Starting phenix.real_space_refine
on Sat Aug 23 15:04:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ip6_35633/08_2025/8ip6_35633.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ip6_35633/08_2025/8ip6_35633.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ip6_35633/08_2025/8ip6_35633.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ip6_35633/08_2025/8ip6_35633.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ip6_35633/08_2025/8ip6_35633.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ip6_35633/08_2025/8ip6_35633.map"
  }
  resolution = 2.9
  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=   0.047
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      65      5.16       5
     Cl      1      4.86       5
     C    8315      2.51       5
     N    2175      2.21       5
     O    2365      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12921
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2584
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
      Conformer: "B"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
          bond proxies already assigned to first conformer: 2613
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
      Conformer: "B"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
          bond proxies already assigned to first conformer: 2613
    Chain: "C"
      Number of atoms: 2584
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
      Conformer: "B"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
          bond proxies already assigned to first conformer: 2613
    Chain: "D"
      Number of atoms: 2584
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
      Conformer: "B"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
          bond proxies already assigned to first conformer: 2613
    Chain: "E"
      Number of atoms: 2584
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
      Conformer: "B"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
          bond proxies already assigned to first conformer: 2613
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.79, per 1000 atoms: 0.37
  Number of scatterers: 12921
  At special positions: 0
  Unit cell: (112.554, 111.54, 141.96, 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)
     Cl      1     17.00
     S      65     16.00
     O    2365      8.00
     N    2175      7.00
     C    8315      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: 0.78
  Conformation dependent library (CDL) restraints added in 815.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3060

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 5 sheets defined
      71.9% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 114 through 119
      removed outlier: 3.761A  pdb=" N   ARG A 119 " --> pdb=" O   ARG A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 172
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 183 through 219
      removed outlier: 3.693A  pdb=" N   ARG A 187 " --> pdb=" O   PRO A 183 " (cutoff:3.500A)
      Proline residue:  A 209  - end of helix
    Processing helix  chain 'A' and resid 227 through 261
      removed outlier: 3.528A  pdb=" N   ILE A 258 " --> pdb=" O   SER A 254 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLU A 261 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 269
      removed outlier: 3.668A  pdb=" N   LEU A 265 " --> pdb=" O   GLU A 261 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   CYS A 269 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 275
      removed outlier: 3.803A  pdb=" N   ASP A 275 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 283
      removed outlier: 4.103A  pdb=" N   LYS A 281 " --> pdb=" O   GLN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 360
      removed outlier: 4.184A  pdb=" N   MET A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLY A 356 " --> pdb=" O   PHE A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 401
    Processing helix  chain 'B' and resid 104 through 112
    Processing helix  chain 'B' and resid 114 through 119
      removed outlier: 3.761A  pdb=" N   ARG B 119 " --> pdb=" O   ARG B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 172
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 183 through 219
      removed outlier: 3.693A  pdb=" N   ARG B 187 " --> pdb=" O   PRO B 183 " (cutoff:3.500A)
      Proline residue:  B 209  - end of helix
    Processing helix  chain 'B' and resid 227 through 261
      removed outlier: 3.528A  pdb=" N   ILE B 258 " --> pdb=" O   SER B 254 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLU B 261 " --> pdb=" O   GLU B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 269
      removed outlier: 3.668A  pdb=" N   LEU B 265 " --> pdb=" O   GLU B 261 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   CYS B 269 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 275
      removed outlier: 3.802A  pdb=" N   ASP B 275 " --> pdb=" O   SER B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 283
      removed outlier: 4.101A  pdb=" N   LYS B 281 " --> pdb=" O   GLN B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 360
      removed outlier: 4.184A  pdb=" N   MET B 355 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLY B 356 " --> pdb=" O   PHE B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 401
    Processing helix  chain 'C' and resid 104 through 112
    Processing helix  chain 'C' and resid 114 through 119
      removed outlier: 3.761A  pdb=" N   ARG C 119 " --> pdb=" O   ARG C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 172
      Proline residue:  C 168  - end of helix
    Processing helix  chain 'C' and resid 183 through 219
      removed outlier: 3.693A  pdb=" N   ARG C 187 " --> pdb=" O   PRO C 183 " (cutoff:3.500A)
      Proline residue:  C 209  - end of helix
    Processing helix  chain 'C' and resid 227 through 261
      removed outlier: 3.528A  pdb=" N   ILE C 258 " --> pdb=" O   SER C 254 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLU C 261 " --> pdb=" O   GLU C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 269
      removed outlier: 3.668A  pdb=" N   LEU C 265 " --> pdb=" O   GLU C 261 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   CYS C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 275
      removed outlier: 3.803A  pdb=" N   ASP C 275 " --> pdb=" O   SER C 271 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 275 through 283
      removed outlier: 4.102A  pdb=" N   LYS C 281 " --> pdb=" O   GLN C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 360
      removed outlier: 4.184A  pdb=" N   MET C 355 " --> pdb=" O   LEU C 351 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLY C 356 " --> pdb=" O   PHE C 352 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 372 through 401
    Processing helix  chain 'D' and resid 104 through 112
    Processing helix  chain 'D' and resid 114 through 119
      removed outlier: 3.761A  pdb=" N   ARG D 119 " --> pdb=" O   ARG D 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 172
      Proline residue:  D 168  - end of helix
    Processing helix  chain 'D' and resid 183 through 219
      removed outlier: 3.693A  pdb=" N   ARG D 187 " --> pdb=" O   PRO D 183 " (cutoff:3.500A)
      Proline residue:  D 209  - end of helix
    Processing helix  chain 'D' and resid 227 through 261
      removed outlier: 3.528A  pdb=" N   ILE D 258 " --> pdb=" O   SER D 254 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLU D 261 " --> pdb=" O   GLU D 257 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 261 through 269
      removed outlier: 3.668A  pdb=" N   LEU D 265 " --> pdb=" O   GLU D 261 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   CYS D 269 " --> pdb=" O   LEU D 265 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 275
      removed outlier: 3.803A  pdb=" N   ASP D 275 " --> pdb=" O   SER D 271 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 283
      removed outlier: 4.102A  pdb=" N   LYS D 281 " --> pdb=" O   GLN D 277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 360
      removed outlier: 4.184A  pdb=" N   MET D 355 " --> pdb=" O   LEU D 351 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   GLY D 356 " --> pdb=" O   PHE D 352 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 372 through 401
    Processing helix  chain 'E' and resid 104 through 112
    Processing helix  chain 'E' and resid 114 through 119
      removed outlier: 3.762A  pdb=" N   ARG E 119 " --> pdb=" O   ARG E 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 159 through 172
      Proline residue:  E 168  - end of helix
    Processing helix  chain 'E' and resid 183 through 219
      removed outlier: 3.693A  pdb=" N   ARG E 187 " --> pdb=" O   PRO E 183 " (cutoff:3.500A)
      Proline residue:  E 209  - end of helix
    Processing helix  chain 'E' and resid 227 through 261
      removed outlier: 3.528A  pdb=" N   ILE E 258 " --> pdb=" O   SER E 254 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLU E 261 " --> pdb=" O   GLU E 257 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 261 through 269
      removed outlier: 3.668A  pdb=" N   LEU E 265 " --> pdb=" O   GLU E 261 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   CYS E 269 " --> pdb=" O   LEU E 265 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 275
      removed outlier: 3.802A  pdb=" N   ASP E 275 " --> pdb=" O   SER E 271 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 275 through 283
      removed outlier: 4.101A  pdb=" N   LYS E 281 " --> pdb=" O   GLN E 277 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 287 through 360
      removed outlier: 4.184A  pdb=" N   MET E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLY E 356 " --> pdb=" O   PHE E 352 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 372 through 401
    Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 103
      removed outlier: 4.220A  pdb=" N   LYS A 141 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 103
      removed outlier: 4.219A  pdb=" N   LYS B 141 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 103
      removed outlier: 4.219A  pdb=" N   LYS C 141 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 97 through 103
      removed outlier: 4.220A  pdb=" N   LYS D 141 " --> pdb=" O   LEU D 152 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 103
      removed outlier: 4.220A  pdb=" N   LYS E 141 " --> pdb=" O   LEU E 152 " (cutoff:3.500A)

    1000 hydrogen bonds defined for protein.
    2905 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: 1.77

  Time building geometry restraints manager: 1.00 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: 4235
        1.34 -     1.46: 1965
        1.46 -     1.57: 6835
        1.57 -     1.69: 0
        1.69 -     1.80: 120
  Bond restraints: 13155
  Sorted by residual:
  bond pdb=" CA  VAL A  82 "
       pdb=" CB  VAL A  82 "
    ideal  model  delta    sigma   weight residual
    1.540  1.520  0.020 2.70e-02 1.37e+03 5.69e-01
  bond pdb=" CA  VAL D  82 "
       pdb=" CB  VAL D  82 "
    ideal  model  delta    sigma   weight residual
    1.540  1.520  0.020 2.70e-02 1.37e+03 5.54e-01
  bond pdb=" CA  VAL E  82 "
       pdb=" CB  VAL E  82 "
    ideal  model  delta    sigma   weight residual
    1.540  1.520  0.020 2.70e-02 1.37e+03 5.48e-01
  bond pdb=" CA  VAL C  82 "
       pdb=" CB  VAL C  82 "
    ideal  model  delta    sigma   weight residual
    1.540  1.520  0.020 2.70e-02 1.37e+03 5.48e-01
  bond pdb=" CA  VAL B  82 "
       pdb=" CB  VAL B  82 "
    ideal  model  delta    sigma   weight residual
    1.540  1.520  0.020 2.70e-02 1.37e+03 5.31e-01
  ... (remaining 13150 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.96: 17213
        0.96 -     1.92: 457
        1.92 -     2.89: 57
        2.89 -     3.85: 28
        3.85 -     4.81: 30
  Bond angle restraints: 17785
  Sorted by residual:
  angle pdb=" C   LEU D 351 "
        pdb=" N   PHE D 352 "
        pdb=" CA  PHE D 352 "
      ideal   model   delta    sigma   weight residual
     121.14  118.24    2.90 1.75e+00 3.27e-01 2.75e+00
  angle pdb=" C   LEU E 351 "
        pdb=" N   PHE E 352 "
        pdb=" CA  PHE E 352 "
      ideal   model   delta    sigma   weight residual
     121.14  118.24    2.90 1.75e+00 3.27e-01 2.75e+00
  angle pdb=" C   LEU B 351 "
        pdb=" N   PHE B 352 "
        pdb=" CA  PHE B 352 "
      ideal   model   delta    sigma   weight residual
     121.14  118.24    2.90 1.75e+00 3.27e-01 2.75e+00
  angle pdb=" C   LEU C 351 "
        pdb=" N   PHE C 352 "
        pdb=" CA  PHE C 352 "
      ideal   model   delta    sigma   weight residual
     121.14  118.27    2.87 1.75e+00 3.27e-01 2.70e+00
  angle pdb=" C   LEU A 351 "
        pdb=" N   PHE A 352 "
        pdb=" CA  PHE A 352 "
      ideal   model   delta    sigma   weight residual
     121.14  118.27    2.87 1.75e+00 3.27e-01 2.69e+00
  ... (remaining 17780 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.49: 7290
       17.49 -    34.99: 585
       34.99 -    52.48: 100
       52.48 -    69.98: 10
       69.98 -    87.47: 10
  Dihedral angle restraints: 7995
    sinusoidal: 3295
      harmonic: 4700
  Sorted by residual:
  dihedral pdb=" CB  GLU E 147 "
           pdb=" CG  GLU E 147 "
           pdb=" CD  GLU E 147 "
           pdb=" OE1 GLU E 147 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.72  -85.72     1      3.00e+01 1.11e-03 9.87e+00
  dihedral pdb=" CB  GLU B 147 "
           pdb=" CG  GLU B 147 "
           pdb=" CD  GLU B 147 "
           pdb=" OE1 GLU B 147 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.69  -85.69     1      3.00e+01 1.11e-03 9.87e+00
  dihedral pdb=" CB  GLU C 147 "
           pdb=" CG  GLU C 147 "
           pdb=" CD  GLU C 147 "
           pdb=" OE1 GLU C 147 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.63  -85.63     1      3.00e+01 1.11e-03 9.85e+00
  ... (remaining 7992 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1383
       0.026 -    0.052: 357
       0.052 -    0.078: 195
       0.078 -    0.104: 92
       0.104 -    0.130: 33
  Chirality restraints: 2060
  Sorted by residual:
  chirality pdb=" CA  LEU B 167 "
            pdb=" N   LEU B 167 "
            pdb=" C   LEU B 167 "
            pdb=" CB  LEU B 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" CA  LEU E 167 "
            pdb=" N   LEU E 167 "
            pdb=" C   LEU E 167 "
            pdb=" CB  LEU E 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  LEU C 167 "
            pdb=" N   LEU C 167 "
            pdb=" C   LEU C 167 "
            pdb=" CB  LEU C 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.05e-01
  ... (remaining 2057 not shown)

  Planarity restraints: 2250
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 163 "   -0.008 2.00e-02 2.50e+03   1.65e-02 2.71e+00
        pdb=" C   LEU C 163 "    0.028 2.00e-02 2.50e+03
        pdb=" O   LEU C 163 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   PHE C 164 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 163 "    0.008 2.00e-02 2.50e+03   1.64e-02 2.69e+00
        pdb=" C   LEU A 163 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   LEU A 163 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE A 164 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E 163 "    0.008 2.00e-02 2.50e+03   1.64e-02 2.68e+00
        pdb=" C   LEU E 163 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   LEU E 163 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE E 164 "    0.010 2.00e-02 2.50e+03
  ... (remaining 2247 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 3744
        2.83 -     3.35: 12582
        3.35 -     3.86: 20753
        3.86 -     4.38: 22868
        4.38 -     4.90: 41705
  Nonbonded interactions: 101652
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU D 185 "
            pdb=" OG  SER D 271 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" OE1 GLU C 185 "
            pdb=" OG  SER C 271 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OE1 GLU B 185 "
            pdb=" OG  SER B 271 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OE1 GLU E 185 "
            pdb=" OG  SER E 271 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OE1 GLU A 185 "
            pdb=" OG  SER A 271 "
     model   vdw
     2.310 3.040
  ... (remaining 101647 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' and (resid 82 through 128 or resid 130 through 401))
  selection = (chain 'B' and (resid 82 through 128 or resid 130 through 401))
  selection = (chain 'C' and (resid 82 through 128 or resid 130 through 401))
  selection = (chain 'D' and (resid 82 through 128 or resid 130 through 401))
  selection = (chain 'E' and (resid 82 through 128 or resid 130 through 401))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     13.260
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.020
  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:7.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
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      :  0.003   0.020  13155  Z= 0.127
  Angle     :  0.427   4.812  17785  Z= 0.233
  Chirality :  0.036   0.130   2060
  Planarity :  0.003   0.028   2250
  Dihedral  : 13.001  87.474   4935
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  4.51 (0.22), residues: 1595
  helix:  4.02 (0.15), residues: 1040
  sheet:  3.02 (0.33), residues: 145
  loop : -0.04 (0.34), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 102 
 TYR   0.014   0.001   TYR C 299 
 PHE   0.014   0.001   PHE D  86 
 TRP   0.004   0.001   TRP E 162 
 HIS   0.002   0.000   HIS B 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (13155)
  covalent geometry    : angle       0.42748 (17785)
  hydrogen bonds       : bond        0.10092 ( 1000)
  hydrogen bonds       : angle       4.02776 ( 2905)

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 0.392 
Fit side-chains
REVERT: A  139 TYR cc_start: 0.9253 (p90) cc_final: 0.8948 (p90)
REVERT: A  257 GLU cc_start: 0.7899 (tt0) cc_final: 0.7659 (tp30)
REVERT: A  382 PHE cc_start: 0.8671 (m-80) cc_final: 0.8433 (m-80)
REVERT: A  383 MET cc_start: 0.5563 (mmp) cc_final: 0.5255 (mpp)
REVERT: B  383 MET cc_start: 0.5257 (mmp) cc_final: 0.4976 (mtm)
REVERT: B  391 ARG cc_start: 0.7934 (mtt180) cc_final: 0.7684 (tpt170)
REVERT: C  383 MET cc_start: 0.5609 (mmp) cc_final: 0.5337 (tpp)
REVERT: D  108 TYR cc_start: 0.8900 (m-10) cc_final: 0.8610 (m-80)
REVERT: D  139 TYR cc_start: 0.9319 (p90) cc_final: 0.9104 (p90)
REVERT: D  190 GLU cc_start: 0.8106 (tt0) cc_final: 0.7856 (tt0)
REVERT: D  257 GLU cc_start: 0.7945 (tt0) cc_final: 0.7643 (tp30)
REVERT: D  383 MET cc_start: 0.5076 (mmp) cc_final: 0.4771 (tpp)
REVERT: D  391 ARG cc_start: 0.7904 (mtt180) cc_final: 0.7516 (tpt170)
REVERT: E  190 GLU cc_start: 0.8239 (tt0) cc_final: 0.7715 (tt0)
REVERT: E  383 MET cc_start: 0.5298 (mmp) cc_final: 0.5051 (mpp)
REVERT: E  391 ARG cc_start: 0.7898 (mtt180) cc_final: 0.7647 (tpt170)
  outliers start: 0
  outliers final: 0
  residues processed: 269
  average time/residue: 0.5582
  time to fit residues: 162.1143
Evaluate side-chains
  178 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    0.0470
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    2.2086

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

Flipped N/Q/H residues before XYZ refinement:
A 194 GLN
A 223 HIS
B 194 GLN
B 223 HIS
C 194 GLN
D 194 GLN
E 223 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.111689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.079132 restraints weight = 64755.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 4.35
r_work: 0.2829 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2821
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2821 r_free = 0.2821    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2821 r_free = 0.2821    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2821
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032  13155  Z= 0.208
  Angle     :  0.578   8.184  17785  Z= 0.294
  Chirality :  0.040   0.144   2060
  Planarity :  0.004   0.029   2250
  Dihedral  :  3.628  14.161   1740
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  9.01 %
    Favored  : 89.37 %
  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:  4.30 (0.21), residues: 1595
  helix:  3.58 (0.15), residues: 1085
  sheet:  2.98 (0.32), residues: 145
  loop :  0.30 (0.37), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 314 
 TYR   0.023   0.002   TYR C 154 
 PHE   0.020   0.002   PHE E  86 
 TRP   0.004   0.001   TRP B 196 
 HIS   0.002   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 (13155)
  covalent geometry    : angle       0.57822 (17785)
  hydrogen bonds       : bond        0.06692 ( 1000)
  hydrogen bonds       : angle       3.74490 ( 2905)

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 186
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9461 (p90) cc_final: 0.9056 (p90)
REVERT: A  250 ILE cc_start: 0.8881 (mp) cc_final: 0.8559 (pt)
REVERT: A  257 GLU cc_start: 0.8657 (tt0) cc_final: 0.7970 (tp30)
REVERT: A  266 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8469 (tp30)
REVERT: A  361 MET cc_start: 0.8665 (ptp) cc_final: 0.7987 (ppp)
REVERT: A  382 PHE cc_start: 0.8488 (m-80) cc_final: 0.8018 (m-80)
REVERT: A  383 MET cc_start: 0.5262 (mmp) cc_final: 0.4982 (mpp)
REVERT: B  154 TYR cc_start: 0.8943 (p90) cc_final: 0.8675 (p90)
REVERT: B  257 GLU cc_start: 0.7988 (tp30) cc_final: 0.7719 (tp30)
REVERT: B  261 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7144 (mp0)
REVERT: B  383 MET cc_start: 0.4737 (mmp) cc_final: 0.4438 (mtm)
REVERT: B  391 ARG cc_start: 0.7871 (mtt180) cc_final: 0.7400 (tpt170)
REVERT: C  383 MET cc_start: 0.5313 (mmp) cc_final: 0.5058 (tpp)
REVERT: C  391 ARG cc_start: 0.7413 (mtt180) cc_final: 0.6934 (tpt170)
REVERT: D  108 TYR cc_start: 0.8787 (m-10) cc_final: 0.8496 (m-80)
REVERT: D  139 TYR cc_start: 0.9499 (p90) cc_final: 0.9236 (p90)
REVERT: D  257 GLU cc_start: 0.8660 (tt0) cc_final: 0.7940 (tp30)
REVERT: D  291 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8485 (mm-30)
REVERT: D  383 MET cc_start: 0.4660 (mmp) cc_final: 0.4322 (tpp)
REVERT: D  391 ARG cc_start: 0.7895 (mtt180) cc_final: 0.7230 (tpt170)
REVERT: E  109 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8109 (pp30)
REVERT: E  383 MET cc_start: 0.5162 (mmp) cc_final: 0.4594 (mpt)
REVERT: E  391 ARG cc_start: 0.7808 (mtt180) cc_final: 0.7333 (tpt170)
  outliers start: 23
  outliers final: 6
  residues processed: 197
  average time/residue: 0.5371
  time to fit residues: 114.7464
Evaluate side-chains
  173 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 166
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 ASP
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  385 SER
Chi-restraints excluded: chain C residue  385 SER
Chi-restraints excluded: chain D residue  338 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 158 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 146 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 154 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 223 HIS
B 223 HIS
E 223 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.111054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.078606 restraints weight = 62155.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 4.26
r_work: 0.2814 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2806
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2806 r_free = 0.2806    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2806 r_free = 0.2806    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2806
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  13155  Z= 0.216
  Angle     :  0.576   8.969  17785  Z= 0.293
  Chirality :  0.040   0.140   2060
  Planarity :  0.004   0.030   2250
  Dihedral  :  3.764  14.447   1740
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  9.79 %
    Favored  : 88.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.02 (0.21), residues: 1595
  helix:  3.33 (0.15), residues: 1105
  sheet:  2.87 (0.33), residues: 145
  loop :  0.13 (0.39), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 337 
 TYR   0.027   0.002   TYR C 154 
 PHE   0.019   0.002   PHE E  86 
 TRP   0.006   0.001   TRP A 389 
 HIS   0.002   0.001   HIS E 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 (13155)
  covalent geometry    : angle       0.57582 (17785)
  hydrogen bonds       : bond        0.06878 ( 1000)
  hydrogen bonds       : angle       3.80565 ( 2905)

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 173
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A  124 MET cc_start: 0.8402 (tpp) cc_final: 0.8200 (tpp)
REVERT: A  139 TYR cc_start: 0.9450 (p90) cc_final: 0.9078 (p90)
REVERT: A  213 GLU cc_start: 0.8595 (tt0) cc_final: 0.8201 (tm-30)
REVERT: A  257 GLU cc_start: 0.8687 (tt0) cc_final: 0.8006 (tp30)
REVERT: A  266 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8421 (tp30)
REVERT: A  361 MET cc_start: 0.8687 (ptp) cc_final: 0.8068 (ppp)
REVERT: A  383 MET cc_start: 0.5493 (mmp) cc_final: 0.5231 (mpp)
REVERT: B  257 GLU cc_start: 0.8108 (tp30) cc_final: 0.7806 (tp30)
REVERT: B  261 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7132 (mp0)
REVERT: B  383 MET cc_start: 0.4680 (mmp) cc_final: 0.4339 (mtm)
REVERT: B  391 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7466 (tpt170)
REVERT: C  137 MET cc_start: 0.9241 (mtm) cc_final: 0.8978 (mtt)
REVERT: C  383 MET cc_start: 0.5226 (mmp) cc_final: 0.4961 (tpp)
REVERT: C  391 ARG cc_start: 0.7452 (mtt180) cc_final: 0.6981 (tpt170)
REVERT: D  108 TYR cc_start: 0.8794 (m-10) cc_final: 0.8533 (m-80)
REVERT: D  139 TYR cc_start: 0.9489 (p90) cc_final: 0.9248 (p90)
REVERT: D  257 GLU cc_start: 0.8704 (tt0) cc_final: 0.7998 (tp30)
REVERT: D  359 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.6681 (t80)
REVERT: D  383 MET cc_start: 0.4630 (mmp) cc_final: 0.4310 (tpp)
REVERT: D  391 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7225 (tpt170)
REVERT: E  109 GLN cc_start: 0.8316 (tm-30) cc_final: 0.8088 (pp30)
REVERT: E  190 GLU cc_start: 0.8957 (tt0) cc_final: 0.8140 (pt0)
REVERT: E  383 MET cc_start: 0.5149 (mmp) cc_final: 0.4552 (mpt)
REVERT: E  391 ARG cc_start: 0.7883 (mtt180) cc_final: 0.7381 (tpt170)
  outliers start: 23
  outliers final: 9
  residues processed: 185
  average time/residue: 0.5384
  time to fit residues: 107.5275
Evaluate side-chains
  174 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 163
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  385 SER
Chi-restraints excluded: chain C residue  385 SER
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain E residue  349 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 111 optimal weight:    0.9990
   chunk 127 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 154 optimal weight:    4.9990
   chunk 147 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 123 optimal weight:    9.9990
   chunk 102 optimal weight:    2.9990
   chunk 158 optimal weight:    7.9990
   chunk 64 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 223 HIS
E 223 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.111647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.079047 restraints weight = 70533.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 4.50
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3046
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3046
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13155  Z= 0.190
  Angle     :  0.543   9.866  17785  Z= 0.277
  Chirality :  0.039   0.134   2060
  Planarity :  0.004   0.031   2250
  Dihedral  :  3.723  14.725   1740
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.13 %
    Favored  : 87.61 %
  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:  4.06 (0.21), residues: 1595
  helix:  3.35 (0.15), residues: 1105
  sheet:  2.88 (0.34), residues: 145
  loop :  0.16 (0.39), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 337 
 TYR   0.027   0.002   TYR C 154 
 PHE   0.016   0.002   PHE E  86 
 TRP   0.004   0.001   TRP B 196 
 HIS   0.002   0.001   HIS E 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (13155)
  covalent geometry    : angle       0.54335 (17785)
  hydrogen bonds       : bond        0.06642 ( 1000)
  hydrogen bonds       : angle       3.74746 ( 2905)

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 175
  time to evaluate  : 0.453 
Fit side-chains
REVERT: A  139 TYR cc_start: 0.9344 (p90) cc_final: 0.8961 (p90)
REVERT: A  213 GLU cc_start: 0.8185 (tt0) cc_final: 0.7920 (tm-30)
REVERT: A  257 GLU cc_start: 0.8352 (tt0) cc_final: 0.7665 (tp30)
REVERT: A  266 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8220 (tp30)
REVERT: A  361 MET cc_start: 0.8644 (ptp) cc_final: 0.8085 (ppp)
REVERT: A  382 PHE cc_start: 0.8429 (m-80) cc_final: 0.8135 (m-80)
REVERT: A  383 MET cc_start: 0.5317 (mmp) cc_final: 0.5006 (mpp)
REVERT: B  257 GLU cc_start: 0.7582 (tp30) cc_final: 0.7222 (tp30)
REVERT: B  261 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6670 (mp0)
REVERT: B  383 MET cc_start: 0.4709 (mmp) cc_final: 0.4358 (mtm)
REVERT: B  391 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7485 (tpt170)
REVERT: C  137 MET cc_start: 0.9084 (mtm) cc_final: 0.8854 (mtm)
REVERT: C  383 MET cc_start: 0.5523 (mmp) cc_final: 0.5246 (tpp)
REVERT: C  391 ARG cc_start: 0.7400 (mtt180) cc_final: 0.6859 (tpt170)
REVERT: D  108 TYR cc_start: 0.8654 (m-10) cc_final: 0.8389 (m-80)
REVERT: D  137 MET cc_start: 0.9077 (mtm) cc_final: 0.8795 (mtt)
REVERT: D  139 TYR cc_start: 0.9388 (p90) cc_final: 0.9116 (p90)
REVERT: D  257 GLU cc_start: 0.8381 (tt0) cc_final: 0.7699 (tp30)
REVERT: D  383 MET cc_start: 0.4656 (mmp) cc_final: 0.4350 (tpp)
REVERT: D  391 ARG cc_start: 0.7904 (mtt180) cc_final: 0.7273 (tpt170)
REVERT: E  109 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7801 (pp30)
REVERT: E  190 GLU cc_start: 0.8401 (tt0) cc_final: 0.7606 (pt0)
REVERT: E  391 ARG cc_start: 0.7937 (mtt180) cc_final: 0.7460 (tpt-90)
  outliers start: 18
  outliers final: 10
  residues processed: 185
  average time/residue: 0.5759
  time to fit residues: 115.0676
Evaluate side-chains
  174 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 163
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  385 SER
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  385 SER
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain E residue  385 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 94 optimal weight:    9.9990
   chunk 91 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 135 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 127 optimal weight:    2.9990
   chunk 121 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 112 optimal weight:    1.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 223 HIS
E 223 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.107770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.075668 restraints weight = 51743.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 4.00
r_work: 0.2828 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2834
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2834
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  13155  Z= 0.204
  Angle     :  0.558  10.308  17785  Z= 0.283
  Chirality :  0.039   0.135   2060
  Planarity :  0.004   0.032   2250
  Dihedral  :  3.747  15.019   1740
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 11.48 %
    Favored  : 86.97 %
  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:  4.04 (0.21), residues: 1595
  helix:  3.34 (0.15), residues: 1105
  sheet:  2.81 (0.34), residues: 145
  loop :  0.17 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 301 
 TYR   0.028   0.002   TYR C 154 
 PHE   0.015   0.002   PHE E  86 
 TRP   0.005   0.001   TRP C 196 
 HIS   0.002   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (13155)
  covalent geometry    : angle       0.55799 (17785)
  hydrogen bonds       : bond        0.06786 ( 1000)
  hydrogen bonds       : angle       3.78306 ( 2905)

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 169
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9463 (p90) cc_final: 0.9101 (p90)
REVERT: A  213 GLU cc_start: 0.8648 (tt0) cc_final: 0.8250 (tm-30)
REVERT: A  257 GLU cc_start: 0.8771 (tt0) cc_final: 0.8095 (tp30)
REVERT: A  266 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8497 (tp30)
REVERT: A  361 MET cc_start: 0.8701 (ptp) cc_final: 0.8078 (ppp)
REVERT: A  382 PHE cc_start: 0.8476 (m-80) cc_final: 0.8170 (m-80)
REVERT: A  383 MET cc_start: 0.5367 (mmp) cc_final: 0.5031 (mpp)
REVERT: B  257 GLU cc_start: 0.8065 (tp30) cc_final: 0.7140 (tp30)
REVERT: B  261 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6552 (mp0)
REVERT: B  383 MET cc_start: 0.4392 (mmp) cc_final: 0.4053 (mtm)
REVERT: B  391 ARG cc_start: 0.7886 (mtt180) cc_final: 0.7440 (tpt170)
REVERT: C  137 MET cc_start: 0.9267 (mtm) cc_final: 0.8974 (mtt)
REVERT: C  383 MET cc_start: 0.5336 (mmp) cc_final: 0.5071 (tpp)
REVERT: C  391 ARG cc_start: 0.7433 (mtt180) cc_final: 0.6892 (tpt170)
REVERT: D  108 TYR cc_start: 0.8839 (m-10) cc_final: 0.8586 (m-80)
REVERT: D  137 MET cc_start: 0.9247 (mtm) cc_final: 0.9011 (mtt)
REVERT: D  139 TYR cc_start: 0.9481 (p90) cc_final: 0.9248 (p90)
REVERT: D  250 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8658 (pt)
REVERT: D  257 GLU cc_start: 0.8725 (tt0) cc_final: 0.8024 (tp30)
REVERT: D  359 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.6918 (t80)
REVERT: D  383 MET cc_start: 0.4586 (mmp) cc_final: 0.4270 (tpp)
REVERT: D  391 ARG cc_start: 0.7911 (mtt180) cc_final: 0.7240 (tpt170)
REVERT: E  109 GLN cc_start: 0.8240 (tm-30) cc_final: 0.7997 (pp30)
REVERT: E  391 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7458 (tpt-90)
  outliers start: 22
  outliers final: 10
  residues processed: 180
  average time/residue: 0.5392
  time to fit residues: 105.2385
Evaluate side-chains
  177 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 164
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  385 SER
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  385 SER
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain E residue  385 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 124 optimal weight:    0.0060
   chunk 77 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 94 optimal weight:    5.9990
   chunk 90 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 138 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.1600

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

Flipped N/Q/H residues before XYZ refinement:
B 223 HIS
E 223 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.113630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.081789 restraints weight = 53289.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 4.01
r_work: 0.2874 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2871
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2871
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13155  Z= 0.138
  Angle     :  0.516  11.287  17785  Z= 0.259
  Chirality :  0.037   0.128   2060
  Planarity :  0.003   0.033   2250
  Dihedral  :  3.580  14.626   1740
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 11.97 %
    Favored  : 86.97 %
  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:  4.23 (0.22), residues: 1595
  helix:  3.48 (0.15), residues: 1105
  sheet:  2.93 (0.34), residues: 145
  loop :  0.26 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 228 
 TYR   0.027   0.002   TYR C 154 
 PHE   0.020   0.001   PHE E 352 
 TRP   0.006   0.001   TRP D 162 
 HIS   0.001   0.000   HIS B 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (13155)
  covalent geometry    : angle       0.51557 (17785)
  hydrogen bonds       : bond        0.06049 ( 1000)
  hydrogen bonds       : angle       3.62211 ( 2905)

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 180
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9462 (p90) cc_final: 0.9074 (p90)
REVERT: A  213 GLU cc_start: 0.8585 (tt0) cc_final: 0.8236 (tm-30)
REVERT: A  257 GLU cc_start: 0.8714 (tt0) cc_final: 0.7974 (tp30)
REVERT: A  266 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8523 (tp30)
REVERT: A  361 MET cc_start: 0.8697 (ptp) cc_final: 0.8084 (ppp)
REVERT: A  382 PHE cc_start: 0.8399 (m-80) cc_final: 0.8121 (m-80)
REVERT: A  383 MET cc_start: 0.5145 (mmp) cc_final: 0.4814 (mpp)
REVERT: B  257 GLU cc_start: 0.7964 (tp30) cc_final: 0.7073 (tp30)
REVERT: B  261 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6281 (mp0)
REVERT: B  383 MET cc_start: 0.4386 (mmp) cc_final: 0.4083 (mtm)
REVERT: B  391 ARG cc_start: 0.7877 (mtt180) cc_final: 0.7332 (tpt170)
REVERT: C  383 MET cc_start: 0.5251 (mmp) cc_final: 0.4989 (tpp)
REVERT: C  391 ARG cc_start: 0.7354 (mtt180) cc_final: 0.6842 (tpt170)
REVERT: D  108 TYR cc_start: 0.8790 (m-10) cc_final: 0.8500 (m-80)
REVERT: D  137 MET cc_start: 0.9148 (mtm) cc_final: 0.8887 (mtt)
REVERT: D  139 TYR cc_start: 0.9467 (p90) cc_final: 0.9191 (p90)
REVERT: D  250 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8627 (pt)
REVERT: D  257 GLU cc_start: 0.8663 (tt0) cc_final: 0.7951 (tp30)
REVERT: D  359 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.6982 (t80)
REVERT: D  383 MET cc_start: 0.4487 (mmp) cc_final: 0.4155 (tpp)
REVERT: D  391 ARG cc_start: 0.7759 (mtt180) cc_final: 0.7167 (tpt170)
REVERT: E  109 GLN cc_start: 0.8256 (tm-30) cc_final: 0.8030 (pp30)
REVERT: E  391 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7517 (tpt-90)
  outliers start: 15
  outliers final: 11
  residues processed: 189
  average time/residue: 0.5563
  time to fit residues: 114.2855
Evaluate side-chains
  185 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 171
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  385 SER
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain D residue  359 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 115 optimal weight:    0.4980
   chunk 133 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 154 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 134 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
B 223 HIS
E 223 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.113503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.081382 restraints weight = 72801.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 4.52
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3059
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3059 r_free = 0.3059    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3059 r_free = 0.3059    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3059
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13155  Z= 0.167
  Angle     :  0.546  11.562  17785  Z= 0.273
  Chirality :  0.038   0.131   2060
  Planarity :  0.003   0.031   2250
  Dihedral  :  3.631  14.999   1740
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 12.46 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  4.17 (0.22), residues: 1595
  helix:  3.42 (0.15), residues: 1105
  sheet:  2.95 (0.34), residues: 145
  loop :  0.25 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 228 
 TYR   0.029   0.002   TYR A 108 
 PHE   0.017   0.001   PHE C 352 
 TRP   0.005   0.001   TRP D 162 
 HIS   0.001   0.001   HIS B 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (13155)
  covalent geometry    : angle       0.54602 (17785)
  hydrogen bonds       : bond        0.06358 ( 1000)
  hydrogen bonds       : angle       3.69854 ( 2905)

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 170
  time to evaluate  : 0.486 
Fit side-chains
REVERT: A  139 TYR cc_start: 0.9369 (p90) cc_final: 0.8973 (p90)
REVERT: A  213 GLU cc_start: 0.8170 (tt0) cc_final: 0.7925 (tm-30)
REVERT: A  257 GLU cc_start: 0.8375 (tt0) cc_final: 0.7698 (tp30)
REVERT: A  266 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8268 (tp30)
REVERT: A  361 MET cc_start: 0.8646 (ptp) cc_final: 0.8079 (ppp)
REVERT: A  382 PHE cc_start: 0.8422 (m-80) cc_final: 0.8178 (m-80)
REVERT: A  383 MET cc_start: 0.5418 (mmp) cc_final: 0.5082 (mpp)
REVERT: B  257 GLU cc_start: 0.7607 (tp30) cc_final: 0.6651 (tp30)
REVERT: B  261 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6055 (mp0)
REVERT: B  383 MET cc_start: 0.4345 (mmp) cc_final: 0.3963 (mtm)
REVERT: B  391 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7355 (tpt170)
REVERT: C  137 MET cc_start: 0.8984 (mtm) cc_final: 0.8748 (mtt)
REVERT: C  383 MET cc_start: 0.5279 (mmp) cc_final: 0.5026 (tpp)
REVERT: C  391 ARG cc_start: 0.7369 (mtt180) cc_final: 0.6882 (tpt170)
REVERT: D  108 TYR cc_start: 0.8700 (m-10) cc_final: 0.8399 (m-80)
REVERT: D  137 MET cc_start: 0.9089 (mtm) cc_final: 0.8791 (mtt)
REVERT: D  139 TYR cc_start: 0.9396 (p90) cc_final: 0.9093 (p90)
REVERT: D  250 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8569 (pt)
REVERT: D  257 GLU cc_start: 0.8385 (tt0) cc_final: 0.7720 (tp30)
REVERT: D  359 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.7094 (t80)
REVERT: D  391 ARG cc_start: 0.7889 (mtt180) cc_final: 0.7284 (tpt170)
REVERT: E  109 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7839 (pp30)
REVERT: E  190 GLU cc_start: 0.8381 (tt0) cc_final: 0.7738 (tt0)
REVERT: E  391 ARG cc_start: 0.7950 (mtt180) cc_final: 0.7468 (tpt-90)
  outliers start: 16
  outliers final: 12
  residues processed: 182
  average time/residue: 0.5605
  time to fit residues: 110.7029
Evaluate side-chains
  179 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 164
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  385 SER
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  385 SER
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain E residue  385 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 101 optimal weight:    0.6980
   chunk 104 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 83 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 106 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B 223 HIS
E 223 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.114725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.083244 restraints weight = 49942.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 3.89
r_work: 0.2910 rms_B_bonded: 4.64 restraints_weight: 0.5000
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2894
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2894
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13155  Z= 0.125
  Angle     :  0.517  12.174  17785  Z= 0.256
  Chirality :  0.037   0.127   2060
  Planarity :  0.003   0.032   2250
  Dihedral  :  3.472  14.411   1740
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 12.75 %
    Favored  : 86.06 %
  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:  4.33 (0.22), residues: 1595
  helix:  3.54 (0.15), residues: 1105
  sheet:  3.02 (0.34), residues: 145
  loop :  0.30 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 228 
 TYR   0.029   0.002   TYR A 108 
 PHE   0.017   0.001   PHE C 352 
 TRP   0.006   0.001   TRP D 162 
 HIS   0.002   0.000   HIS E 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (13155)
  covalent geometry    : angle       0.51682 (17785)
  hydrogen bonds       : bond        0.05691 ( 1000)
  hydrogen bonds       : angle       3.53791 ( 2905)

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 182
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9458 (p90) cc_final: 0.9032 (p90)
REVERT: A  213 GLU cc_start: 0.8554 (tt0) cc_final: 0.8235 (tm-30)
REVERT: A  257 GLU cc_start: 0.8673 (tt0) cc_final: 0.7940 (tp30)
REVERT: A  266 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8516 (tp30)
REVERT: A  382 PHE cc_start: 0.8388 (m-80) cc_final: 0.8096 (m-80)
REVERT: A  383 MET cc_start: 0.5210 (mmp) cc_final: 0.4939 (mpp)
REVERT: B  257 GLU cc_start: 0.7894 (tp30) cc_final: 0.6663 (tp30)
REVERT: B  261 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.5823 (mp0)
REVERT: B  383 MET cc_start: 0.4182 (mmp) cc_final: 0.3841 (mtm)
REVERT: B  391 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7350 (tpt170)
REVERT: C  359 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.7084 (m-80)
REVERT: C  383 MET cc_start: 0.5139 (mmp) cc_final: 0.4899 (tpp)
REVERT: C  391 ARG cc_start: 0.7428 (mtt180) cc_final: 0.6888 (tpt170)
REVERT: D  108 TYR cc_start: 0.8788 (m-10) cc_final: 0.8513 (m-80)
REVERT: D  137 MET cc_start: 0.9121 (mtm) cc_final: 0.8878 (mtt)
REVERT: D  139 TYR cc_start: 0.9474 (p90) cc_final: 0.9214 (p90)
REVERT: D  250 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8595 (pt)
REVERT: D  257 GLU cc_start: 0.8644 (tt0) cc_final: 0.7926 (tp30)
REVERT: D  352 PHE cc_start: 0.8467 (m-80) cc_final: 0.8225 (m-80)
REVERT: D  359 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.7146 (t80)
REVERT: D  391 ARG cc_start: 0.7907 (mtt180) cc_final: 0.7231 (tpt170)
REVERT: E  109 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7990 (pp30)
REVERT: E  250 ILE cc_start: 0.8862 (mm) cc_final: 0.8538 (pt)
REVERT: E  391 ARG cc_start: 0.7860 (mtt180) cc_final: 0.7397 (tpt-90)
  outliers start: 17
  outliers final: 8
  residues processed: 192
  average time/residue: 0.5815
  time to fit residues: 120.7333
Evaluate side-chains
  183 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 171
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain E residue  349 LEU
Chi-restraints excluded: chain E residue  385 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   chunk 155 optimal weight:    8.9990
   chunk 153 optimal weight:    4.9990
   chunk 105 optimal weight:   10.0000
   chunk 113 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
B 223 HIS
E 223 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.107780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.075867 restraints weight = 54717.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 4.04
r_work: 0.2824 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2834
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2834
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  13155  Z= 0.216
  Angle     :  0.595  13.008  17785  Z= 0.296
  Chirality :  0.040   0.137   2060
  Planarity :  0.004   0.032   2250
  Dihedral  :  3.699  15.271   1740
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 13.38 %
    Favored  : 85.56 %
  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:  4.08 (0.21), residues: 1595
  helix:  3.35 (0.15), residues: 1105
  sheet:  2.93 (0.35), residues: 145
  loop :  0.23 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 301 
 TYR   0.035   0.003   TYR A 108 
 PHE   0.015   0.002   PHE E  86 
 TRP   0.005   0.001   TRP B 375 
 HIS   0.002   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 (13155)
  covalent geometry    : angle       0.59526 (17785)
  hydrogen bonds       : bond        0.06762 ( 1000)
  hydrogen bonds       : angle       3.80561 ( 2905)

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 172
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9474 (p90) cc_final: 0.9131 (p90)
REVERT: A  213 GLU cc_start: 0.8648 (tt0) cc_final: 0.8274 (tm-30)
REVERT: A  257 GLU cc_start: 0.8793 (tt0) cc_final: 0.8080 (tp30)
REVERT: A  266 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8517 (tp30)
REVERT: A  382 PHE cc_start: 0.8516 (m-80) cc_final: 0.8302 (m-80)
REVERT: A  383 MET cc_start: 0.5474 (mmp) cc_final: 0.5168 (mpp)
REVERT: B  257 GLU cc_start: 0.8115 (tp30) cc_final: 0.7813 (tp30)
REVERT: B  383 MET cc_start: 0.4242 (mmp) cc_final: 0.3878 (mtm)
REVERT: B  391 ARG cc_start: 0.7911 (mtt180) cc_final: 0.7455 (tpt170)
REVERT: C  383 MET cc_start: 0.5256 (mmp) cc_final: 0.4996 (tpp)
REVERT: C  391 ARG cc_start: 0.7464 (mtt180) cc_final: 0.6936 (tpt170)
REVERT: D  108 TYR cc_start: 0.8891 (m-10) cc_final: 0.8614 (m-80)
REVERT: D  137 MET cc_start: 0.9290 (mtm) cc_final: 0.9081 (mtt)
REVERT: D  139 TYR cc_start: 0.9484 (p90) cc_final: 0.9277 (p90)
REVERT: D  250 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8759 (pt)
REVERT: D  257 GLU cc_start: 0.8741 (tt0) cc_final: 0.8060 (tp30)
REVERT: D  352 PHE cc_start: 0.8526 (m-80) cc_final: 0.8310 (m-80)
REVERT: D  391 ARG cc_start: 0.7849 (mtt180) cc_final: 0.7227 (tpt170)
REVERT: E  391 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7410 (tpt170)
  outliers start: 15
  outliers final: 9
  residues processed: 183
  average time/residue: 0.5478
  time to fit residues: 108.7789
Evaluate side-chains
  174 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 164
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  385 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 122 optimal weight:    2.9990
   chunk 144 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 84 optimal weight:    4.9990
   chunk 116 optimal weight:    7.9990
   chunk 117 optimal weight:    0.7980
   chunk 72 optimal weight:    0.4980
   chunk 67 optimal weight:    0.3980
   chunk 83 optimal weight:    0.5980
   chunk 135 optimal weight:    4.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 223 HIS
E 223 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.115325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.083118 restraints weight = 63471.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 4.37
r_work: 0.2901 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2885
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2885 r_free = 0.2885    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2885 r_free = 0.2885    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2885
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13155  Z= 0.121
  Angle     :  0.542  13.466  17785  Z= 0.266
  Chirality :  0.037   0.142   2060
  Planarity :  0.003   0.031   2250
  Dihedral  :  3.499  14.660   1740
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 13.73 %
    Favored  : 85.42 %
  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:  4.25 (0.21), residues: 1595
  helix:  3.51 (0.15), residues: 1085
  sheet:  3.02 (0.34), residues: 145
  loop :  0.34 (0.38), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 301 
 TYR   0.032   0.002   TYR A 108 
 PHE   0.020   0.001   PHE A 352 
 TRP   0.008   0.001   TRP D 162 
 HIS   0.002   0.000   HIS B 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (13155)
  covalent geometry    : angle       0.54239 (17785)
  hydrogen bonds       : bond        0.05683 ( 1000)
  hydrogen bonds       : angle       3.58096 ( 2905)

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 178
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9440 (p90) cc_final: 0.8995 (p90)
REVERT: A  213 GLU cc_start: 0.8559 (tt0) cc_final: 0.8243 (tm-30)
REVERT: A  250 ILE cc_start: 0.8876 (mm) cc_final: 0.8553 (pt)
REVERT: A  257 GLU cc_start: 0.8684 (tt0) cc_final: 0.7951 (tp30)
REVERT: A  266 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8518 (tp30)
REVERT: A  382 PHE cc_start: 0.8403 (m-80) cc_final: 0.8091 (m-80)
REVERT: A  383 MET cc_start: 0.5249 (mmp) cc_final: 0.4949 (mpp)
REVERT: B  250 ILE cc_start: 0.8800 (mm) cc_final: 0.8593 (pt)
REVERT: B  257 GLU cc_start: 0.7853 (tp30) cc_final: 0.6977 (tp30)
REVERT: B  261 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.5985 (mp0)
REVERT: B  355 MET cc_start: 0.7987 (ttm) cc_final: 0.7743 (ttp)
REVERT: B  383 MET cc_start: 0.4034 (mmp) cc_final: 0.3679 (mtm)
REVERT: B  391 ARG cc_start: 0.7770 (mtt180) cc_final: 0.7392 (tpt170)
REVERT: C  383 MET cc_start: 0.5171 (mmp) cc_final: 0.4899 (tpp)
REVERT: C  391 ARG cc_start: 0.7365 (mtt180) cc_final: 0.6854 (tpt170)
REVERT: D  108 TYR cc_start: 0.8775 (m-10) cc_final: 0.8535 (m-80)
REVERT: D  137 MET cc_start: 0.9124 (mtm) cc_final: 0.8883 (mtt)
REVERT: D  139 TYR cc_start: 0.9468 (p90) cc_final: 0.9181 (p90)
REVERT: D  250 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8609 (pt)
REVERT: D  257 GLU cc_start: 0.8664 (tt0) cc_final: 0.7951 (tp30)
REVERT: D  352 PHE cc_start: 0.8440 (m-80) cc_final: 0.8203 (m-80)
REVERT: E  109 GLN cc_start: 0.8259 (tm-30) cc_final: 0.8005 (pp30)
REVERT: E  391 ARG cc_start: 0.7818 (mtt180) cc_final: 0.7302 (tpt170)
  outliers start: 12
  outliers final: 6
  residues processed: 187
  average time/residue: 0.5343
  time to fit residues: 108.6453
Evaluate side-chains
  181 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 173
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain E residue   97 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 141 optimal weight:    4.9990
   chunk 146 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 107 optimal weight:    0.8980
   chunk 96 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 139 optimal weight:    0.8980
   chunk 90 optimal weight:    0.5980
   chunk 104 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 223 HIS
E 223 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.114900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.082502 restraints weight = 67967.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 4.57
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3104
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3104
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13155  Z= 0.127
  Angle     :  0.544  13.214  17785  Z= 0.267
  Chirality :  0.037   0.138   2060
  Planarity :  0.003   0.033   2250
  Dihedral  :  3.471  14.468   1740
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 13.87 %
    Favored  : 85.56 %
  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:  4.26 (0.22), residues: 1595
  helix:  3.47 (0.15), residues: 1105
  sheet:  3.02 (0.35), residues: 145
  loop :  0.32 (0.41), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 301 
 TYR   0.035   0.002   TYR A 108 
 PHE   0.021   0.001   PHE E 352 
 TRP   0.006   0.001   TRP D 162 
 HIS   0.002   0.000   HIS E 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (13155)
  covalent geometry    : angle       0.54425 (17785)
  hydrogen bonds       : bond        0.05699 ( 1000)
  hydrogen bonds       : angle       3.59506 ( 2905)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4015.43 seconds
wall clock time: 68 minutes 57.89 seconds (4137.89 seconds total)