Starting phenix.real_space_refine
on Wed Jul 30 23:35:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ip4_35631/07_2025/8ip4_35631.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ip4_35631/07_2025/8ip4_35631.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ip4_35631/07_2025/8ip4_35631.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ip4_35631/07_2025/8ip4_35631.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ip4_35631/07_2025/8ip4_35631.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ip4_35631/07_2025/8ip4_35631.cif"
  }
  resolution = 2.7
  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=   0.025
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: 6
    Type Number    sf(0)   Gaussians
     Mg      2      5.21       5
     S      65      5.16       5
     Cl      1      4.86       5
     C    8315      2.51       5
     N    2175      2.21       5
     O    2375      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: 12933
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 2585
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2577
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 23
          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, 2577
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 23
          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: 2614
    Chain: "B"
      Number of atoms: 2585
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2577
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 23
          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, 2577
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 23
          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: 2614
    Chain: "C"
      Number of atoms: 2585
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2577
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 23
          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, 2577
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 23
          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: 2614
    Chain: "D"
      Number of atoms: 2585
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2577
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 23
          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, 2577
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 23
          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: 2614
    Chain: "E"
      Number of atoms: 2585
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2577
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 23
          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, 2577
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 23
          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: 2614
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CL': 1, ' MG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 13.96, per 1000 atoms: 1.08
  Number of scatterers: 12933
  At special positions: 0
  Unit cell: (110.67, 108.81, 140.43, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      65     16.00
     Mg      2     11.99
     O    2375      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: 3.28
  Conformation dependent library (CDL) restraints added in 3.1 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
      72.2% alpha, 9.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 114 through 119
      removed outlier: 3.531A  pdb=" N   ARG A 119 " --> pdb=" O   ARG A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 172
      removed outlier: 4.720A  pdb=" N   TRP A 162 " --> pdb=" O   ASN A 158 " (cutoff:3.500A)
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 183 through 219
      removed outlier: 3.611A  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: 3.917A  pdb=" N   GLU A 261 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 269
      removed outlier: 3.533A  pdb=" N   LEU A 265 " --> pdb=" O   GLU A 261 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   CYS A 269 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 275
      removed outlier: 3.851A  pdb=" N   ASP A 275 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 283
      removed outlier: 4.164A  pdb=" N   LYS A 281 " --> pdb=" O   GLN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 360
      removed outlier: 3.788A  pdb=" N   MET A 355 " --> pdb=" O   LEU A 351 " (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: 3.531A  pdb=" N   ARG B 119 " --> pdb=" O   ARG B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 172
      removed outlier: 4.720A  pdb=" N   TRP B 162 " --> pdb=" O   ASN B 158 " (cutoff:3.500A)
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 183 through 219
      removed outlier: 3.611A  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: 3.917A  pdb=" N   GLU B 261 " --> pdb=" O   GLU B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 269
      removed outlier: 3.533A  pdb=" N   LEU B 265 " --> pdb=" O   GLU B 261 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   CYS B 269 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 275
      removed outlier: 3.850A  pdb=" N   ASP B 275 " --> pdb=" O   SER B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 283
      removed outlier: 4.165A  pdb=" N   LYS B 281 " --> pdb=" O   GLN B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 360
      removed outlier: 3.789A  pdb=" N   MET B 355 " --> pdb=" O   LEU B 351 " (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: 3.530A  pdb=" N   ARG C 119 " --> pdb=" O   ARG C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 158 through 172
      removed outlier: 4.721A  pdb=" N   TRP C 162 " --> pdb=" O   ASN C 158 " (cutoff:3.500A)
      Proline residue:  C 168  - end of helix
    Processing helix  chain 'C' and resid 183 through 219
      removed outlier: 3.611A  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: 3.917A  pdb=" N   GLU C 261 " --> pdb=" O   GLU C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 269
      removed outlier: 3.533A  pdb=" N   LEU C 265 " --> pdb=" O   GLU C 261 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   CYS C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 275
      removed outlier: 3.851A  pdb=" N   ASP C 275 " --> pdb=" O   SER C 271 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 275 through 283
      removed outlier: 4.164A  pdb=" N   LYS C 281 " --> pdb=" O   GLN C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 360
      removed outlier: 3.789A  pdb=" N   MET C 355 " --> pdb=" O   LEU C 351 " (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: 3.531A  pdb=" N   ARG D 119 " --> pdb=" O   ARG D 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 158 through 172
      removed outlier: 4.720A  pdb=" N   TRP D 162 " --> pdb=" O   ASN D 158 " (cutoff:3.500A)
      Proline residue:  D 168  - end of helix
    Processing helix  chain 'D' and resid 183 through 219
      removed outlier: 3.611A  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: 3.917A  pdb=" N   GLU D 261 " --> pdb=" O   GLU D 257 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 261 through 269
      removed outlier: 3.533A  pdb=" N   LEU D 265 " --> pdb=" O   GLU D 261 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   CYS D 269 " --> pdb=" O   LEU D 265 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 275
      removed outlier: 3.850A  pdb=" N   ASP D 275 " --> pdb=" O   SER D 271 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 283
      removed outlier: 4.164A  pdb=" N   LYS D 281 " --> pdb=" O   GLN D 277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 360
      removed outlier: 3.788A  pdb=" N   MET D 355 " --> pdb=" O   LEU D 351 " (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: 3.531A  pdb=" N   ARG E 119 " --> pdb=" O   ARG E 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 158 through 172
      removed outlier: 4.720A  pdb=" N   TRP E 162 " --> pdb=" O   ASN E 158 " (cutoff:3.500A)
      Proline residue:  E 168  - end of helix
    Processing helix  chain 'E' and resid 183 through 219
      removed outlier: 3.611A  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: 3.917A  pdb=" N   GLU E 261 " --> pdb=" O   GLU E 257 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 261 through 269
      removed outlier: 3.532A  pdb=" N   LEU E 265 " --> pdb=" O   GLU E 261 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   CYS E 269 " --> pdb=" O   LEU E 265 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 275
      removed outlier: 3.850A  pdb=" N   ASP E 275 " --> pdb=" O   SER E 271 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 275 through 283
      removed outlier: 4.164A  pdb=" N   LYS E 281 " --> pdb=" O   GLN E 277 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 287 through 360
      removed outlier: 3.789A  pdb=" N   MET E 355 " --> pdb=" O   LEU E 351 " (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: 4.082A  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: 4.083A  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: 4.083A  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: 4.082A  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: 4.083A  pdb=" N   LYS E 141 " --> pdb=" O   LEU E 152 " (cutoff:3.500A)

    1010 hydrogen bonds defined for protein.
    2965 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: 4.06

  Time building geometry restraints manager: 3.89 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: 4230
        1.34 -     1.46: 2363
        1.46 -     1.58: 6447
        1.58 -     1.69: 0
        1.69 -     1.81: 120
  Bond restraints: 13160
  Sorted by residual:
  bond pdb=" C   LEU B 182 "
       pdb=" N   PRO B 183 "
    ideal  model  delta    sigma   weight residual
    1.331  1.346 -0.015 1.21e-02 6.83e+03 1.49e+00
  bond pdb=" C   LEU D 182 "
       pdb=" N   PRO D 183 "
    ideal  model  delta    sigma   weight residual
    1.331  1.346 -0.014 1.21e-02 6.83e+03 1.38e+00
  bond pdb=" C   LEU E 182 "
       pdb=" N   PRO E 183 "
    ideal  model  delta    sigma   weight residual
    1.331  1.345 -0.014 1.21e-02 6.83e+03 1.29e+00
  bond pdb=" C   LEU A 182 "
       pdb=" N   PRO A 183 "
    ideal  model  delta    sigma   weight residual
    1.331  1.345 -0.013 1.21e-02 6.83e+03 1.23e+00
  bond pdb=" C   LEU C 182 "
       pdb=" N   PRO C 183 "
    ideal  model  delta    sigma   weight residual
    1.331  1.344 -0.013 1.21e-02 6.83e+03 1.16e+00
  ... (remaining 13155 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 17314
        1.04 -     2.08: 342
        2.08 -     3.12: 83
        3.12 -     4.16: 26
        4.16 -     5.20: 25
  Bond angle restraints: 17790
  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
     121.66  118.21    3.45 1.76e+00 3.23e-01 3.85e+00
  angle pdb=" C   LEU E 351 "
        pdb=" N   PHE E 352 "
        pdb=" CA  PHE E 352 "
      ideal   model   delta    sigma   weight residual
     121.66  118.22    3.44 1.76e+00 3.23e-01 3.83e+00
  angle pdb=" C   LEU C 351 "
        pdb=" N   PHE C 352 "
        pdb=" CA  PHE C 352 "
      ideal   model   delta    sigma   weight residual
     121.66  118.22    3.44 1.76e+00 3.23e-01 3.82e+00
  angle pdb=" C   LEU B 351 "
        pdb=" N   PHE B 352 "
        pdb=" CA  PHE B 352 "
      ideal   model   delta    sigma   weight residual
     121.66  118.24    3.42 1.76e+00 3.23e-01 3.77e+00
  angle pdb=" C   LEU A 351 "
        pdb=" N   PHE A 352 "
        pdb=" CA  PHE A 352 "
      ideal   model   delta    sigma   weight residual
     121.66  118.25    3.41 1.76e+00 3.23e-01 3.76e+00
  ... (remaining 17785 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.30: 6947
       13.30 -    26.60: 688
       26.60 -    39.90: 310
       39.90 -    53.20: 45
       53.20 -    66.50: 10
  Dihedral angle restraints: 8000
    sinusoidal: 3300
      harmonic: 4700
  Sorted by residual:
  dihedral pdb=" CG  LYS D 104 "
           pdb=" CD  LYS D 104 "
           pdb=" CE  LYS D 104 "
           pdb=" NZ  LYS D 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.72  -57.72     3      1.50e+01 4.44e-03 9.45e+00
  dihedral pdb=" CG  LYS C 104 "
           pdb=" CD  LYS C 104 "
           pdb=" CE  LYS C 104 "
           pdb=" NZ  LYS C 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.69  -57.69     3      1.50e+01 4.44e-03 9.45e+00
  dihedral pdb=" CG  LYS E 104 "
           pdb=" CD  LYS E 104 "
           pdb=" CE  LYS E 104 "
           pdb=" NZ  LYS E 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.68  -57.68     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 7997 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1521
       0.030 -    0.060: 329
       0.060 -    0.091: 134
       0.091 -    0.121: 62
       0.121 -    0.151: 14
  Chirality restraints: 2060
  Sorted by residual:
  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    2.36    0.15 2.00e-01 2.50e+01 5.69e-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    2.36    0.15 2.00e-01 2.50e+01 5.59e-01
  chirality pdb=" CA  LEU D 167 "
            pdb=" N   LEU D 167 "
            pdb=" C   LEU D 167 "
            pdb=" CB  LEU D 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.53e-01
  ... (remaining 2057 not shown)

  Planarity restraints: 2250
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 145 "   -0.033 5.00e-02 4.00e+02   5.00e-02 4.00e+00
        pdb=" N   PRO D 146 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO D 146 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO D 146 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 145 "   -0.033 5.00e-02 4.00e+02   4.97e-02 3.95e+00
        pdb=" N   PRO C 146 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO C 146 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 146 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 145 "    0.033 5.00e-02 4.00e+02   4.97e-02 3.95e+00
        pdb=" N   PRO A 146 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 146 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 146 "    0.028 5.00e-02 4.00e+02
  ... (remaining 2247 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 4028
        2.84 -     3.35: 12930
        3.35 -     3.87: 21750
        3.87 -     4.38: 25115
        4.38 -     4.90: 43911
  Nonbonded interactions: 107734
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D 179 "
            pdb=" OE1 GLU D 190 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OG1 THR C 179 "
            pdb=" OE1 GLU C 190 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OG1 THR B 179 "
            pdb=" OE1 GLU B 190 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" OG1 THR A 179 "
            pdb=" OE1 GLU A 190 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" OG1 THR E 179 "
            pdb=" OE1 GLU E 190 "
     model   vdw
     2.320 3.040
  ... (remaining 107729 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 82 through 128 or resid 130 through 401))
  selection = (chain 'B' and (resid 82 through 128 or resid 130 through 401))
  selection = (chain 'C' and (resid 82 through 128 or resid 130 through 401))
  selection = (chain 'D' and (resid 82 through 128 or resid 130 through 401))
  selection = (chain 'E' and (resid 82 through 128 or resid 130 through 401))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     40.140
  Find NCS groups from input model:        0.780
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   56.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
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      :  0.002   0.022  13160  Z= 0.110
  Angle     :  0.442   5.196  17790  Z= 0.237
  Chirality :  0.036   0.151   2060
  Planarity :  0.004   0.050   2250
  Dihedral  : 12.813  66.498   4940
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.99 (0.21), residues: 1595
  helix:  3.48 (0.15), residues: 1085
  sheet:  1.45 (0.39), residues: 145
  loop :  0.39 (0.36), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 162 
 HIS   0.003   0.001   HIS A 122 
 PHE   0.014   0.001   PHE D 352 
 TYR   0.008   0.001   TYR C 299 
 ARG   0.002   0.000   ARG B 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08125 ( 1010)
  hydrogen bonds       : angle       4.08005 ( 2965)
  covalent geometry    : bond        0.00203 (13160)
  covalent geometry    : angle       0.44157 (17790)

*********************** 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
  290 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 290
  time to evaluate  : 1.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 GLN cc_start: 0.8540 (mt0) cc_final: 0.8333 (pm20)
REVERT: A  223 HIS cc_start: 0.8476 (m170) cc_final: 0.8144 (m-70)
REVERT: A  383 MET cc_start: 0.7776 (mmp) cc_final: 0.7520 (mpp)
REVERT: A  390 ARG cc_start: 0.7629 (mtt180) cc_final: 0.7196 (mpt180)
REVERT: A  391 ARG cc_start: 0.7405 (ttm-80) cc_final: 0.7044 (ttt180)
REVERT: B  121 GLN cc_start: 0.8605 (mt0) cc_final: 0.8352 (pm20)
REVERT: B  158 ASN cc_start: 0.9048 (m-40) cc_final: 0.8617 (t0)
REVERT: B  222 LYS cc_start: 0.8631 (pptt) cc_final: 0.8334 (pptt)
REVERT: B  383 MET cc_start: 0.7732 (mmp) cc_final: 0.7448 (mmt)
REVERT: B  390 ARG cc_start: 0.7511 (mtt180) cc_final: 0.7004 (mpt180)
REVERT: B  391 ARG cc_start: 0.7263 (ttm-80) cc_final: 0.6742 (ttt180)
REVERT: C  390 ARG cc_start: 0.7619 (mtt180) cc_final: 0.7049 (mpt180)
REVERT: C  391 ARG cc_start: 0.7249 (ttm-80) cc_final: 0.6795 (tmt170)
REVERT: D  121 GLN cc_start: 0.8661 (mt0) cc_final: 0.8443 (pm20)
REVERT: D  154 TYR cc_start: 0.8649 (p90) cc_final: 0.8384 (p90)
REVERT: D  253 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7883 (mm-30)
REVERT: D  261 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7601 (mp0)
REVERT: D  292 MET cc_start: 0.8802 (tpp) cc_final: 0.8482 (tpp)
REVERT: D  383 MET cc_start: 0.7792 (mmp) cc_final: 0.7556 (mpp)
REVERT: D  390 ARG cc_start: 0.7567 (mtt180) cc_final: 0.7232 (mpt180)
REVERT: D  391 ARG cc_start: 0.7312 (ttm-80) cc_final: 0.6672 (ttt180)
REVERT: E  292 MET cc_start: 0.8771 (tpp) cc_final: 0.8309 (tpp)
REVERT: E  383 MET cc_start: 0.7991 (mmp) cc_final: 0.7748 (mpp)
REVERT: E  390 ARG cc_start: 0.7614 (mtt180) cc_final: 0.7197 (mpt180)
REVERT: E  391 ARG cc_start: 0.7342 (ttm-80) cc_final: 0.6965 (ttt180)
  outliers start: 0
  outliers final: 1
  residues processed: 290
  average time/residue: 1.5182
  time to fit residues: 472.2660
Evaluate side-chains
  172 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 171
  time to evaluate  : 1.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  351 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 135 optimal weight:    3.9990
   chunk 121 optimal weight:    3.9990
   chunk 67 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 81 optimal weight:    0.7980
   chunk 64 optimal weight:    6.9990
   chunk 125 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 93 optimal weight:    7.9990
   chunk 145 optimal weight:    1.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 194 GLN
D 158 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.099601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.073180 restraints weight = 50649.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 3.92
r_work: 0.2765 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2768
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2768 r_free = 0.2768    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2768 r_free = 0.2768    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2768
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  13160  Z= 0.269
  Angle     :  0.601   9.602  17790  Z= 0.305
  Chirality :  0.043   0.232   2060
  Planarity :  0.005   0.051   2250
  Dihedral  :  3.824  14.667   1742
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  :  9.26 %
    Favored  : 88.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.60 (0.21), residues: 1595
  helix:  3.06 (0.15), residues: 1085
  sheet:  1.43 (0.38), residues: 145
  loop :  0.67 (0.38), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 196 
 HIS   0.004   0.001   HIS A 122 
 PHE   0.019   0.002   PHE A  86 
 TYR   0.026   0.003   TYR E 154 
 ARG   0.008   0.001   ARG A 301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04887 ( 1010)
  hydrogen bonds       : angle       3.97255 ( 2965)
  covalent geometry    : bond        0.00624 (13160)
  covalent geometry    : angle       0.60081 (17790)

*********************** 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
  192 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 162
  time to evaluate  : 1.410 
Fit side-chains
REVERT: A  390 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7194 (mpt180)
REVERT: A  391 ARG cc_start: 0.7593 (ttm-80) cc_final: 0.7119 (ttt180)
REVERT: B  222 LYS cc_start: 0.8602 (pptt) cc_final: 0.8287 (pptt)
REVERT: B  292 MET cc_start: 0.8935 (tpp) cc_final: 0.8390 (tpp)
REVERT: B  390 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7062 (mpt180)
REVERT: B  391 ARG cc_start: 0.7475 (ttm-80) cc_final: 0.6800 (tmt170)
REVERT: C  390 ARG cc_start: 0.7702 (mtt180) cc_final: 0.6967 (mpt180)
REVERT: C  391 ARG cc_start: 0.7509 (ttm-80) cc_final: 0.6776 (tmt170)
REVERT: D  253 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8233 (mm-30)
REVERT: D  261 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7700 (mp0)
REVERT: D  383 MET cc_start: 0.7807 (mmp) cc_final: 0.7572 (mpp)
REVERT: D  390 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7186 (mpt180)
REVERT: D  391 ARG cc_start: 0.7563 (ttm-80) cc_final: 0.6710 (ttt180)
REVERT: E  383 MET cc_start: 0.7997 (mmp) cc_final: 0.7723 (mpp)
REVERT: E  390 ARG cc_start: 0.7837 (mtt180) cc_final: 0.7227 (mpt180)
REVERT: E  391 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.7029 (ttt180)
  outliers start: 30
  outliers final: 9
  residues processed: 184
  average time/residue: 1.1420
  time to fit residues: 230.9346
Evaluate side-chains
  154 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 145
  time to evaluate  : 1.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 MET
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain C residue  297 GLU
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  338 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 136 optimal weight:    0.0570
   chunk 74 optimal weight:    0.9990
   chunk 78 optimal weight:    0.1980
   chunk 47 optimal weight:    0.7980
   chunk 84 optimal weight:    8.9990
   chunk 57 optimal weight:    4.9990
   chunk 157 optimal weight:   10.0000
   chunk 85 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
D 158 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.102715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.076511 restraints weight = 57573.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 4.21
r_work: 0.2781 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2840
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.1727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  13160  Z= 0.112
  Angle     :  0.490   9.468  17790  Z= 0.249
  Chirality :  0.039   0.241   2060
  Planarity :  0.004   0.053   2250
  Dihedral  :  3.629  13.310   1740
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  :  9.40 %
    Favored  : 88.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.68 (0.21), residues: 1595
  helix:  3.12 (0.15), residues: 1085
  sheet:  1.46 (0.39), residues: 145
  loop :  0.67 (0.37), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 162 
 HIS   0.004   0.001   HIS A 122 
 PHE   0.016   0.001   PHE C 352 
 TYR   0.021   0.002   TYR E 154 
 ARG   0.008   0.001   ARG A 301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04227 ( 1010)
  hydrogen bonds       : angle       3.72550 ( 2965)
  covalent geometry    : bond        0.00232 (13160)
  covalent geometry    : angle       0.48984 (17790)

*********************** 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
  201 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 171
  time to evaluate  : 1.417 
Fit side-chains
   revert: symmetry clash
REVERT: A  390 ARG cc_start: 0.7794 (mtt180) cc_final: 0.7160 (mpt180)
REVERT: A  391 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.7140 (ttt180)
REVERT: B  222 LYS cc_start: 0.8561 (pptt) cc_final: 0.8235 (pptt)
REVERT: B  390 ARG cc_start: 0.7646 (mtt180) cc_final: 0.6963 (mpt180)
REVERT: B  391 ARG cc_start: 0.7471 (ttm-80) cc_final: 0.6752 (tmt170)
REVERT: C  292 MET cc_start: 0.8907 (tpp) cc_final: 0.8346 (tpp)
REVERT: C  390 ARG cc_start: 0.7746 (mtt180) cc_final: 0.7028 (mpt180)
REVERT: C  391 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.6792 (tmt170)
REVERT: D  253 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8101 (mm-30)
REVERT: D  261 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7692 (mp0)
REVERT: D  390 ARG cc_start: 0.7751 (mtt180) cc_final: 0.7202 (mpt180)
REVERT: D  391 ARG cc_start: 0.7577 (ttm-80) cc_final: 0.6716 (ttt180)
REVERT: E   94 GLN cc_start: 0.8714 (mm110) cc_final: 0.8505 (mp10)
REVERT: E  137 MET cc_start: 0.9268 (mtm) cc_final: 0.9055 (mpp)
REVERT: E  390 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7138 (mpt180)
REVERT: E  391 ARG cc_start: 0.7599 (ttm-80) cc_final: 0.7099 (ttt180)
  outliers start: 30
  outliers final: 3
  residues processed: 186
  average time/residue: 1.2248
  time to fit residues: 249.6005
Evaluate side-chains
  159 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 156
  time to evaluate  : 1.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain C residue  297 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 133 optimal weight:    3.9990
   chunk 95 optimal weight:    4.9990
   chunk 150 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 112 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 106 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
D 158 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.095024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.069017 restraints weight = 49226.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 3.88
r_work: 0.2729 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2775
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2775 r_free = 0.2775    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2775 r_free = 0.2775    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2775
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  13160  Z= 0.238
  Angle     :  0.566   8.977  17790  Z= 0.287
  Chirality :  0.042   0.222   2060
  Planarity :  0.005   0.052   2250
  Dihedral  :  3.802  14.761   1740
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 10.67 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.44 (0.21), residues: 1595
  helix:  2.88 (0.15), residues: 1105
  sheet:  1.50 (0.39), residues: 145
  loop :  0.61 (0.39), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 375 
 HIS   0.004   0.001   HIS A 122 
 PHE   0.022   0.002   PHE A 374 
 TYR   0.032   0.003   TYR E 154 
 ARG   0.006   0.001   ARG A 301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04787 ( 1010)
  hydrogen bonds       : angle       3.98275 ( 2965)
  covalent geometry    : bond        0.00553 (13160)
  covalent geometry    : angle       0.56583 (17790)

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

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 156
  time to evaluate  : 1.406 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.9052 (ptm)
REVERT: A  390 ARG cc_start: 0.7860 (mtt180) cc_final: 0.7293 (mpt180)
REVERT: A  391 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.7157 (ttt180)
REVERT: B  292 MET cc_start: 0.8929 (tpp) cc_final: 0.8365 (tpp)
REVERT: B  390 ARG cc_start: 0.7670 (mtt180) cc_final: 0.7056 (mpt180)
REVERT: B  391 ARG cc_start: 0.7509 (ttm-80) cc_final: 0.6846 (tmt170)
REVERT: C  390 ARG cc_start: 0.7731 (mtt180) cc_final: 0.6999 (mpt180)
REVERT: C  391 ARG cc_start: 0.7588 (ttm-80) cc_final: 0.6870 (tmt170)
REVERT: D  253 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8295 (mm-30)
REVERT: D  261 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7687 (mp0)
REVERT: D  292 MET cc_start: 0.9029 (tpp) cc_final: 0.8623 (tpp)
REVERT: D  390 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7182 (mpt180)
REVERT: D  391 ARG cc_start: 0.7623 (ttm-80) cc_final: 0.6767 (ttt180)
REVERT: E  390 ARG cc_start: 0.7873 (mtt180) cc_final: 0.7250 (mpt180)
REVERT: E  391 ARG cc_start: 0.7545 (ttm-80) cc_final: 0.7051 (ttt180)
  outliers start: 30
  outliers final: 10
  residues processed: 175
  average time/residue: 1.1802
  time to fit residues: 226.1757
Evaluate side-chains
  158 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 1.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain C residue  297 GLU
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain C residue  383 MET
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  387 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 158 optimal weight:    7.9990
   chunk 89 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 113 optimal weight:    0.8980
   chunk 120 optimal weight:    1.9990
   overall best weight:    1.3384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.096187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.069810 restraints weight = 64568.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 4.34
r_work: 0.2779 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2784
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13160  Z= 0.154
  Angle     :  0.506   9.358  17790  Z= 0.258
  Chirality :  0.040   0.248   2060
  Planarity :  0.004   0.052   2250
  Dihedral  :  3.729  14.831   1740
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.79 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.48 (0.21), residues: 1595
  helix:  2.91 (0.15), residues: 1105
  sheet:  1.52 (0.40), residues: 145
  loop :  0.60 (0.39), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 375 
 HIS   0.004   0.001   HIS A 122 
 PHE   0.022   0.001   PHE A 374 
 TYR   0.034   0.002   TYR E 154 
 ARG   0.007   0.000   ARG E 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04482 ( 1010)
  hydrogen bonds       : angle       3.89306 ( 2965)
  covalent geometry    : bond        0.00350 (13160)
  covalent geometry    : angle       0.50599 (17790)

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

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 161
  time to evaluate  : 1.470 
Fit side-chains
   revert: symmetry clash
REVERT: A  390 ARG cc_start: 0.7774 (mtt180) cc_final: 0.7194 (mpt180)
REVERT: A  391 ARG cc_start: 0.7581 (ttm-80) cc_final: 0.7074 (ttt180)
REVERT: B  390 ARG cc_start: 0.7628 (mtt180) cc_final: 0.6967 (mpt180)
REVERT: B  391 ARG cc_start: 0.7468 (ttm-80) cc_final: 0.6841 (tmt170)
REVERT: C  390 ARG cc_start: 0.7655 (mtt180) cc_final: 0.6919 (mpt180)
REVERT: C  391 ARG cc_start: 0.7505 (ttm-80) cc_final: 0.6791 (tmt170)
REVERT: D  253 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8266 (mm-30)
REVERT: D  261 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7653 (mp0)
REVERT: D  292 MET cc_start: 0.8995 (tpp) cc_final: 0.8587 (tpp)
REVERT: D  390 ARG cc_start: 0.7704 (mtt180) cc_final: 0.7154 (mpt180)
REVERT: D  391 ARG cc_start: 0.7568 (ttm-80) cc_final: 0.6710 (ttt180)
REVERT: E  390 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7203 (mpt180)
REVERT: E  391 ARG cc_start: 0.7567 (ttm-80) cc_final: 0.7080 (ttt180)
  outliers start: 25
  outliers final: 9
  residues processed: 175
  average time/residue: 1.1306
  time to fit residues: 218.1567
Evaluate side-chains
  162 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 153
  time to evaluate  : 1.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain C residue  297 GLU
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  387 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 116 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 137 optimal weight:    8.9990
   chunk 131 optimal weight:    0.8980
   chunk 89 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 146 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   overall best weight:    1.5584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.095933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.070952 restraints weight = 35400.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 3.35
r_work: 0.2829 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2823
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2823 r_free = 0.2823    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2823 r_free = 0.2823    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2823
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13160  Z= 0.170
  Angle     :  0.526  10.202  17790  Z= 0.264
  Chirality :  0.040   0.262   2060
  Planarity :  0.004   0.051   2250
  Dihedral  :  3.726  14.647   1740
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 11.93 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.46 (0.21), residues: 1595
  helix:  2.88 (0.15), residues: 1105
  sheet:  1.58 (0.40), residues: 145
  loop :  0.61 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 389 
 HIS   0.004   0.001   HIS A 122 
 PHE   0.021   0.002   PHE A 374 
 TYR   0.035   0.003   TYR B 154 
 ARG   0.010   0.000   ARG E 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04529 ( 1010)
  hydrogen bonds       : angle       3.92237 ( 2965)
  covalent geometry    : bond        0.00390 (13160)
  covalent geometry    : angle       0.52589 (17790)

*********************** 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
  180 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 157
  time to evaluate  : 1.550 
Fit side-chains
   revert: symmetry clash
REVERT: A  390 ARG cc_start: 0.7781 (mtt180) cc_final: 0.7212 (mpt180)
REVERT: A  391 ARG cc_start: 0.7574 (ttm-80) cc_final: 0.7030 (ttt180)
REVERT: B  390 ARG cc_start: 0.7610 (mtt180) cc_final: 0.6960 (mpt180)
REVERT: B  391 ARG cc_start: 0.7449 (ttm-80) cc_final: 0.6854 (tmt170)
REVERT: C  390 ARG cc_start: 0.7647 (mtt180) cc_final: 0.6925 (mpt180)
REVERT: C  391 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.6798 (tmt170)
REVERT: D  253 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8237 (mm-30)
REVERT: D  261 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7635 (mp0)
REVERT: D  292 MET cc_start: 0.8990 (tpp) cc_final: 0.8569 (tpp)
REVERT: D  390 ARG cc_start: 0.7717 (mtt180) cc_final: 0.7162 (mpt180)
REVERT: D  391 ARG cc_start: 0.7560 (ttm-80) cc_final: 0.6720 (ttt180)
REVERT: E  390 ARG cc_start: 0.7813 (mtt180) cc_final: 0.7200 (mpt180)
REVERT: E  391 ARG cc_start: 0.7532 (ttm-80) cc_final: 0.7044 (ttt180)
  outliers start: 23
  outliers final: 11
  residues processed: 171
  average time/residue: 1.1438
  time to fit residues: 215.3221
Evaluate side-chains
  165 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 154
  time to evaluate  : 1.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain C residue  101 GLU
Chi-restraints excluded: chain C residue  297 GLU
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  387 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 152 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 147 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0670
   chunk 132 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 109 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.8920

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.101612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.075602 restraints weight = 52807.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 4.02
r_work: 0.2810 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2803
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2803
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13160  Z= 0.126
  Angle     :  0.489   9.207  17790  Z= 0.249
  Chirality :  0.039   0.261   2060
  Planarity :  0.004   0.052   2250
  Dihedral  :  3.644  14.475   1740
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 13.05 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.54 (0.21), residues: 1595
  helix:  2.95 (0.15), residues: 1105
  sheet:  1.65 (0.40), residues: 145
  loop :  0.59 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 162 
 HIS   0.004   0.001   HIS A 122 
 PHE   0.020   0.001   PHE A 374 
 TYR   0.035   0.002   TYR B 154 
 ARG   0.009   0.000   ARG E 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04322 ( 1010)
  hydrogen bonds       : angle       3.82241 ( 2965)
  covalent geometry    : bond        0.00275 (13160)
  covalent geometry    : angle       0.48854 (17790)

*********************** 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
  180 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 165
  time to evaluate  : 1.462 
Fit side-chains
   revert: symmetry clash
REVERT: A  390 ARG cc_start: 0.7811 (mtt180) cc_final: 0.7243 (mpt180)
REVERT: A  391 ARG cc_start: 0.7631 (ttm-80) cc_final: 0.7080 (ttt180)
REVERT: B  253 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8182 (mm-30)
REVERT: B  390 ARG cc_start: 0.7659 (mtt180) cc_final: 0.6985 (mpt180)
REVERT: B  391 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.6878 (tmt170)
REVERT: C  267 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8580 (mt-10)
REVERT: C  335 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8989 (mtm)
REVERT: C  390 ARG cc_start: 0.7671 (mtt180) cc_final: 0.6946 (mpt180)
REVERT: C  391 ARG cc_start: 0.7560 (ttm-80) cc_final: 0.6844 (tmt170)
REVERT: D  253 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8260 (mm-30)
REVERT: D  261 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7647 (mp0)
REVERT: D  292 MET cc_start: 0.8998 (tpp) cc_final: 0.8557 (tpp)
REVERT: D  390 ARG cc_start: 0.7770 (mtt180) cc_final: 0.7204 (mpt180)
REVERT: D  391 ARG cc_start: 0.7628 (ttm-80) cc_final: 0.6780 (ttt180)
REVERT: E   94 GLN cc_start: 0.8740 (mm110) cc_final: 0.8476 (mp10)
REVERT: E  390 ARG cc_start: 0.7790 (mtt180) cc_final: 0.7172 (mpt180)
REVERT: E  391 ARG cc_start: 0.7574 (ttm-80) cc_final: 0.7082 (ttt180)
  outliers start: 15
  outliers final: 8
  residues processed: 175
  average time/residue: 1.1211
  time to fit residues: 216.4876
Evaluate side-chains
  167 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 158
  time to evaluate  : 1.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain C residue  297 GLU
Chi-restraints excluded: chain C residue  335 MET
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  387 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 119 optimal weight:    0.9980
   chunk 117 optimal weight:    0.8980
   chunk 110 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 123 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.9784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.101594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.075231 restraints weight = 55894.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 4.14
r_work: 0.2790 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13160  Z= 0.131
  Angle     :  0.500  10.056  17790  Z= 0.252
  Chirality :  0.040   0.252   2060
  Planarity :  0.004   0.052   2250
  Dihedral  :  3.612  14.393   1740
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 13.05 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.55 (0.21), residues: 1595
  helix:  2.96 (0.15), residues: 1105
  sheet:  1.65 (0.40), residues: 145
  loop :  0.55 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 389 
 HIS   0.004   0.001   HIS A 122 
 PHE   0.017   0.001   PHE E 352 
 TYR   0.033   0.002   TYR B 154 
 ARG   0.009   0.000   ARG E 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04334 ( 1010)
  hydrogen bonds       : angle       3.78699 ( 2965)
  covalent geometry    : bond        0.00288 (13160)
  covalent geometry    : angle       0.49955 (17790)

*********************** 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
  176 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 159
  time to evaluate  : 1.414 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.8942 (mtp)
REVERT: A  390 ARG cc_start: 0.7800 (mtt180) cc_final: 0.7184 (mpt180)
REVERT: A  391 ARG cc_start: 0.7622 (ttm-80) cc_final: 0.6854 (ttt180)
REVERT: B  253 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8165 (mm-30)
REVERT: B  390 ARG cc_start: 0.7635 (mtt180) cc_final: 0.6963 (mpt180)
REVERT: B  391 ARG cc_start: 0.7475 (ttm-80) cc_final: 0.6827 (tmt170)
REVERT: C  335 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8982 (mtm)
REVERT: C  390 ARG cc_start: 0.7660 (mtt180) cc_final: 0.6933 (mpt180)
REVERT: C  391 ARG cc_start: 0.7575 (ttm-80) cc_final: 0.6852 (tmt170)
REVERT: D  253 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8262 (mm-30)
REVERT: D  261 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7648 (mp0)
REVERT: D  292 MET cc_start: 0.8983 (tpp) cc_final: 0.8560 (tpp)
REVERT: D  297 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8377 (tp30)
REVERT: D  390 ARG cc_start: 0.7766 (mtt180) cc_final: 0.7194 (mpt180)
REVERT: D  391 ARG cc_start: 0.7625 (ttm-80) cc_final: 0.6772 (ttt180)
REVERT: E  390 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7154 (mpt180)
REVERT: E  391 ARG cc_start: 0.7579 (ttm-80) cc_final: 0.7089 (ttt180)
  outliers start: 17
  outliers final: 10
  residues processed: 168
  average time/residue: 1.1283
  time to fit residues: 208.3229
Evaluate side-chains
  167 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 154
  time to evaluate  : 1.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  137 MET
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain C residue  297 GLU
Chi-restraints excluded: chain C residue  335 MET
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain D residue  297 GLU
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  387 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 136 optimal weight:    3.9990
   chunk 60 optimal weight:   10.0000
   chunk 157 optimal weight:    8.9990
   chunk 114 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0010
   chunk 109 optimal weight:    4.9990
   chunk 89 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 63 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.9994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.095317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.069231 restraints weight = 51878.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 3.97
r_work: 0.2736 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2783
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2783
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  13160  Z= 0.206
  Angle     :  0.538   9.098  17790  Z= 0.273
  Chirality :  0.041   0.243   2060
  Planarity :  0.004   0.051   2250
  Dihedral  :  3.762  15.337   1740
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 13.33 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.38 (0.21), residues: 1595
  helix:  2.82 (0.15), residues: 1105
  sheet:  1.64 (0.40), residues: 145
  loop :  0.52 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 389 
 HIS   0.004   0.001   HIS A 122 
 PHE   0.024   0.002   PHE C 374 
 TYR   0.035   0.003   TYR B 154 
 ARG   0.009   0.000   ARG E 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04689 ( 1010)
  hydrogen bonds       : angle       3.96235 ( 2965)
  covalent geometry    : bond        0.00477 (13160)
  covalent geometry    : angle       0.53763 (17790)

*********************** 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
  171 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 1.549 
Fit side-chains
REVERT: A  137 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.8936 (mtp)
REVERT: A  390 ARG cc_start: 0.7812 (mtt180) cc_final: 0.7242 (mpt180)
REVERT: A  391 ARG cc_start: 0.7627 (ttm-80) cc_final: 0.6830 (ttt180)
REVERT: B  253 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8210 (mm-30)
REVERT: B  292 MET cc_start: 0.8938 (tpp) cc_final: 0.8360 (tpp)
REVERT: B  390 ARG cc_start: 0.7634 (mtt180) cc_final: 0.6985 (mpt180)
REVERT: B  391 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.6889 (tmt170)
REVERT: C  335 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8934 (mtm)
REVERT: C  390 ARG cc_start: 0.7658 (mtt180) cc_final: 0.6938 (mpt180)
REVERT: C  391 ARG cc_start: 0.7538 (ttm-80) cc_final: 0.6802 (tmt170)
REVERT: D  253 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8283 (mm-30)
REVERT: D  261 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7680 (mp0)
REVERT: D  390 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7205 (mpt180)
REVERT: D  391 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.6712 (ttt180)
REVERT: E  304 ASP cc_start: 0.8855 (t0) cc_final: 0.8638 (t0)
REVERT: E  390 ARG cc_start: 0.7816 (mtt180) cc_final: 0.7207 (mpt180)
REVERT: E  391 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.7115 (ttt180)
  outliers start: 18
  outliers final: 12
  residues processed: 164
  average time/residue: 1.1747
  time to fit residues: 211.7840
Evaluate side-chains
  164 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 150
  time to evaluate  : 1.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  137 MET
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain C residue  297 GLU
Chi-restraints excluded: chain C residue  335 MET
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain D residue  297 GLU
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  355 MET
Chi-restraints excluded: chain E residue  338 LEU
Chi-restraints excluded: chain E residue  387 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 130 optimal weight:    0.9990
   chunk 131 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 118 optimal weight:    0.9990
   chunk 123 optimal weight:    4.9990
   chunk 72 optimal weight:    0.0570
   chunk 115 optimal weight:    0.0770
   chunk 27 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.5858

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.102377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.076418 restraints weight = 49721.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 3.95
r_work: 0.2824 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2849
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2849
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  13160  Z= 0.116
  Angle     :  0.494  11.059  17790  Z= 0.250
  Chirality :  0.039   0.261   2060
  Planarity :  0.004   0.053   2250
  Dihedral  :  3.630  14.085   1740
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 14.18 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.39 (0.21), residues: 1595
  helix:  2.87 (0.15), residues: 1105
  sheet:  1.64 (0.41), residues: 145
  loop :  0.41 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 389 
 HIS   0.004   0.001   HIS D 122 
 PHE   0.026   0.001   PHE C 374 
 TYR   0.032   0.002   TYR B 154 
 ARG   0.008   0.000   ARG E 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04302 ( 1010)
  hydrogen bonds       : angle       3.79978 ( 2965)
  covalent geometry    : bond        0.00240 (13160)
  covalent geometry    : angle       0.49395 (17790)

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

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 167
  time to evaluate  : 1.623 
Fit side-chains
   revert: symmetry clash
REVERT: A  390 ARG cc_start: 0.7815 (mtt180) cc_final: 0.7227 (mpt180)
REVERT: A  391 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.6830 (ttt180)
REVERT: B   93 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8429 (mttm)
REVERT: B  253 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8140 (mm-30)
REVERT: B  390 ARG cc_start: 0.7593 (mtt180) cc_final: 0.6942 (mpt180)
REVERT: B  391 ARG cc_start: 0.7467 (ttm-80) cc_final: 0.6862 (tmt170)
REVERT: C  390 ARG cc_start: 0.7626 (mtt180) cc_final: 0.6907 (mpt180)
REVERT: C  391 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.6851 (tmt170)
REVERT: D  253 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8245 (mm-30)
REVERT: D  261 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7626 (mp0)
REVERT: D  292 MET cc_start: 0.8956 (tpp) cc_final: 0.8620 (tpp)
REVERT: D  297 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8296 (tp30)
REVERT: D  390 ARG cc_start: 0.7747 (mtt180) cc_final: 0.7177 (mpt180)
REVERT: D  391 ARG cc_start: 0.7607 (ttm-80) cc_final: 0.6783 (tmt170)
REVERT: E   94 GLN cc_start: 0.8712 (mm110) cc_final: 0.8494 (mp10)
REVERT: E  390 ARG cc_start: 0.7792 (mtt180) cc_final: 0.7166 (mpt180)
REVERT: E  391 ARG cc_start: 0.7584 (ttm-80) cc_final: 0.7098 (ttt180)
  outliers start: 9
  outliers final: 7
  residues processed: 173
  average time/residue: 1.1766
  time to fit residues: 224.3596
Evaluate side-chains
  167 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 159
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain C residue  297 GLU
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain D residue  297 GLU
Chi-restraints excluded: chain E residue  387 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 67 optimal weight:    0.0010
   chunk 31 optimal weight:    0.8980
   chunk 159 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0670
   chunk 113 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 123 optimal weight:    5.9990
   chunk 136 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 51 optimal weight:    0.4980
   overall best weight:    0.4724

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.102480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.076805 restraints weight = 44727.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 3.77
r_work: 0.2843 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2837
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2837
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  13160  Z= 0.114
  Angle     :  0.491   9.251  17790  Z= 0.253
  Chirality :  0.040   0.265   2060
  Planarity :  0.004   0.053   2250
  Dihedral  :  3.579  14.911   1740
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 14.11 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.47 (0.21), residues: 1595
  helix:  2.95 (0.15), residues: 1105
  sheet:  1.53 (0.41), residues: 145
  loop :  0.40 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 389 
 HIS   0.004   0.001   HIS A 122 
 PHE   0.025   0.001   PHE C 374 
 TYR   0.035   0.002   TYR D 154 
 ARG   0.008   0.000   ARG E 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04236 ( 1010)
  hydrogen bonds       : angle       3.72631 ( 2965)
  covalent geometry    : bond        0.00236 (13160)
  covalent geometry    : angle       0.49077 (17790)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10073.23 seconds
wall clock time: 172 minutes 40.26 seconds (10360.26 seconds total)