Starting phenix.real_space_refine
on Wed Jul 30 23:35:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ip6_35633/07_2025/8ip6_35633.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ip6_35633/07_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_35633/07_2025/8ip6_35633.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ip6_35633/07_2025/8ip6_35633.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ip6_35633/07_2025/8ip6_35633.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ip6_35633/07_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-5711/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: 14.31, per 1000 atoms: 1.11
  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: 3.32
  Conformation dependent library (CDL) restraints added in 3.3 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: 1.31
  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: 3.63

  Time building geometry restraints manager: 3.88 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:             0.780
  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:             0.020
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     40.130
  Find NCS groups from input model:        0.680
  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:             0.000
  Load rotamer database and sin/cos tables:15.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   57.860
-------------------------------------------------------------------------------
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  : 1.759 
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: 1.3551
  time to fit residues: 394.2738
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  : 1.530 
-------------------------------------------------------------------------------
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 = 34)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.079946 restraints weight = 65192.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 4.30
r_work: 0.2808 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2807
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    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 = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2807
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
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  : 1.527 
Fit side-chains
REVERT: A  124 MET cc_start: 0.8489 (tpp) cc_final: 0.8264 (tpp)
REVERT: A  139 TYR cc_start: 0.9470 (p90) cc_final: 0.9069 (p90)
REVERT: A  257 GLU cc_start: 0.8715 (tt0) cc_final: 0.8003 (tp30)
REVERT: A  266 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8509 (tp30)
REVERT: A  361 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8035 (ppp)
REVERT: A  382 PHE cc_start: 0.8513 (m-80) cc_final: 0.8080 (m-80)
REVERT: A  383 MET cc_start: 0.5333 (mmp) cc_final: 0.5059 (mpp)
REVERT: B  257 GLU cc_start: 0.8059 (tp30) cc_final: 0.7795 (tp30)
REVERT: B  261 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7242 (mp0)
REVERT: B  383 MET cc_start: 0.4655 (mmp) cc_final: 0.4347 (mtm)
REVERT: B  391 ARG cc_start: 0.7896 (mtt180) cc_final: 0.7427 (tpt170)
REVERT: C  383 MET cc_start: 0.5330 (mmp) cc_final: 0.5073 (tpp)
REVERT: C  391 ARG cc_start: 0.7434 (mtt180) cc_final: 0.6960 (tpt170)
REVERT: D  108 TYR cc_start: 0.8816 (m-10) cc_final: 0.8538 (m-80)
REVERT: D  139 TYR cc_start: 0.9489 (p90) cc_final: 0.9230 (p90)
REVERT: D  257 GLU cc_start: 0.8671 (tt0) cc_final: 0.7932 (tp30)
REVERT: D  291 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8532 (mm-30)
REVERT: D  383 MET cc_start: 0.4683 (mmp) cc_final: 0.4351 (tpp)
REVERT: D  391 ARG cc_start: 0.7904 (mtt180) cc_final: 0.7240 (tpt170)
REVERT: E  109 GLN cc_start: 0.8363 (tm-30) cc_final: 0.8105 (pp30)
REVERT: E  190 GLU cc_start: 0.8997 (tt0) cc_final: 0.8178 (pt0)
REVERT: E  383 MET cc_start: 0.5171 (mmp) cc_final: 0.4605 (mpt)
REVERT: E  391 ARG cc_start: 0.7820 (mtt180) cc_final: 0.7337 (tpt170)
  outliers start: 27
  outliers final: 7
  residues processed: 192
  average time/residue: 1.3428
  time to fit residues: 279.8400
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  : 1.497 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 44 optimal weight:    0.9990
   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:    0.8980
   overall best weight:    0.8782

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.115164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.082944 restraints weight = 60682.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 4.25
r_work: 0.2886 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2880
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2881
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
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     :  0.512   9.364  17785  Z= 0.259
  Chirality :  0.037   0.129   2060
  Planarity :  0.003   0.031   2250
  Dihedral  :  3.513  14.446   1740
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  9.58 %
    Favored  : 88.94 %
  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:  4.42 (0.21), residues: 1595
  helix:  3.61 (0.15), residues: 1090
  sheet:  3.03 (0.33), residues: 145
  loop :  0.51 (0.38), residues: 360

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   0.015   0.001   PHE C 352 
 TYR   0.027   0.002   TYR B 154 
 ARG   0.005   0.000   ARG B 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05848 ( 1000)
  hydrogen bonds       : angle       3.55738 ( 2905)
  covalent geometry    : bond        0.00265 (13155)
  covalent geometry    : angle       0.51180 (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
  209 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 188
  time to evaluate  : 1.461 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9463 (p90) cc_final: 0.9021 (p90)
REVERT: A  257 GLU cc_start: 0.8684 (tt0) cc_final: 0.7938 (tp30)
REVERT: A  266 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8486 (tp30)
REVERT: A  383 MET cc_start: 0.5262 (mmp) cc_final: 0.5008 (mpp)
REVERT: B  257 GLU cc_start: 0.8043 (tp30) cc_final: 0.7676 (tp30)
REVERT: B  261 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6866 (mp0)
REVERT: B  383 MET cc_start: 0.4754 (mmp) cc_final: 0.4427 (mtm)
REVERT: B  391 ARG cc_start: 0.7899 (mtt180) cc_final: 0.7438 (tpt170)
REVERT: C  137 MET cc_start: 0.9075 (mtm) cc_final: 0.8787 (mtt)
REVERT: C  383 MET cc_start: 0.5253 (mmp) cc_final: 0.4990 (tpp)
REVERT: C  391 ARG cc_start: 0.7396 (mtt180) cc_final: 0.6893 (tpt170)
REVERT: D  108 TYR cc_start: 0.8770 (m-10) cc_final: 0.8501 (m-80)
REVERT: D  139 TYR cc_start: 0.9505 (p90) cc_final: 0.9243 (p90)
REVERT: D  190 GLU cc_start: 0.8903 (tt0) cc_final: 0.8298 (tt0)
REVERT: D  257 GLU cc_start: 0.8717 (tt0) cc_final: 0.8000 (tp30)
REVERT: D  291 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8397 (mm-30)
REVERT: D  383 MET cc_start: 0.4562 (mmp) cc_final: 0.4228 (tpp)
REVERT: D  391 ARG cc_start: 0.7852 (mtt180) cc_final: 0.7217 (tpt170)
REVERT: E  266 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8440 (tp30)
REVERT: E  383 MET cc_start: 0.5047 (mmp) cc_final: 0.4470 (mpt)
REVERT: E  391 ARG cc_start: 0.7838 (mtt180) cc_final: 0.7357 (tpt170)
  outliers start: 21
  outliers final: 10
  residues processed: 199
  average time/residue: 1.3019
  time to fit residues: 281.6833
Evaluate side-chains
  180 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 169
  time to evaluate  : 1.574 
-------------------------------------------------------------------------------
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  349 LEU
Chi-restraints excluded: chain E residue  350 SER
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:    0.6980
   chunk 1 optimal weight:    0.4980
   chunk 29 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    1.7784

-------------------------------------------------------------------------------
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 = 0.3608 r_free = 0.3608 target = 0.113603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.081544 restraints weight = 64808.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 4.38
r_work: 0.2844 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2817
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2817 r_free = 0.2817    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2817 r_free = 0.2817    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2817
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  13155  Z= 0.175
  Angle     :  0.539   9.914  17785  Z= 0.274
  Chirality :  0.038   0.134   2060
  Planarity :  0.003   0.031   2250
  Dihedral  :  3.630  14.537   1740
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 11.48 %
    Favored  : 87.54 %
  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:  4.21 (0.21), residues: 1595
  helix:  3.44 (0.15), residues: 1105
  sheet:  3.08 (0.33), residues: 145
  loop :  0.24 (0.39), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 196 
 HIS   0.002   0.001   HIS E 288 
 PHE   0.017   0.002   PHE E 352 
 TYR   0.027   0.002   TYR C 154 
 ARG   0.004   0.000   ARG A 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06407 ( 1000)
  hydrogen bonds       : angle       3.67277 ( 2905)
  covalent geometry    : bond        0.00402 (13155)
  covalent geometry    : angle       0.53915 (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
  182 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 168
  time to evaluate  : 1.571 
Fit side-chains
REVERT: A  139 TYR cc_start: 0.9464 (p90) cc_final: 0.9075 (p90)
REVERT: A  213 GLU cc_start: 0.8597 (tt0) cc_final: 0.8206 (tm-30)
REVERT: A  257 GLU cc_start: 0.8688 (tt0) cc_final: 0.7952 (tp30)
REVERT: A  266 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8527 (tp30)
REVERT: A  361 MET cc_start: 0.8680 (ptp) cc_final: 0.8043 (ppp)
REVERT: A  383 MET cc_start: 0.5307 (mmp) cc_final: 0.5015 (mpp)
REVERT: B  257 GLU cc_start: 0.7915 (tp30) cc_final: 0.7512 (tp30)
REVERT: B  261 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6981 (mp0)
REVERT: B  383 MET cc_start: 0.4383 (mmp) cc_final: 0.4044 (mtm)
REVERT: B  391 ARG cc_start: 0.7899 (mtt180) cc_final: 0.7374 (tpt170)
REVERT: C  383 MET cc_start: 0.5161 (mmp) cc_final: 0.4891 (tpp)
REVERT: C  391 ARG cc_start: 0.7405 (mtt180) cc_final: 0.6870 (tpt170)
REVERT: D  108 TYR cc_start: 0.8762 (m-10) cc_final: 0.8507 (m-80)
REVERT: D  139 TYR cc_start: 0.9479 (p90) cc_final: 0.9238 (p90)
REVERT: D  257 GLU cc_start: 0.8678 (tt0) cc_final: 0.7974 (tp30)
REVERT: D  291 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8400 (mm-30)
REVERT: D  383 MET cc_start: 0.4580 (mmp) cc_final: 0.4281 (mpp)
REVERT: D  391 ARG cc_start: 0.7898 (mtt180) cc_final: 0.7225 (tpt170)
REVERT: E  190 GLU cc_start: 0.8919 (tt0) cc_final: 0.8102 (pt0)
REVERT: E  383 MET cc_start: 0.4974 (mmp) cc_final: 0.4401 (mpt)
REVERT: E  391 ARG cc_start: 0.7854 (mtt180) cc_final: 0.7313 (tpt170)
  outliers start: 14
  outliers final: 8
  residues processed: 179
  average time/residue: 1.2966
  time to fit residues: 252.2214
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  : 1.427 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 138 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 136 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 137 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 156 optimal weight:   20.0000
   chunk 71 optimal weight:    0.8980
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.3627 r_free = 0.3627 target = 0.113491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.081062 restraints weight = 72565.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 4.60
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3092
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3092
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13155  Z= 0.137
  Angle     :  0.516  10.472  17785  Z= 0.259
  Chirality :  0.037   0.130   2060
  Planarity :  0.003   0.033   2250
  Dihedral  :  3.536  14.338   1740
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 12.32 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  4.35 (0.21), residues: 1595
  helix:  3.57 (0.15), residues: 1085
  sheet:  3.07 (0.33), residues: 145
  loop :  0.44 (0.38), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 162 
 HIS   0.002   0.000   HIS B 223 
 PHE   0.016   0.001   PHE C 352 
 TYR   0.027   0.002   TYR C 154 
 ARG   0.005   0.000   ARG E 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05977 ( 1000)
  hydrogen bonds       : angle       3.59397 ( 2905)
  covalent geometry    : bond        0.00293 (13155)
  covalent geometry    : angle       0.51641 (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
  187 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 173
  time to evaluate  : 1.496 
Fit side-chains
REVERT: A  139 TYR cc_start: 0.9356 (p90) cc_final: 0.8868 (p90)
REVERT: A  213 GLU cc_start: 0.8159 (tt0) cc_final: 0.7927 (tm-30)
REVERT: A  257 GLU cc_start: 0.8400 (tt0) cc_final: 0.7700 (tp30)
REVERT: A  266 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8332 (tp30)
REVERT: A  361 MET cc_start: 0.8615 (ptp) cc_final: 0.8037 (ppp)
REVERT: A  383 MET cc_start: 0.5586 (mmp) cc_final: 0.5288 (mpp)
REVERT: B  257 GLU cc_start: 0.7586 (tp30) cc_final: 0.6380 (tp30)
REVERT: B  261 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.5567 (mp0)
REVERT: B  383 MET cc_start: 0.4488 (mmp) cc_final: 0.4090 (mtm)
REVERT: B  391 ARG cc_start: 0.7852 (mtt180) cc_final: 0.7345 (tpt170)
REVERT: C  383 MET cc_start: 0.5225 (mmp) cc_final: 0.4953 (tpp)
REVERT: C  391 ARG cc_start: 0.7416 (mtt180) cc_final: 0.6948 (tpt170)
REVERT: D  108 TYR cc_start: 0.8660 (m-10) cc_final: 0.8391 (m-80)
REVERT: D  137 MET cc_start: 0.8908 (mtm) cc_final: 0.8635 (mtt)
REVERT: D  139 TYR cc_start: 0.9410 (p90) cc_final: 0.9080 (p90)
REVERT: D  257 GLU cc_start: 0.8394 (tt0) cc_final: 0.7708 (tp30)
REVERT: D  291 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8022 (mm-30)
REVERT: D  359 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6668 (t80)
REVERT: D  383 MET cc_start: 0.4859 (mmp) cc_final: 0.4544 (mpp)
REVERT: D  391 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7287 (tpt170)
REVERT: E  190 GLU cc_start: 0.8384 (tt0) cc_final: 0.7598 (pt0)
REVERT: E  383 MET cc_start: 0.5128 (mmp) cc_final: 0.4558 (mpt)
REVERT: E  391 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7428 (tpt-90)
  outliers start: 14
  outliers final: 5
  residues processed: 182
  average time/residue: 1.3007
  time to fit residues: 258.1015
Evaluate side-chains
  171 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 164
  time to evaluate  : 1.710 
-------------------------------------------------------------------------------
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  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  359 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 97 optimal weight:    0.6980
   chunk 109 optimal weight:    0.5980
   chunk 83 optimal weight:    4.9990
   chunk 63 optimal weight:    8.9990
   chunk 42 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 111 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    1.6384

-------------------------------------------------------------------------------
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 = 0.3610 r_free = 0.3610 target = 0.113592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.081272 restraints weight = 73247.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 4.57
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3047
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  13155  Z= 0.166
  Angle     :  0.537  11.010  17785  Z= 0.270
  Chirality :  0.038   0.178   2060
  Planarity :  0.003   0.033   2250
  Dihedral  :  3.620  14.755   1740
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 12.54 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.17 (0.21), residues: 1595
  helix:  3.40 (0.15), residues: 1105
  sheet:  3.11 (0.34), residues: 145
  loop :  0.25 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 196 
 HIS   0.002   0.001   HIS E 122 
 PHE   0.017   0.001   PHE E 352 
 TYR   0.028   0.002   TYR B 108 
 ARG   0.004   0.000   ARG E 301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06291 ( 1000)
  hydrogen bonds       : angle       3.66732 ( 2905)
  covalent geometry    : bond        0.00377 (13155)
  covalent geometry    : angle       0.53693 (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
  179 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 166
  time to evaluate  : 1.580 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9364 (p90) cc_final: 0.8887 (p90)
REVERT: A  213 GLU cc_start: 0.8153 (tt0) cc_final: 0.7915 (tm-30)
REVERT: A  257 GLU cc_start: 0.8367 (tt0) cc_final: 0.7676 (tp30)
REVERT: A  266 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8380 (tp30)
REVERT: A  361 MET cc_start: 0.8614 (ptp) cc_final: 0.8043 (ppp)
REVERT: A  383 MET cc_start: 0.5571 (mmp) cc_final: 0.5277 (mpp)
REVERT: B  257 GLU cc_start: 0.7576 (tp30) cc_final: 0.6636 (tp30)
REVERT: B  261 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.5903 (mp0)
REVERT: B  383 MET cc_start: 0.4264 (mmp) cc_final: 0.3912 (mtm)
REVERT: B  391 ARG cc_start: 0.7845 (mtt180) cc_final: 0.7346 (tpt170)
REVERT: C  359 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.7120 (m-80)
REVERT: C  383 MET cc_start: 0.5260 (mmp) cc_final: 0.4983 (tpp)
REVERT: C  391 ARG cc_start: 0.7411 (mtt180) cc_final: 0.6911 (tpt170)
REVERT: D  108 TYR cc_start: 0.8658 (m-10) cc_final: 0.8389 (m-80)
REVERT: D  139 TYR cc_start: 0.9387 (p90) cc_final: 0.9075 (p90)
REVERT: D  257 GLU cc_start: 0.8387 (tt0) cc_final: 0.7708 (tp30)
REVERT: D  359 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.6900 (t80)
REVERT: D  383 MET cc_start: 0.4877 (mmp) cc_final: 0.4572 (mpp)
REVERT: D  391 ARG cc_start: 0.7766 (mtt180) cc_final: 0.7203 (tpt170)
REVERT: E  383 MET cc_start: 0.5135 (mmp) cc_final: 0.4562 (mpt)
REVERT: E  391 ARG cc_start: 0.7911 (mtt180) cc_final: 0.7441 (tpt-90)
  outliers start: 13
  outliers final: 8
  residues processed: 175
  average time/residue: 1.2734
  time to fit residues: 243.4289
Evaluate side-chains
  171 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 160
  time to evaluate  : 1.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  256 LEU
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain C residue  385 SER
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain E residue  385 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 110 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 139 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 77 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   chunk 154 optimal weight:    0.9980
   chunk 147 optimal weight:    4.9990
   chunk 131 optimal weight:    2.9990
   chunk 92 optimal weight:   10.0000
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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 = 0.3608 r_free = 0.3608 target = 0.112404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.080087 restraints weight = 68811.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 4.44
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3074
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  13155  Z= 0.161
  Angle     :  0.542  12.111  17785  Z= 0.271
  Chirality :  0.038   0.170   2060
  Planarity :  0.003   0.032   2250
  Dihedral  :  3.602  14.864   1740
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 12.61 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  4.17 (0.21), residues: 1595
  helix:  3.41 (0.15), residues: 1105
  sheet:  3.07 (0.34), residues: 145
  loop :  0.24 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 162 
 HIS   0.001   0.001   HIS B 223 
 PHE   0.017   0.001   PHE C 352 
 TYR   0.030   0.002   TYR B 108 
 ARG   0.003   0.000   ARG A 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06255 ( 1000)
  hydrogen bonds       : angle       3.67617 ( 2905)
  covalent geometry    : bond        0.00363 (13155)
  covalent geometry    : angle       0.54248 (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
  185 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 171
  time to evaluate  : 1.596 
Fit side-chains
REVERT: A  139 TYR cc_start: 0.9352 (p90) cc_final: 0.8877 (p90)
REVERT: A  213 GLU cc_start: 0.8153 (tt0) cc_final: 0.7920 (tm-30)
REVERT: A  257 GLU cc_start: 0.8397 (tt0) cc_final: 0.7716 (tp30)
REVERT: A  266 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8353 (tp30)
REVERT: A  361 MET cc_start: 0.8623 (ptp) cc_final: 0.8072 (ppp)
REVERT: A  382 PHE cc_start: 0.8423 (m-80) cc_final: 0.8103 (m-80)
REVERT: A  383 MET cc_start: 0.5343 (mmp) cc_final: 0.5011 (mpp)
REVERT: B  257 GLU cc_start: 0.7619 (tp30) cc_final: 0.6662 (tp30)
REVERT: B  261 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.5910 (mp0)
REVERT: B  383 MET cc_start: 0.4255 (mmp) cc_final: 0.3902 (mtm)
REVERT: B  391 ARG cc_start: 0.7834 (mtt180) cc_final: 0.7348 (tpt170)
REVERT: C  383 MET cc_start: 0.5215 (mmp) cc_final: 0.4944 (tpp)
REVERT: C  391 ARG cc_start: 0.7348 (mtt180) cc_final: 0.6762 (tpt170)
REVERT: D  108 TYR cc_start: 0.8689 (m-10) cc_final: 0.8424 (m-80)
REVERT: D  139 TYR cc_start: 0.9406 (p90) cc_final: 0.9143 (p90)
REVERT: D  257 GLU cc_start: 0.8369 (tt0) cc_final: 0.7693 (tp30)
REVERT: D  359 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.6954 (t80)
REVERT: D  383 MET cc_start: 0.4741 (mmp) cc_final: 0.4430 (mpp)
REVERT: D  391 ARG cc_start: 0.7730 (mtt180) cc_final: 0.7045 (tpt170)
REVERT: E  190 GLU cc_start: 0.8385 (tt0) cc_final: 0.7739 (tt0)
REVERT: E  391 ARG cc_start: 0.7921 (mtt180) cc_final: 0.7451 (tpt-90)
  outliers start: 14
  outliers final: 10
  residues processed: 181
  average time/residue: 1.2802
  time to fit residues: 252.9230
Evaluate side-chains
  176 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 164
  time to evaluate  : 1.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  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  359 PHE
Chi-restraints excluded: chain E residue  385 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 145 optimal weight:    3.9990
   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:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 94 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 151 optimal weight:    0.8980
   chunk 88 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 = 0.3582 r_free = 0.3582 target = 0.107929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.075382 restraints weight = 72710.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 4.59
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031  13155  Z= 0.203
  Angle     :  0.573  12.432  17785  Z= 0.286
  Chirality :  0.039   0.161   2060
  Planarity :  0.004   0.032   2250
  Dihedral  :  3.723  15.381   1740
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 12.96 %
    Favored  : 86.13 %
  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:  4.06 (0.21), residues: 1595
  helix:  3.32 (0.15), residues: 1105
  sheet:  3.00 (0.34), residues: 145
  loop :  0.25 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 196 
 HIS   0.002   0.001   HIS C 232 
 PHE   0.019   0.002   PHE E 352 
 TYR   0.031   0.003   TYR B 108 
 ARG   0.006   0.000   ARG E 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06709 ( 1000)
  hydrogen bonds       : angle       3.77978 ( 2905)
  covalent geometry    : bond        0.00474 (13155)
  covalent geometry    : angle       0.57322 (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
  178 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 165
  time to evaluate  : 1.531 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9365 (p90) cc_final: 0.8995 (p90)
REVERT: A  213 GLU cc_start: 0.8206 (tt0) cc_final: 0.7978 (tm-30)
REVERT: A  257 GLU cc_start: 0.8417 (tt0) cc_final: 0.7765 (tp30)
REVERT: A  266 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8348 (tp30)
REVERT: A  361 MET cc_start: 0.8625 (ptp) cc_final: 0.8087 (ppp)
REVERT: A  382 PHE cc_start: 0.8470 (m-80) cc_final: 0.8258 (m-80)
REVERT: A  383 MET cc_start: 0.5505 (mmp) cc_final: 0.5187 (mpp)
REVERT: B  257 GLU cc_start: 0.7714 (tp30) cc_final: 0.6735 (tp30)
REVERT: B  261 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6243 (mp0)
REVERT: B  383 MET cc_start: 0.4387 (mmp) cc_final: 0.3987 (mtm)
REVERT: B  391 ARG cc_start: 0.7868 (mtt180) cc_final: 0.7448 (tpt170)
REVERT: C  383 MET cc_start: 0.5441 (mmp) cc_final: 0.5181 (tpp)
REVERT: C  391 ARG cc_start: 0.7505 (mtt180) cc_final: 0.7091 (tpt170)
REVERT: D  108 TYR cc_start: 0.8735 (m-10) cc_final: 0.8463 (m-80)
REVERT: D  137 MET cc_start: 0.9128 (mtm) cc_final: 0.8862 (mtm)
REVERT: D  139 TYR cc_start: 0.9399 (p90) cc_final: 0.9139 (p90)
REVERT: D  257 GLU cc_start: 0.8328 (tt0) cc_final: 0.7663 (tp30)
REVERT: D  352 PHE cc_start: 0.8490 (m-80) cc_final: 0.8232 (m-80)
REVERT: D  391 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7350 (tpt170)
REVERT: E  391 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7537 (tpt-90)
  outliers start: 13
  outliers final: 10
  residues processed: 176
  average time/residue: 1.3148
  time to fit residues: 251.7475
Evaluate side-chains
  172 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 161
  time to evaluate  : 1.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 E residue   97 VAL
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:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 105 optimal weight:    0.7980
   chunk 92 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 144 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3608 r_free = 0.3608 target = 0.112751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.080858 restraints weight = 54529.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 4.13
r_work: 0.2845 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2845
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2845
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  13155  Z= 0.158
  Angle     :  0.551  13.204  17785  Z= 0.272
  Chirality :  0.038   0.165   2060
  Planarity :  0.003   0.033   2250
  Dihedral  :  3.643  15.226   1740
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 13.38 %
    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:  4.13 (0.21), residues: 1595
  helix:  3.37 (0.15), residues: 1105
  sheet:  3.02 (0.34), residues: 145
  loop :  0.26 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 196 
 HIS   0.001   0.001   HIS C 371 
 PHE   0.016   0.001   PHE C 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        0.06293 ( 1000)
  hydrogen bonds       : angle       3.69921 ( 2905)
  covalent geometry    : bond        0.00355 (13155)
  covalent geometry    : angle       0.55056 (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
  179 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 166
  time to evaluate  : 1.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9445 (p90) cc_final: 0.9059 (p90)
REVERT: A  213 GLU cc_start: 0.8576 (tt0) cc_final: 0.8192 (tm-30)
REVERT: A  257 GLU cc_start: 0.8700 (tt0) cc_final: 0.7969 (tp30)
REVERT: A  266 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8479 (tp30)
REVERT: A  382 PHE cc_start: 0.8414 (m-80) cc_final: 0.8151 (m-80)
REVERT: A  383 MET cc_start: 0.5182 (mmp) cc_final: 0.4864 (mpp)
REVERT: B  257 GLU cc_start: 0.7898 (tp30) cc_final: 0.6920 (tp30)
REVERT: B  261 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6306 (mp0)
REVERT: B  383 MET cc_start: 0.4109 (mmp) cc_final: 0.3743 (mtm)
REVERT: B  391 ARG cc_start: 0.7841 (mtt180) cc_final: 0.7364 (tpt170)
REVERT: C  383 MET cc_start: 0.5186 (mmp) cc_final: 0.4909 (tpp)
REVERT: C  391 ARG cc_start: 0.7532 (mtt180) cc_final: 0.7137 (tpt170)
REVERT: D  108 TYR cc_start: 0.8772 (m-10) cc_final: 0.8531 (m-80)
REVERT: D  137 MET cc_start: 0.9135 (mtm) cc_final: 0.8913 (mtt)
REVERT: D  139 TYR cc_start: 0.9455 (p90) cc_final: 0.9213 (p90)
REVERT: D  257 GLU cc_start: 0.8652 (tt0) cc_final: 0.7903 (tp30)
REVERT: D  352 PHE cc_start: 0.8443 (m-80) cc_final: 0.8201 (m-80)
REVERT: D  391 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7225 (tpt170)
REVERT: E  391 ARG cc_start: 0.7886 (mtt180) cc_final: 0.7398 (tpt-90)
  outliers start: 13
  outliers final: 11
  residues processed: 177
  average time/residue: 1.2609
  time to fit residues: 243.5442
Evaluate side-chains
  172 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 160
  time to evaluate  : 1.464 
-------------------------------------------------------------------------------
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 E residue   97 VAL
Chi-restraints excluded: chain E residue  385 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 134 optimal weight:    2.9990
   chunk 140 optimal weight:    0.6980
   chunk 148 optimal weight:   10.0000
   chunk 130 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 84 optimal weight:    8.9990
   chunk 75 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 115 optimal weight:    0.0270
   overall best weight:    0.9442

-------------------------------------------------------------------------------
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 = 0.3633 r_free = 0.3633 target = 0.114252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.081891 restraints weight = 67476.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 4.54
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3081
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3081 r_free = 0.3081    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 = 0.3081 r_free = 0.3081    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3081
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13155  Z= 0.130
  Angle     :  0.536  13.364  17785  Z= 0.264
  Chirality :  0.037   0.166   2060
  Planarity :  0.003   0.033   2250
  Dihedral  :  3.556  14.991   1740
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 13.45 %
    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:  4.21 (0.22), residues: 1595
  helix:  3.42 (0.15), residues: 1105
  sheet:  3.12 (0.34), residues: 145
  loop :  0.27 (0.40), residues: 345

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   0.016   0.001   PHE C 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        0.05887 ( 1000)
  hydrogen bonds       : angle       3.62046 ( 2905)
  covalent geometry    : bond        0.00270 (13155)
  covalent geometry    : angle       0.53561 (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
  189 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 177
  time to evaluate  : 1.567 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9361 (p90) cc_final: 0.8936 (p90)
REVERT: A  250 ILE cc_start: 0.8787 (mm) cc_final: 0.8509 (pt)
REVERT: A  257 GLU cc_start: 0.8380 (tt0) cc_final: 0.7685 (tp30)
REVERT: A  266 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8357 (tp30)
REVERT: A  382 PHE cc_start: 0.8398 (m-80) cc_final: 0.8126 (m-80)
REVERT: A  383 MET cc_start: 0.5308 (mmp) cc_final: 0.4976 (mpp)
REVERT: B  250 ILE cc_start: 0.8775 (mm) cc_final: 0.8543 (pt)
REVERT: B  257 GLU cc_start: 0.7565 (tp30) cc_final: 0.6650 (tp30)
REVERT: B  261 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.5797 (mp0)
REVERT: B  383 MET cc_start: 0.4255 (mmp) cc_final: 0.3883 (mtm)
REVERT: B  391 ARG cc_start: 0.7790 (mtt180) cc_final: 0.7463 (tpt170)
REVERT: C  109 GLN cc_start: 0.8894 (tp40) cc_final: 0.8676 (tp40)
REVERT: C  359 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.7242 (m-80)
REVERT: C  383 MET cc_start: 0.5447 (mmp) cc_final: 0.5181 (tpp)
REVERT: C  391 ARG cc_start: 0.7557 (mtt180) cc_final: 0.7172 (tpt170)
REVERT: D  108 TYR cc_start: 0.8672 (m-10) cc_final: 0.8408 (m-80)
REVERT: D  137 MET cc_start: 0.9034 (mtm) cc_final: 0.8747 (mtt)
REVERT: D  139 TYR cc_start: 0.9407 (p90) cc_final: 0.9136 (p90)
REVERT: D  257 GLU cc_start: 0.8380 (tt0) cc_final: 0.7656 (tp30)
REVERT: D  352 PHE cc_start: 0.8432 (m-80) cc_final: 0.8178 (m-80)
REVERT: E  190 GLU cc_start: 0.8353 (tt0) cc_final: 0.7701 (tt0)
REVERT: E  383 MET cc_start: 0.5084 (mmt) cc_final: 0.4431 (mtt)
REVERT: E  391 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7470 (tpt-90)
  outliers start: 12
  outliers final: 9
  residues processed: 187
  average time/residue: 1.2655
  time to fit residues: 258.4795
Evaluate side-chains
  181 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 170
  time to evaluate  : 1.657 
-------------------------------------------------------------------------------
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  359 PHE
Chi-restraints excluded: chain E residue   97 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 60 optimal weight:    0.0010
   chunk 24 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0970
   chunk 105 optimal weight:    0.0030
   chunk 43 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 125 optimal weight:    8.9990
   chunk 64 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 110 optimal weight:    0.6980
   overall best weight:    0.3594

-------------------------------------------------------------------------------
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 = 0.3673 r_free = 0.3673 target = 0.116743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.084660 restraints weight = 65822.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 4.54
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3127
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3127
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  13155  Z= 0.117
  Angle     :  0.532  13.390  17785  Z= 0.260
  Chirality :  0.037   0.176   2060
  Planarity :  0.003   0.035   2250
  Dihedral  :  3.398  14.009   1740
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 13.80 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  4.32 (0.22), residues: 1595
  helix:  3.57 (0.15), residues: 1085
  sheet:  3.07 (0.34), residues: 145
  loop :  0.36 (0.39), 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   0.023   0.001   PHE E 352 
 TYR   0.027   0.002   TYR B 108 
 ARG   0.005   0.000   ARG E 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05246 ( 1000)
  hydrogen bonds       : angle       3.48210 ( 2905)
  covalent geometry    : bond        0.00218 (13155)
  covalent geometry    : angle       0.53219 (17785)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9001.55 seconds
wall clock time: 154 minutes 37.49 seconds (9277.49 seconds total)