Starting phenix.real_space_refine
on Thu May 15 07:34:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ip6_35633/05_2025/8ip6_35633.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ip6_35633/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ip6_35633/05_2025/8ip6_35633.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ip6_35633/05_2025/8ip6_35633.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ip6_35633/05_2025/8ip6_35633.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ip6_35633/05_2025/8ip6_35633.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.047
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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: 13.71, per 1000 atoms: 1.06
  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: 3.26
  Conformation dependent library (CDL) restraints added in 3.2 seconds
  

  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: 1.26
  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: 3.71

  Time building geometry restraints manager: 3.80 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:             0.840
  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:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     38.180
  Find NCS groups from input model:        0.650
  Set up NCS constraints:                  0.080
  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:             0.010
  Load rotamer database and sin/cos tables:11.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.520
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.004   0.001   TRP E 162 
 HIS   0.002   0.000   HIS B 371 
 PHE   0.014   0.001   PHE D  86 
 TYR   0.014   0.001   TYR C 299 
 ARG   0.001   0.000   ARG E 102 

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

*********************** 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  : 1.368 
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: 1.2576
  time to fit residues: 366.5508
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  : 1.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 135 optimal weight:    5.9990
   chunk 121 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 41 optimal weight:    0.3980
   chunk 81 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   chunk 125 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 93 optimal weight:    5.9990
   chunk 145 optimal weight:    3.9990
   overall best weight:    2.6788

-------------------------------------------------------------------------------
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 = 0.3589 r_free = 0.3589 target = 0.112434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.079947 restraints weight = 65192.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3032 rms_B_bonded: 4.30
r_work: 0.2810 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2803
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803    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 = 0.2803 r_free = 0.2803    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2803
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035  13155  Z= 0.243
  Angle     :  0.606   8.215  17785  Z= 0.308
  Chirality :  0.041   0.146   2060
  Planarity :  0.004   0.029   2250
  Dihedral  :  3.733  14.384   1740
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  :  8.73 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.11 (0.21), residues: 1595
  helix:  3.41 (0.15), residues: 1105
  sheet:  2.94 (0.33), residues: 145
  loop :  0.07 (0.38), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 196 
 HIS   0.003   0.001   HIS E 122 
 PHE   0.022   0.002   PHE E  86 
 TYR   0.024   0.002   TYR C 154 
 ARG   0.005   0.001   ARG A 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07033 ( 1000)
  hydrogen bonds       : angle       3.83393 ( 2905)
  covalent geometry    : bond        0.00572 (13155)
  covalent geometry    : angle       0.60572 (17785)

*********************** 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
  206 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 179
  time to evaluate  : 1.390 
Fit side-chains
REVERT: A  124 MET cc_start: 0.8483 (tpp) cc_final: 0.8259 (tpp)
REVERT: A  139 TYR cc_start: 0.9468 (p90) cc_final: 0.9067 (p90)
REVERT: A  257 GLU cc_start: 0.8710 (tt0) cc_final: 0.7999 (tp30)
REVERT: A  266 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8503 (tp30)
REVERT: A  361 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8028 (ppp)
REVERT: A  382 PHE cc_start: 0.8516 (m-80) cc_final: 0.8078 (m-80)
REVERT: A  383 MET cc_start: 0.5338 (mmp) cc_final: 0.5062 (mpp)
REVERT: B  257 GLU cc_start: 0.8055 (tp30) cc_final: 0.7791 (tp30)
REVERT: B  261 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7235 (mp0)
REVERT: B  383 MET cc_start: 0.4665 (mmp) cc_final: 0.4356 (mtm)
REVERT: B  391 ARG cc_start: 0.7893 (mtt180) cc_final: 0.7429 (tpt170)
REVERT: C  383 MET cc_start: 0.5335 (mmp) cc_final: 0.5077 (tpp)
REVERT: C  391 ARG cc_start: 0.7427 (mtt180) cc_final: 0.6955 (tpt170)
REVERT: D  108 TYR cc_start: 0.8813 (m-10) cc_final: 0.8535 (m-80)
REVERT: D  139 TYR cc_start: 0.9488 (p90) cc_final: 0.9228 (p90)
REVERT: D  257 GLU cc_start: 0.8666 (tt0) cc_final: 0.7926 (tp30)
REVERT: D  291 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8530 (mm-30)
REVERT: D  383 MET cc_start: 0.4687 (mmp) cc_final: 0.4354 (tpp)
REVERT: D  391 ARG cc_start: 0.7903 (mtt180) cc_final: 0.7241 (tpt170)
REVERT: E  109 GLN cc_start: 0.8361 (tm-30) cc_final: 0.8103 (pp30)
REVERT: E  190 GLU cc_start: 0.8992 (tt0) cc_final: 0.8170 (pt0)
REVERT: E  383 MET cc_start: 0.5186 (mmp) cc_final: 0.4612 (mpt)
REVERT: E  391 ARG cc_start: 0.7818 (mtt180) cc_final: 0.7338 (tpt170)
  outliers start: 27
  outliers final: 7
  residues processed: 192
  average time/residue: 1.2656
  time to fit residues: 264.0565
Evaluate side-chains
  172 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 163
  time to evaluate  : 1.461 
-------------------------------------------------------------------------------
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  361 MET
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
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9980
   chunk 149 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 101 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.115054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.082846 restraints weight = 60789.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3093 rms_B_bonded: 4.26
r_work: 0.2877 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2877
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2877
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13155  Z= 0.130
  Angle     :  0.513   9.262  17785  Z= 0.260
  Chirality :  0.037   0.131   2060
  Planarity :  0.003   0.031   2250
  Dihedral  :  3.525  14.575   1740
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  9.86 %
    Favored  : 88.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.40 (0.21), residues: 1595
  helix:  3.60 (0.15), residues: 1090
  sheet:  3.03 (0.33), residues: 145
  loop :  0.50 (0.38), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 162 
 HIS   0.002   0.000   HIS E 223 
 PHE   0.014   0.001   PHE C 352 
 TYR   0.027   0.002   TYR C 154 
 ARG   0.005   0.000   ARG B 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05898 ( 1000)
  hydrogen bonds       : angle       3.56295 ( 2905)
  covalent geometry    : bond        0.00266 (13155)
  covalent geometry    : angle       0.51299 (17785)

*********************** 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
  206 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 188
  time to evaluate  : 1.482 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9458 (p90) cc_final: 0.9014 (p90)
REVERT: A  257 GLU cc_start: 0.8683 (tt0) cc_final: 0.7936 (tp30)
REVERT: A  266 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8472 (tp30)
REVERT: A  383 MET cc_start: 0.5259 (mmp) cc_final: 0.5004 (mpp)
REVERT: B  257 GLU cc_start: 0.8031 (tp30) cc_final: 0.7662 (tp30)
REVERT: B  261 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6867 (mp0)
REVERT: B  383 MET cc_start: 0.4745 (mmp) cc_final: 0.4417 (mtm)
REVERT: B  391 ARG cc_start: 0.7895 (mtt180) cc_final: 0.7437 (tpt170)
REVERT: C  137 MET cc_start: 0.9065 (mtm) cc_final: 0.8780 (mtt)
REVERT: C  383 MET cc_start: 0.5252 (mmp) cc_final: 0.4989 (tpp)
REVERT: C  391 ARG cc_start: 0.7387 (mtt180) cc_final: 0.6890 (tpt170)
REVERT: D  108 TYR cc_start: 0.8764 (m-10) cc_final: 0.8495 (m-80)
REVERT: D  139 TYR cc_start: 0.9499 (p90) cc_final: 0.9247 (p90)
REVERT: D  190 GLU cc_start: 0.8897 (tt0) cc_final: 0.8290 (tt0)
REVERT: D  257 GLU cc_start: 0.8704 (tt0) cc_final: 0.7983 (tp30)
REVERT: D  291 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8412 (mm-30)
REVERT: D  383 MET cc_start: 0.4532 (mmp) cc_final: 0.4198 (tpp)
REVERT: D  391 ARG cc_start: 0.7847 (mtt180) cc_final: 0.7215 (tpt170)
REVERT: E  266 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8427 (tp30)
REVERT: E  383 MET cc_start: 0.5056 (mmp) cc_final: 0.4475 (mpt)
REVERT: E  391 ARG cc_start: 0.7839 (mtt180) cc_final: 0.7357 (tpt170)
  outliers start: 18
  outliers final: 8
  residues processed: 198
  average time/residue: 1.3148
  time to fit residues: 283.2433
Evaluate side-chains
  180 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 171
  time to evaluate  : 1.377 
-------------------------------------------------------------------------------
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  385 SER
Chi-restraints excluded: chain C residue  256 LEU
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 157 optimal weight:   10.0000
   chunk 110 optimal weight:    5.9990
   chunk 120 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3596 r_free = 0.3596 target = 0.111789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.079519 restraints weight = 63689.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 4.31
r_work: 0.2823 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2815
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2815 r_free = 0.2815    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2815 r_free = 0.2815    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2815
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  13155  Z= 0.202
  Angle     :  0.557   9.799  17785  Z= 0.284
  Chirality :  0.039   0.136   2060
  Planarity :  0.004   0.031   2250
  Dihedral  :  3.700  14.731   1740
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.48 %
    Favored  : 87.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.13 (0.21), residues: 1595
  helix:  3.38 (0.15), residues: 1105
  sheet:  3.05 (0.33), residues: 145
  loop :  0.21 (0.39), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 196 
 HIS   0.002   0.001   HIS A 288 
 PHE   0.017   0.002   PHE E  86 
 TYR   0.027   0.002   TYR C 154 
 ARG   0.005   0.000   ARG E 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06679 ( 1000)
  hydrogen bonds       : angle       3.74339 ( 2905)
  covalent geometry    : bond        0.00470 (13155)
  covalent geometry    : angle       0.55742 (17785)

*********************** 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
  186 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 170
  time to evaluate  : 1.479 
Fit side-chains
REVERT: A  139 TYR cc_start: 0.9465 (p90) cc_final: 0.9083 (p90)
REVERT: A  257 GLU cc_start: 0.8715 (tt0) cc_final: 0.7979 (tp30)
REVERT: A  266 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8458 (tp30)
REVERT: A  361 MET cc_start: 0.8686 (ptp) cc_final: 0.8051 (ppp)
REVERT: A  383 MET cc_start: 0.5334 (mmp) cc_final: 0.5054 (mpp)
REVERT: B  257 GLU cc_start: 0.7988 (tp30) cc_final: 0.7642 (tp30)
REVERT: B  261 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7102 (mp0)
REVERT: B  383 MET cc_start: 0.4392 (mmp) cc_final: 0.4049 (mtm)
REVERT: B  391 ARG cc_start: 0.7907 (mtt180) cc_final: 0.7388 (tpt170)
REVERT: C  137 MET cc_start: 0.9211 (mtm) cc_final: 0.9001 (mtt)
REVERT: C  383 MET cc_start: 0.5204 (mmp) cc_final: 0.4934 (tpp)
REVERT: C  391 ARG cc_start: 0.7409 (mtt180) cc_final: 0.6887 (tpt170)
REVERT: D  108 TYR cc_start: 0.8791 (m-10) cc_final: 0.8534 (m-80)
REVERT: D  137 MET cc_start: 0.9172 (mtm) cc_final: 0.8923 (mtt)
REVERT: D  139 TYR cc_start: 0.9465 (p90) cc_final: 0.9227 (p90)
REVERT: D  257 GLU cc_start: 0.8692 (tt0) cc_final: 0.7996 (tp30)
REVERT: D  383 MET cc_start: 0.4542 (mmp) cc_final: 0.4236 (mpp)
REVERT: D  391 ARG cc_start: 0.7902 (mtt180) cc_final: 0.7242 (tpt170)
REVERT: E  190 GLU cc_start: 0.8952 (tt0) cc_final: 0.8123 (pt0)
REVERT: E  383 MET cc_start: 0.5012 (mmp) cc_final: 0.4437 (mpt)
REVERT: E  391 ARG cc_start: 0.7878 (mtt180) cc_final: 0.7372 (tpt170)
  outliers start: 16
  outliers final: 8
  residues processed: 182
  average time/residue: 1.2860
  time to fit residues: 254.3673
Evaluate side-chains
  170 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 161
  time to evaluate  : 1.553 
-------------------------------------------------------------------------------
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  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 E residue  385 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 158 optimal weight:   10.0000
   chunk 138 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 136 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 137 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 156 optimal weight:   20.0000
   chunk 71 optimal weight:    2.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3569 r_free = 0.3569 target = 0.107211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.074401 restraints weight = 76449.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 4.73
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3029
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3029
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039  13155  Z= 0.235
  Angle     :  0.587  10.438  17785  Z= 0.298
  Chirality :  0.040   0.137   2060
  Planarity :  0.004   0.031   2250
  Dihedral  :  3.821  15.305   1740
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.90 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.95 (0.21), residues: 1595
  helix:  3.26 (0.15), residues: 1105
  sheet:  2.85 (0.34), residues: 145
  loop :  0.18 (0.39), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 196 
 HIS   0.002   0.001   HIS A 288 
 PHE   0.016   0.002   PHE E  86 
 TYR   0.029   0.003   TYR B 108 
 ARG   0.005   0.000   ARG E 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07027 ( 1000)
  hydrogen bonds       : angle       3.86809 ( 2905)
  covalent geometry    : bond        0.00553 (13155)
  covalent geometry    : angle       0.58657 (17785)

*********************** 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
  186 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 168
  time to evaluate  : 1.565 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9349 (p90) cc_final: 0.8953 (p90)
REVERT: A  213 GLU cc_start: 0.8205 (tt0) cc_final: 0.7950 (tm-30)
REVERT: A  257 GLU cc_start: 0.8410 (tt0) cc_final: 0.7773 (tp30)
REVERT: A  266 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8307 (tp30)
REVERT: A  361 MET cc_start: 0.8593 (ptp) cc_final: 0.8038 (ppp)
REVERT: A  382 PHE cc_start: 0.8468 (m-80) cc_final: 0.8191 (m-80)
REVERT: A  383 MET cc_start: 0.5531 (mmp) cc_final: 0.5184 (mpp)
REVERT: B  257 GLU cc_start: 0.7663 (tp30) cc_final: 0.7265 (tp30)
REVERT: B  261 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6761 (mp0)
REVERT: B  383 MET cc_start: 0.4552 (mmp) cc_final: 0.4198 (mtm)
REVERT: B  391 ARG cc_start: 0.7871 (mtt180) cc_final: 0.7410 (tpt170)
REVERT: C  137 MET cc_start: 0.9091 (mtm) cc_final: 0.8765 (mtt)
REVERT: C  383 MET cc_start: 0.5491 (mmp) cc_final: 0.5224 (tpp)
REVERT: C  391 ARG cc_start: 0.7431 (mtt180) cc_final: 0.6918 (tpt170)
REVERT: D  108 TYR cc_start: 0.8687 (m-10) cc_final: 0.8417 (m-80)
REVERT: D  137 MET cc_start: 0.9116 (mtm) cc_final: 0.8829 (mtt)
REVERT: D  139 TYR cc_start: 0.9381 (p90) cc_final: 0.9117 (p90)
REVERT: D  257 GLU cc_start: 0.8346 (tt0) cc_final: 0.7721 (tp30)
REVERT: D  383 MET cc_start: 0.4742 (mmp) cc_final: 0.4420 (tpp)
REVERT: D  391 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7288 (tpt170)
REVERT: E  391 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7502 (tpt-90)
  outliers start: 18
  outliers final: 10
  residues processed: 180
  average time/residue: 1.2836
  time to fit residues: 250.9022
Evaluate side-chains
  175 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 164
  time to evaluate  : 1.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  390 ARG
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 64 optimal weight:    5.9990
   chunk 97 optimal weight:    0.8980
   chunk 109 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 111 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.9182

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.114382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.082032 restraints weight = 65826.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 4.40
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2140

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= 0.128
  Angle     :  0.514  11.208  17785  Z= 0.257
  Chirality :  0.037   0.186   2060
  Planarity :  0.003   0.034   2250
  Dihedral  :  3.555  14.721   1740
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 12.75 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.29 (0.21), residues: 1595
  helix:  3.53 (0.15), residues: 1085
  sheet:  3.03 (0.34), residues: 145
  loop :  0.42 (0.38), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 162 
 HIS   0.002   0.000   HIS E 223 
 PHE   0.018   0.001   PHE A 352 
 TYR   0.028   0.002   TYR C 154 
 ARG   0.004   0.000   ARG E 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05867 ( 1000)
  hydrogen bonds       : angle       3.60134 ( 2905)
  covalent geometry    : bond        0.00261 (13155)
  covalent geometry    : angle       0.51354 (17785)

*********************** 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
  186 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 175
  time to evaluate  : 1.412 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9359 (p90) cc_final: 0.8938 (p90)
REVERT: A  213 GLU cc_start: 0.8146 (tt0) cc_final: 0.7940 (tm-30)
REVERT: A  257 GLU cc_start: 0.8349 (tt0) cc_final: 0.7652 (tp30)
REVERT: A  266 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8339 (tp30)
REVERT: A  382 PHE cc_start: 0.8369 (m-80) cc_final: 0.8060 (m-80)
REVERT: A  383 MET cc_start: 0.5327 (mmp) cc_final: 0.4997 (mpp)
REVERT: B  257 GLU cc_start: 0.7591 (tp30) cc_final: 0.6416 (tp30)
REVERT: B  261 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.5587 (mp0)
REVERT: B  383 MET cc_start: 0.4449 (mmp) cc_final: 0.4127 (mtm)
REVERT: B  391 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7332 (tpt170)
REVERT: C  137 MET cc_start: 0.9037 (mtm) cc_final: 0.8797 (mtt)
REVERT: C  383 MET cc_start: 0.5313 (mmp) cc_final: 0.5019 (tpp)
REVERT: C  391 ARG cc_start: 0.7373 (mtt180) cc_final: 0.6893 (tpt170)
REVERT: D  108 TYR cc_start: 0.8661 (m-10) cc_final: 0.8392 (m-80)
REVERT: D  137 MET cc_start: 0.9067 (mtm) cc_final: 0.8770 (mtt)
REVERT: D  139 TYR cc_start: 0.9404 (p90) cc_final: 0.9094 (p90)
REVERT: D  257 GLU cc_start: 0.8354 (tt0) cc_final: 0.7661 (tp30)
REVERT: D  383 MET cc_start: 0.4732 (mmp) cc_final: 0.4423 (mpp)
REVERT: D  391 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7225 (tpt170)
REVERT: E  391 ARG cc_start: 0.7973 (mtt180) cc_final: 0.7547 (tpt-90)
  outliers start: 11
  outliers final: 6
  residues processed: 183
  average time/residue: 1.2171
  time to fit residues: 242.6862
Evaluate side-chains
  170 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 163
  time to evaluate  : 1.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 SER
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  385 SER
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  390 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 110 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 139 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 20 optimal weight:    0.0570
   chunk 154 optimal weight:    5.9990
   chunk 147 optimal weight:    2.9990
   chunk 131 optimal weight:    0.7980
   chunk 92 optimal weight:   20.0000
   overall best weight:    1.3502

-------------------------------------------------------------------------------
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 = 0.3620 r_free = 0.3620 target = 0.113499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.081165 restraints weight = 69494.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 4.50
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3064
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.2190

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= 0.148
  Angle     :  0.539  11.590  17785  Z= 0.268
  Chirality :  0.038   0.169   2060
  Planarity :  0.003   0.032   2250
  Dihedral  :  3.584  14.818   1740
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 12.82 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.20 (0.22), residues: 1595
  helix:  3.42 (0.15), residues: 1105
  sheet:  3.08 (0.34), residues: 145
  loop :  0.31 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 162 
 HIS   0.001   0.001   HIS E 223 
 PHE   0.017   0.001   PHE E 352 
 TYR   0.028   0.002   TYR B 108 
 ARG   0.003   0.000   ARG E 301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06093 ( 1000)
  hydrogen bonds       : angle       3.63924 ( 2905)
  covalent geometry    : bond        0.00327 (13155)
  covalent geometry    : angle       0.53859 (17785)

*********************** 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
  187 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 173
  time to evaluate  : 1.400 
Fit side-chains
REVERT: A  139 TYR cc_start: 0.9371 (p90) cc_final: 0.8966 (p90)
REVERT: A  213 GLU cc_start: 0.8157 (tt0) cc_final: 0.7948 (tm-30)
REVERT: A  257 GLU cc_start: 0.8373 (tt0) cc_final: 0.7678 (tp30)
REVERT: A  266 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8330 (tp30)
REVERT: A  383 MET cc_start: 0.5337 (mmp) cc_final: 0.5016 (mpp)
REVERT: B  257 GLU cc_start: 0.7543 (tp30) cc_final: 0.6499 (tp30)
REVERT: B  261 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.5658 (mp0)
REVERT: B  383 MET cc_start: 0.4322 (mmp) cc_final: 0.3939 (mtm)
REVERT: B  391 ARG cc_start: 0.7825 (mtt180) cc_final: 0.7348 (tpt170)
REVERT: C  137 MET cc_start: 0.9044 (mtm) cc_final: 0.8773 (mtt)
REVERT: C  297 GLU cc_start: 0.8117 (tt0) cc_final: 0.7806 (tt0)
REVERT: C  359 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7140 (m-80)
REVERT: C  383 MET cc_start: 0.5325 (mmp) cc_final: 0.5063 (tpp)
REVERT: C  391 ARG cc_start: 0.7302 (mtt180) cc_final: 0.6805 (tpt170)
REVERT: D  108 TYR cc_start: 0.8697 (m-10) cc_final: 0.8411 (m-80)
REVERT: D  137 MET cc_start: 0.9061 (mtm) cc_final: 0.8773 (mtt)
REVERT: D  139 TYR cc_start: 0.9400 (p90) cc_final: 0.9100 (p90)
REVERT: D  257 GLU cc_start: 0.8372 (tt0) cc_final: 0.7686 (tp30)
REVERT: D  383 MET cc_start: 0.4720 (mmp) cc_final: 0.4418 (mpp)
REVERT: D  391 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7271 (tpt170)
REVERT: E  190 GLU cc_start: 0.8374 (tt0) cc_final: 0.7727 (tt0)
REVERT: E  391 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7487 (tpt-90)
  outliers start: 14
  outliers final: 10
  residues processed: 182
  average time/residue: 1.2098
  time to fit residues: 240.0958
Evaluate side-chains
  177 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 165
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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  359 PHE
Chi-restraints excluded: chain C residue  385 SER
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  390 ARG
Chi-restraints excluded: chain E residue  349 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 145 optimal weight:    0.9990
   chunk 155 optimal weight:    9.9990
   chunk 54 optimal weight:    4.9990
   chunk 106 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 69 optimal weight:    0.7980
   chunk 94 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 151 optimal weight:    0.9980
   chunk 88 optimal weight:    3.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.3613 r_free = 0.3613 target = 0.112960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.080687 restraints weight = 71157.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 4.59
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3050
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3050
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13155  Z= 0.161
  Angle     :  0.554  12.338  17785  Z= 0.276
  Chirality :  0.038   0.160   2060
  Planarity :  0.003   0.032   2250
  Dihedral  :  3.618  14.905   1740
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 13.24 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.12 (0.21), residues: 1595
  helix:  3.36 (0.15), residues: 1105
  sheet:  3.03 (0.34), residues: 145
  loop :  0.29 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 162 
 HIS   0.002   0.001   HIS B 223 
 PHE   0.018   0.001   PHE A 352 
 TYR   0.030   0.002   TYR B 108 
 ARG   0.005   0.000   ARG E 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06261 ( 1000)
  hydrogen bonds       : angle       3.69324 ( 2905)
  covalent geometry    : bond        0.00364 (13155)
  covalent geometry    : angle       0.55359 (17785)

*********************** 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
  185 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 171
  time to evaluate  : 1.564 
Fit side-chains
REVERT: A  139 TYR cc_start: 0.9359 (p90) cc_final: 0.8914 (p90)
REVERT: A  250 ILE cc_start: 0.8852 (mm) cc_final: 0.8493 (pt)
REVERT: A  257 GLU cc_start: 0.8377 (tt0) cc_final: 0.7683 (tp30)
REVERT: A  266 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8259 (tp30)
REVERT: A  382 PHE cc_start: 0.8396 (m-80) cc_final: 0.8131 (m-80)
REVERT: A  383 MET cc_start: 0.5417 (mmp) cc_final: 0.5103 (mpp)
REVERT: B  257 GLU cc_start: 0.7591 (tp30) cc_final: 0.6622 (tp30)
REVERT: B  261 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6004 (mp0)
REVERT: B  383 MET cc_start: 0.4356 (mmp) cc_final: 0.3969 (mtm)
REVERT: B  391 ARG cc_start: 0.7906 (mtt180) cc_final: 0.7426 (tpt170)
REVERT: C  137 MET cc_start: 0.9090 (mtm) cc_final: 0.8862 (mtm)
REVERT: C  297 GLU cc_start: 0.8128 (tt0) cc_final: 0.7794 (tt0)
REVERT: C  383 MET cc_start: 0.5380 (mmp) cc_final: 0.5112 (tpp)
REVERT: C  391 ARG cc_start: 0.7443 (mtt180) cc_final: 0.6964 (tpt170)
REVERT: D  108 TYR cc_start: 0.8691 (m-10) cc_final: 0.8407 (m-80)
REVERT: D  137 MET cc_start: 0.8985 (mtm) cc_final: 0.8723 (mtt)
REVERT: D  139 TYR cc_start: 0.9395 (p90) cc_final: 0.9143 (p90)
REVERT: D  257 GLU cc_start: 0.8367 (tt0) cc_final: 0.7680 (tp30)
REVERT: D  352 PHE cc_start: 0.8335 (m-80) cc_final: 0.8109 (m-80)
REVERT: D  391 ARG cc_start: 0.7774 (mtt180) cc_final: 0.7028 (tpt170)
REVERT: E  190 GLU cc_start: 0.8390 (tt0) cc_final: 0.7743 (tt0)
REVERT: E  391 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7452 (tpt-90)
  outliers start: 14
  outliers final: 12
  residues processed: 183
  average time/residue: 1.2414
  time to fit residues: 248.0384
Evaluate side-chains
  180 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 167
  time to evaluate  : 1.368 
-------------------------------------------------------------------------------
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 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  338 LEU
Chi-restraints excluded: chain E residue   97 VAL
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 26 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 62 optimal weight:    8.9990
   chunk 105 optimal weight:    2.9990
   chunk 92 optimal weight:    0.2980
   chunk 57 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 144 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.3620 r_free = 0.3620 target = 0.113542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.081814 restraints weight = 54853.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 4.11
r_work: 0.2838 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2853
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2853
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.2271

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= 0.150
  Angle     :  0.561  13.066  17785  Z= 0.276
  Chirality :  0.038   0.160   2060
  Planarity :  0.003   0.033   2250
  Dihedral  :  3.588  14.820   1740
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 13.24 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.16 (0.21), residues: 1595
  helix:  3.39 (0.15), residues: 1105
  sheet:  3.01 (0.34), residues: 145
  loop :  0.30 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 162 
 HIS   0.002   0.001   HIS B 223 
 PHE   0.013   0.001   PHE B 352 
 TYR   0.031   0.002   TYR B 108 
 ARG   0.005   0.000   ARG E 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06153 ( 1000)
  hydrogen bonds       : angle       3.66692 ( 2905)
  covalent geometry    : bond        0.00334 (13155)
  covalent geometry    : angle       0.56117 (17785)

*********************** 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
  183 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 167
  time to evaluate  : 1.551 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9407 (p90) cc_final: 0.9000 (p90)
REVERT: A  257 GLU cc_start: 0.8728 (tt0) cc_final: 0.7992 (tp30)
REVERT: A  266 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8539 (tp30)
REVERT: A  361 MET cc_start: 0.8646 (ptp) cc_final: 0.8012 (ppp)
REVERT: A  383 MET cc_start: 0.5147 (mmp) cc_final: 0.4860 (mpp)
REVERT: B  257 GLU cc_start: 0.7915 (tp30) cc_final: 0.6931 (tp30)
REVERT: B  261 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6300 (mp0)
REVERT: B  383 MET cc_start: 0.4024 (mmp) cc_final: 0.3678 (mtm)
REVERT: B  391 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7458 (tpt170)
REVERT: C  137 MET cc_start: 0.9184 (mtm) cc_final: 0.8942 (mtt)
REVERT: C  297 GLU cc_start: 0.8479 (tt0) cc_final: 0.8193 (tt0)
REVERT: C  383 MET cc_start: 0.5166 (mmp) cc_final: 0.4917 (tpp)
REVERT: C  391 ARG cc_start: 0.7542 (mtt180) cc_final: 0.7151 (tpt170)
REVERT: D  108 TYR cc_start: 0.8794 (m-10) cc_final: 0.8513 (m-80)
REVERT: D  137 MET cc_start: 0.9134 (mtm) cc_final: 0.8884 (mtt)
REVERT: D  139 TYR cc_start: 0.9460 (p90) cc_final: 0.9229 (p90)
REVERT: D  257 GLU cc_start: 0.8689 (tt0) cc_final: 0.7973 (tp30)
REVERT: D  352 PHE cc_start: 0.8406 (m-80) cc_final: 0.8202 (m-80)
REVERT: D  391 ARG cc_start: 0.7854 (mtt180) cc_final: 0.7248 (tpt170)
REVERT: E  190 GLU cc_start: 0.8893 (tt0) cc_final: 0.8231 (tt0)
REVERT: E  391 ARG cc_start: 0.7875 (mtt180) cc_final: 0.7392 (tpt-90)
  outliers start: 16
  outliers final: 13
  residues processed: 180
  average time/residue: 1.2627
  time to fit residues: 247.4020
Evaluate side-chains
  174 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 160
  time to evaluate  : 1.529 
-------------------------------------------------------------------------------
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  261 GLU
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  338 LEU
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  349 LEU
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 134 optimal weight:    2.9990
   chunk 140 optimal weight:    1.9990
   chunk 148 optimal weight:    9.9990
   chunk 130 optimal weight:    0.8980
   chunk 59 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 84 optimal weight:   20.0000
   chunk 75 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 115 optimal weight:    3.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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 = 0.3581 r_free = 0.3581 target = 0.107918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.075330 restraints weight = 69833.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 4.58
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3027
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3027
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2381

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= 0.202
  Angle     :  0.592  13.457  17785  Z= 0.293
  Chirality :  0.039   0.151   2060
  Planarity :  0.004   0.032   2250
  Dihedral  :  3.704  15.254   1740
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 13.45 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.04 (0.21), residues: 1595
  helix:  3.30 (0.15), residues: 1105
  sheet:  2.89 (0.35), residues: 145
  loop :  0.29 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 196 
 HIS   0.002   0.001   HIS E 288 
 PHE   0.016   0.002   PHE A 352 
 TYR   0.036   0.003   TYR A 108 
 ARG   0.006   0.000   ARG E 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06631 ( 1000)
  hydrogen bonds       : angle       3.78903 ( 2905)
  covalent geometry    : bond        0.00471 (13155)
  covalent geometry    : angle       0.59173 (17785)

********************** 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
  176 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 162
  time to evaluate  : 1.419 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9313 (p90) cc_final: 0.8932 (p90)
REVERT: A  213 GLU cc_start: 0.8127 (tt0) cc_final: 0.7891 (tm-30)
REVERT: A  257 GLU cc_start: 0.8426 (tt0) cc_final: 0.7751 (tp30)
REVERT: A  266 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8307 (tp30)
REVERT: A  382 PHE cc_start: 0.8447 (m-80) cc_final: 0.8230 (m-80)
REVERT: A  383 MET cc_start: 0.5363 (mmp) cc_final: 0.5019 (mpp)
REVERT: B  257 GLU cc_start: 0.7602 (tp30) cc_final: 0.6611 (tp30)
REVERT: B  261 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6121 (mp0)
REVERT: B  383 MET cc_start: 0.4267 (mmp) cc_final: 0.3902 (mtm)
REVERT: B  391 ARG cc_start: 0.7935 (mtt180) cc_final: 0.7523 (tpt170)
REVERT: C  137 MET cc_start: 0.9142 (mtm) cc_final: 0.8876 (mtm)
REVERT: C  297 GLU cc_start: 0.8112 (tt0) cc_final: 0.7804 (tt0)
REVERT: C  383 MET cc_start: 0.5419 (mmp) cc_final: 0.5133 (tpp)
REVERT: C  391 ARG cc_start: 0.7606 (mtt180) cc_final: 0.7230 (tpt170)
REVERT: D  108 TYR cc_start: 0.8717 (m-10) cc_final: 0.8458 (m-80)
REVERT: D  137 MET cc_start: 0.9078 (mtm) cc_final: 0.8760 (mtt)
REVERT: D  139 TYR cc_start: 0.9393 (p90) cc_final: 0.9140 (p90)
REVERT: D  257 GLU cc_start: 0.8318 (tt0) cc_final: 0.7622 (tp30)
REVERT: D  352 PHE cc_start: 0.8446 (m-80) cc_final: 0.8212 (m-80)
REVERT: D  391 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7307 (tpt170)
REVERT: E  190 GLU cc_start: 0.8408 (tt0) cc_final: 0.7798 (tt0)
REVERT: E  391 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7497 (tpt-90)
  outliers start: 14
  outliers final: 12
  residues processed: 174
  average time/residue: 1.2754
  time to fit residues: 242.3711
Evaluate side-chains
  169 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 156
  time to evaluate  : 1.395 
-------------------------------------------------------------------------------
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  261 GLU
Chi-restraints excluded: chain B residue  385 SER
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  385 SER
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  349 LEU
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 60 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 105 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 125 optimal weight:    6.9990
   chunk 64 optimal weight:    5.9990
   chunk 77 optimal weight:    0.6980
   chunk 110 optimal weight:    4.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.3587 r_free = 0.3587 target = 0.108396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.075983 restraints weight = 68107.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 4.52
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3036
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3036
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13155  Z= 0.187
  Angle     :  0.585  13.372  17785  Z= 0.290
  Chirality :  0.039   0.154   2060
  Planarity :  0.004   0.032   2250
  Dihedral  :  3.717  15.455   1740
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 13.24 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.99 (0.21), residues: 1595
  helix:  3.27 (0.15), residues: 1105
  sheet:  2.89 (0.35), residues: 145
  loop :  0.27 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 196 
 HIS   0.002   0.001   HIS B 223 
 PHE   0.018   0.002   PHE E 352 
 TYR   0.035   0.003   TYR A 108 
 ARG   0.005   0.000   ARG E 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06558 ( 1000)
  hydrogen bonds       : angle       3.79519 ( 2905)
  covalent geometry    : bond        0.00432 (13155)
  covalent geometry    : angle       0.58455 (17785)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8425.79 seconds
wall clock time: 145 minutes 39.15 seconds (8739.15 seconds total)