weight = 46746.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.059661 restraints weight = 25737.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.061197 restraints weight = 17147.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.062296 restraints weight = 12817.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.063113 restraints weight = 10284.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.3394

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= 0.153
  Angle     :  0.622   9.559  19730  Z= 0.314
  Chirality :  0.042   0.161   2290
  Planarity :  0.004   0.048   2490
  Dihedral  :  3.968  16.409   1925
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 10.57 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.21), residues: 1735
  helix:  2.30 (0.17), residues: 950
  sheet: -0.23 (0.30), residues: 280
  loop : -1.53 (0.27), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  96 
 TYR   0.016   0.001   TYR A 327 
 PHE   0.015   0.001   PHE B 306 
 TRP   0.007   0.001   TRP E  61 
 HIS   0.002   0.001   HIS C 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (14525)
  covalent geometry    : angle       0.62166 (19730)
  hydrogen bonds       : bond        0.04323 (  880)
  hydrogen bonds       : angle       4.37785 ( 2565)

*********************** 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
  169 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 126
  time to evaluate  : 0.602 
Fit side-chains
REVERT: A   61 TRP cc_start: 0.9018 (t60) cc_final: 0.8538 (t60)
REVERT: A  112 MET cc_start: 0.8417 (mtm) cc_final: 0.8211 (mtt)
REVERT: A  138 MET cc_start: 0.8076 (tmm) cc_final: 0.6699 (tmm)
REVERT: B   74 GLN cc_start: 0.8908 (tt0) cc_final: 0.8670 (tp-100)
REVERT: B  134 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8188 (m-40)
REVERT: B  138 MET cc_start: 0.8248 (ttp) cc_final: 0.7700 (tmm)
REVERT: C   74 GLN cc_start: 0.8996 (tt0) cc_final: 0.8555 (tp-100)
REVERT: C  138 MET cc_start: 0.8147 (ttp) cc_final: 0.7701 (tmm)
REVERT: D   32 MET cc_start: 0.8007 (mtp) cc_final: 0.7666 (mtm)
REVERT: D   74 GLN cc_start: 0.8903 (tt0) cc_final: 0.8506 (tp-100)
REVERT: D  295 THR cc_start: 0.9572 (OUTLIER) cc_final: 0.9369 (t)
REVERT: D  296 ILE cc_start: 0.9231 (pt) cc_final: 0.8777 (mt)
REVERT: E  138 MET cc_start: 0.8260 (ttp) cc_final: 0.7550 (tmm)
  outliers start: 43
  outliers final: 28
  residues processed: 158
  average time/residue: 0.0855
  time to fit residues: 23.2887
Evaluate side-chains
  144 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 114
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
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  343 VAL
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  134 ASN
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  135 CYS
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  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 D residue  343 VAL
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 123 optimal weight:    0.9990
   chunk 140 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9980
   chunk 130 optimal weight:    0.9980
   chunk 169 optimal weight:    2.9990
   chunk 143 optimal weight:    4.9990
   chunk 132 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9990
   chunk 134 optimal weight:    0.0040
   chunk 121 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    0.7996

-------------------------------------------------------------------------------
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  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 ** 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 = 0.3334 r_free = 0.3334 target = 0.071002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.058493 restraints weight = 46494.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.060634 restraints weight = 26224.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.062198 restraints weight = 17867.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.063312 restraints weight = 13457.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.064123 restraints weight = 10867.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14525  Z= 0.129
  Angle     :  0.615  13.341  19730  Z= 0.307
  Chirality :  0.042   0.189   2290
  Planarity :  0.003   0.046   2490
  Dihedral  :  3.836  16.242   1925
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 11.59 %
    Favored  : 86.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.21), residues: 1735
  helix:  2.33 (0.17), residues: 955
  sheet:  0.19 (0.31), residues: 270
  loop : -1.44 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 165 
 TYR   0.015   0.001   TYR A 327 
 PHE   0.014   0.001   PHE B 306 
 TRP   0.007   0.001   TRP E  61 
 HIS   0.004   0.001   HIS C  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (14525)
  covalent geometry    : angle       0.61454 (19730)
  hydrogen bonds       : bond        0.04085 (  880)
  hydrogen bonds       : angle       4.17043 ( 2565)

*********************** 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
  159 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 124
  time to evaluate  : 0.593 
Fit side-chains
REVERT: A  138 MET cc_start: 0.7989 (tmm) cc_final: 0.6631 (tmm)
REVERT: B  134 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8150 (m-40)
REVERT: B  138 MET cc_start: 0.8091 (ttp) cc_final: 0.7686 (tmm)
REVERT: B  295 THR cc_start: 0.9500 (t) cc_final: 0.9268 (t)
REVERT: C   74 GLN cc_start: 0.8923 (tt0) cc_final: 0.8562 (tp-100)
REVERT: C  138 MET cc_start: 0.8097 (ttp) cc_final: 0.7729 (tmm)
REVERT: D   32 MET cc_start: 0.7937 (mtp) cc_final: 0.7602 (mtm)
REVERT: D   74 GLN cc_start: 0.8837 (tt0) cc_final: 0.8541 (tp-100)
REVERT: D  296 ILE cc_start: 0.9164 (pt) cc_final: 0.8857 (mt)
REVERT: E  138 MET cc_start: 0.8206 (ttp) cc_final: 0.6765 (tmm)
  outliers start: 35
  outliers final: 26
  residues processed: 151
  average time/residue: 0.0833
  time to fit residues: 21.7076
Evaluate side-chains
  147 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
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   60 THR
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  134 ASN
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  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 15 optimal weight:    6.9990
   chunk 155 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9990
   chunk 142 optimal weight:    1.9990
   chunk 152 optimal weight:    5.9990
   chunk 146 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 131 optimal weight:    3.9990
   chunk 3 optimal weight:    7.9990
   chunk 105 optimal weight:    6.9990
   overall best weight:    1.1986

-------------------------------------------------------------------------------
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  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 ** 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 = 0.3327 r_free = 0.3327 target = 0.070605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.058073 restraints weight = 46361.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.060254 restraints weight = 26124.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.061801 restraints weight = 17669.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.062907 restraints weight = 13312.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.063720 restraints weight = 10739.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.3675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  14525  Z= 0.140
  Angle     :  0.618  12.992  19730  Z= 0.307
  Chirality :  0.042   0.201   2290
  Planarity :  0.003   0.047   2490
  Dihedral  :  3.788  16.739   1925
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.17 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.21), residues: 1735
  helix:  2.39 (0.17), residues: 955
  sheet:  0.37 (0.33), residues: 255
  loop : -1.37 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 153 
 TYR   0.018   0.001   TYR C 327 
 PHE   0.030   0.001   PHE B 306 
 TRP   0.007   0.001   TRP E  61 
 HIS   0.002   0.000   HIS C 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (14525)
  covalent geometry    : angle       0.61837 (19730)
  hydrogen bonds       : bond        0.04020 (  880)
  hydrogen bonds       : angle       4.14559 ( 2565)

*********************** 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
  153 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 0.563 
Fit side-chains
REVERT: A  138 MET cc_start: 0.7986 (tmm) cc_final: 0.6609 (tmm)
REVERT: B  134 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.8146 (m-40)
REVERT: B  138 MET cc_start: 0.8147 (ttp) cc_final: 0.7653 (tmm)
REVERT: B  295 THR cc_start: 0.9494 (t) cc_final: 0.9283 (t)
REVERT: C   74 GLN cc_start: 0.9003 (tt0) cc_final: 0.8625 (tp-100)
REVERT: C  138 MET cc_start: 0.8141 (ttp) cc_final: 0.7671 (tmm)
REVERT: C  302 MET cc_start: 0.8484 (mmp) cc_final: 0.8266 (mmp)
REVERT: D   32 MET cc_start: 0.8023 (mtp) cc_final: 0.7607 (mtm)
REVERT: D   74 GLN cc_start: 0.8919 (tt0) cc_final: 0.8571 (tp-100)
REVERT: D  296 ILE cc_start: 0.9208 (pt) cc_final: 0.8903 (mt)
  outliers start: 31
  outliers final: 24
  residues processed: 145
  average time/residue: 0.0850
  time to fit residues: 21.4092
Evaluate side-chains
  140 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
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  247 THR
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  134 ASN
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  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 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 164 optimal weight:    2.9990
   chunk 73 optimal weight:    9.9990
   chunk 153 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0030
   chunk 17 optimal weight:    2.9990
   chunk 132 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 106 optimal weight:    0.0980
   chunk 90 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
A 314 ASN
B 314 ASN
C  95 GLN
C 314 ASN
** D  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 314 ASN
E  83 HIS
E 314 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.071554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.059059 restraints weight = 46387.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.061264 restraints weight = 26306.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.062817 restraints weight = 17800.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.063906 restraints weight = 13399.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.064686 restraints weight = 10865.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.3806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  14525  Z= 0.120
  Angle     :  0.607  11.032  19730  Z= 0.302
  Chirality :  0.042   0.185   2290
  Planarity :  0.003   0.046   2490
  Dihedral  :  3.736  17.376   1925
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 12.17 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.21), residues: 1735
  helix:  2.50 (0.17), residues: 950
  sheet:  0.68 (0.32), residues: 260
  loop : -1.50 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 158 
 TYR   0.014   0.001   TYR C 327 
 PHE   0.014   0.001   PHE B 306 
 TRP   0.005   0.001   TRP E  61 
 HIS   0.002   0.000   HIS D 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (14525)
  covalent geometry    : angle       0.60675 (19730)
  hydrogen bonds       : bond        0.03849 (  880)
  hydrogen bonds       : angle       4.00522 ( 2565)

*********************** 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
  147 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 0.622 
Fit side-chains
REVERT: A  138 MET cc_start: 0.7962 (tmm) cc_final: 0.6643 (tmm)
REVERT: B  134 ASN cc_start: 0.8411 (m110) cc_final: 0.8121 (m-40)
REVERT: B  138 MET cc_start: 0.8023 (ttp) cc_final: 0.7369 (tmm)
REVERT: B  291 MET cc_start: 0.8969 (tpp) cc_final: 0.8670 (tpp)
REVERT: B  295 THR cc_start: 0.9414 (t) cc_final: 0.9177 (t)
REVERT: C   74 GLN cc_start: 0.8923 (tt0) cc_final: 0.8618 (tp-100)
REVERT: C  138 MET cc_start: 0.7967 (ttp) cc_final: 0.7627 (tmm)
REVERT: C  291 MET cc_start: 0.9019 (mmt) cc_final: 0.8739 (tpp)
REVERT: D   32 MET cc_start: 0.7833 (mtp) cc_final: 0.7437 (mtm)
REVERT: D   74 GLN cc_start: 0.8848 (tt0) cc_final: 0.8571 (tp-100)
REVERT: D  296 ILE cc_start: 0.9082 (pt) cc_final: 0.8877 (mt)
REVERT: E  138 MET cc_start: 0.8174 (ttp) cc_final: 0.7607 (tmm)
  outliers start: 27
  outliers final: 21
  residues processed: 142
  average time/residue: 0.0855
  time to fit residues: 21.1045
Evaluate side-chains
  133 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  239 VAL
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  239 VAL
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  135 CYS
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  239 VAL
Chi-restraints excluded: chain D residue  299 THR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 123 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 68 optimal weight:    0.5980
   chunk 12 optimal weight:    3.9990
   chunk 105 optimal weight:    8.9990
   chunk 107 optimal weight:    2.9990
   chunk 46 optimal weight:   10.0000
   chunk 146 optimal weight:    0.9980
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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  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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.070221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.057522 restraints weight = 46728.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.059638 restraints weight = 27030.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.061147 restraints weight = 18467.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.062234 restraints weight = 14052.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.062975 restraints weight = 11441.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.3868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  14525  Z= 0.163
  Angle     :  0.621  12.538  19730  Z= 0.310
  Chirality :  0.042   0.196   2290
  Planarity :  0.004   0.048   2490
  Dihedral  :  3.744  18.071   1925
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.36 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.21), residues: 1735
  helix:  2.51 (0.17), residues: 945
  sheet:  0.52 (0.33), residues: 255
  loop : -1.43 (0.27), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 216 
 TYR   0.016   0.001   TYR D 327 
 PHE   0.021   0.001   PHE C 306 
 TRP   0.008   0.001   TRP E  61 
 HIS   0.002   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (14525)
  covalent geometry    : angle       0.62095 (19730)
  hydrogen bonds       : bond        0.03940 (  880)
  hydrogen bonds       : angle       4.08974 ( 2565)

*********************** 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
  144 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 0.630 
Fit side-chains
REVERT: A  112 MET cc_start: 0.8307 (mtm) cc_final: 0.8098 (mtt)
REVERT: A  138 MET cc_start: 0.8063 (tmm) cc_final: 0.6651 (tmm)
REVERT: B   74 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8590 (tm-30)
REVERT: B  134 ASN cc_start: 0.8492 (m110) cc_final: 0.8158 (m-40)
REVERT: B  138 MET cc_start: 0.8102 (ttp) cc_final: 0.7709 (tmm)
REVERT: B  295 THR cc_start: 0.9449 (t) cc_final: 0.9210 (t)
REVERT: C   74 GLN cc_start: 0.8949 (tt0) cc_final: 0.8648 (tp-100)
REVERT: C  138 MET cc_start: 0.8042 (ttp) cc_final: 0.7576 (tmm)
REVERT: C  291 MET cc_start: 0.9218 (mmt) cc_final: 0.8868 (mmp)
REVERT: D   32 MET cc_start: 0.7993 (mtp) cc_final: 0.7627 (mtm)
REVERT: D   74 GLN cc_start: 0.8884 (tt0) cc_final: 0.8609 (tp-100)
REVERT: D  296 ILE cc_start: 0.9115 (pt) cc_final: 0.8882 (mt)
REVERT: E  138 MET cc_start: 0.8298 (ttp) cc_final: 0.7435 (tmm)
  outliers start: 31
  outliers final: 29
  residues processed: 138
  average time/residue: 0.0884
  time to fit residues: 21.1630
Evaluate side-chains
  139 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
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 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  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  135 CYS
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  331 LEU
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  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 69 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 123 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   chunk 106 optimal weight:    0.1980
   chunk 65 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 39 optimal weight:   10.0000
   chunk 98 optimal weight:    0.9980
   chunk 158 optimal weight:    0.3980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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  95 GLN
C 314 ASN
** D  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 314 ASN
E 314 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.071114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.058605 restraints weight = 46370.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.060775 restraints weight = 26401.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.062304 restraints weight = 17909.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.063408 restraints weight = 13545.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.064174 restraints weight = 10957.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
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   0.048  14525  Z= 0.122
  Angle     :  0.614  13.945  19730  Z= 0.305
  Chirality :  0.042   0.184   2290
  Planarity :  0.003   0.046   2490
  Dihedral  :  3.732  17.444   1925
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 12.93 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.62 (0.21), residues: 1735
  helix:  2.51 (0.17), residues: 945
  sheet:  0.73 (0.33), residues: 260
  loop : -1.53 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  69 
 TYR   0.016   0.001   TYR C 327 
 PHE   0.022   0.001   PHE C 306 
 TRP   0.006   0.001   TRP E  61 
 HIS   0.002   0.000   HIS B  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (14525)
  covalent geometry    : angle       0.61362 (19730)
  hydrogen bonds       : bond        0.03838 (  880)
  hydrogen bonds       : angle       3.99146 ( 2565)

********************** 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
  137 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.630 
Fit side-chains
REVERT: A  112 MET cc_start: 0.8286 (mtm) cc_final: 0.8057 (mtt)
REVERT: A  138 MET cc_start: 0.8044 (tmm) cc_final: 0.6455 (tmm)
REVERT: B   74 GLN cc_start: 0.8880 (tp-100) cc_final: 0.8542 (tm-30)
REVERT: B  134 ASN cc_start: 0.8461 (m110) cc_final: 0.8132 (m-40)
REVERT: B  138 MET cc_start: 0.8053 (ttp) cc_final: 0.7387 (tmm)
REVERT: B  291 MET cc_start: 0.8922 (tpp) cc_final: 0.8462 (tpp)
REVERT: B  295 THR cc_start: 0.9383 (t) cc_final: 0.9154 (t)
REVERT: C   74 GLN cc_start: 0.8896 (tt0) cc_final: 0.8627 (tp-100)
REVERT: C  138 MET cc_start: 0.8012 (ttp) cc_final: 0.7645 (tmm)
REVERT: D   32 MET cc_start: 0.7930 (mtp) cc_final: 0.7553 (mtm)
REVERT: D   74 GLN cc_start: 0.8814 (tt0) cc_final: 0.8541 (tp-100)
REVERT: D  296 ILE cc_start: 0.9112 (pt) cc_final: 0.8889 (mt)
REVERT: E  138 MET cc_start: 0.8293 (ttp) cc_final: 0.7560 (tmm)
  outliers start: 22
  outliers final: 22
  residues processed: 131
  average time/residue: 0.0897
  time to fit residues: 20.3851
Evaluate side-chains
  135 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  132 THR
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  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  331 LEU
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  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  232 LEU
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 156 optimal weight:    6.9990
   chunk 58 optimal weight:    0.7980
   chunk 90 optimal weight:    0.4980
   chunk 138 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 168 optimal weight:    5.9990
   chunk 167 optimal weight:    0.1980
   chunk 69 optimal weight:    0.3980
   chunk 96 optimal weight:    0.8980
   chunk 39 optimal weight:    0.2980
   chunk 66 optimal weight:    4.9990
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 314 ASN
B 140 GLN
B 314 ASN
C  95 GLN
C 314 ASN
D  83 HIS
** D 140 GLN ** 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 = 0.3358 r_free = 0.3358 target = 0.071965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.059450 restraints weight = 46286.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.061599 restraints weight = 26479.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.063146 restraints weight = 17981.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.064277 restraints weight = 13570.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.064990 restraints weight = 10939.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.4022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14525  Z= 0.117
  Angle     :  0.603  13.983  19730  Z= 0.299
  Chirality :  0.041   0.176   2290
  Planarity :  0.003   0.046   2490
  Dihedral  :  3.671  17.197   1925
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 13.25 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.21), residues: 1735
  helix:  2.52 (0.17), residues: 945
  sheet:  0.83 (0.33), residues: 260
  loop : -1.53 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 202 
 TYR   0.016   0.001   TYR C 327 
 PHE   0.021   0.001   PHE C 306 
 TRP   0.006   0.000   TRP A  61 
 HIS   0.002   0.000   HIS B  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (14525)
  covalent geometry    : angle       0.60313 (19730)
  hydrogen bonds       : bond        0.03721 (  880)
  hydrogen bonds       : angle       3.92118 ( 2565)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1965.80 seconds
wall clock time: 35 minutes 5.50 seconds (2105.50 seconds total)