Starting phenix.real_space_refine
on Wed Jul 30 22:22:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ip5_35632/07_2025/8ip5_35632.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ip5_35632/07_2025/8ip5_35632.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ip5_35632/07_2025/8ip5_35632.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ip5_35632/07_2025/8ip5_35632.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ip5_35632/07_2025/8ip5_35632.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ip5_35632/07_2025/8ip5_35632.cif"
  }
  resolution = 2.5
  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=   0.027
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    2370      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: 12928
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 2584
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
      Conformer: "B"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
          bond proxies already assigned to first conformer: 2613
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
      Conformer: "B"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
          bond proxies already assigned to first conformer: 2613
    Chain: "C"
      Number of atoms: 2584
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
      Conformer: "B"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
          bond proxies already assigned to first conformer: 2613
    Chain: "D"
      Number of atoms: 2584
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
      Conformer: "B"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
          bond proxies already assigned to first conformer: 2613
    Chain: "E"
      Number of atoms: 2584
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
      Conformer: "B"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
          bond proxies already assigned to first conformer: 2613
    Chain: "A"
      Number of atoms: 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: "C"
      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: 13.95, per 1000 atoms: 1.08
  Number of scatterers: 12928
  At special positions: 0
  Unit cell: (108.81, 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    2370      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: 3.12
  Conformation dependent library (CDL) restraints added in 2.9 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, 9.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 114 through 119
      removed outlier: 3.642A  pdb=" N   ARG A 119 " --> pdb=" O   ARG A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 173
      removed outlier: 4.238A  pdb=" N   LEU A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 183 through 219
      removed outlier: 3.645A  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: 3.865A  pdb=" N   GLU A 261 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 269
      removed outlier: 3.552A  pdb=" N   LEU A 265 " --> pdb=" O   GLU A 261 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   CYS A 269 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 275
      removed outlier: 3.866A  pdb=" N   ASP A 275 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 283
      removed outlier: 4.123A  pdb=" N   LYS A 281 " --> pdb=" O   GLN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 359
      removed outlier: 3.850A  pdb=" N   PHE A 359 " --> pdb=" O   MET A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 401
      removed outlier: 4.548A  pdb=" N   TRP A 375 " --> pdb=" O   HIS A 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 112
    Processing helix  chain 'B' and resid 114 through 119
      removed outlier: 3.642A  pdb=" N   ARG B 119 " --> pdb=" O   ARG B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 173
      removed outlier: 4.239A  pdb=" N   LEU B 167 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 183 through 219
      removed outlier: 3.646A  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: 3.865A  pdb=" N   GLU B 261 " --> pdb=" O   GLU B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 269
      removed outlier: 3.551A  pdb=" N   LEU B 265 " --> pdb=" O   GLU B 261 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   CYS B 269 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 275
      removed outlier: 3.866A  pdb=" N   ASP B 275 " --> pdb=" O   SER B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 283
      removed outlier: 4.122A  pdb=" N   LYS B 281 " --> pdb=" O   GLN B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 359
      removed outlier: 3.851A  pdb=" N   PHE B 359 " --> pdb=" O   MET B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 401
      removed outlier: 4.550A  pdb=" N   TRP B 375 " --> pdb=" O   HIS B 371 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 112
    Processing helix  chain 'C' and resid 114 through 119
      removed outlier: 3.642A  pdb=" N   ARG C 119 " --> pdb=" O   ARG C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 173
      removed outlier: 4.239A  pdb=" N   LEU C 167 " --> pdb=" O   LEU C 163 " (cutoff:3.500A)
      Proline residue:  C 168  - end of helix
    Processing helix  chain 'C' and resid 183 through 219
      removed outlier: 3.645A  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: 3.865A  pdb=" N   GLU C 261 " --> pdb=" O   GLU C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 269
      removed outlier: 3.552A  pdb=" N   LEU C 265 " --> pdb=" O   GLU C 261 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   CYS C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 275
      removed outlier: 3.866A  pdb=" N   ASP C 275 " --> pdb=" O   SER C 271 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 275 through 283
      removed outlier: 4.122A  pdb=" N   LYS C 281 " --> pdb=" O   GLN C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 359
      removed outlier: 3.851A  pdb=" N   PHE C 359 " --> pdb=" O   MET C 355 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 371 through 401
      removed outlier: 4.549A  pdb=" N   TRP C 375 " --> pdb=" O   HIS C 371 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 112
    Processing helix  chain 'D' and resid 114 through 119
      removed outlier: 3.642A  pdb=" N   ARG D 119 " --> pdb=" O   ARG D 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 173
      removed outlier: 4.238A  pdb=" N   LEU D 167 " --> pdb=" O   LEU D 163 " (cutoff:3.500A)
      Proline residue:  D 168  - end of helix
    Processing helix  chain 'D' and resid 183 through 219
      removed outlier: 3.646A  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: 3.865A  pdb=" N   GLU D 261 " --> pdb=" O   GLU D 257 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 261 through 269
      removed outlier: 3.552A  pdb=" N   LEU D 265 " --> pdb=" O   GLU D 261 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   CYS D 269 " --> pdb=" O   LEU D 265 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 275
      removed outlier: 3.866A  pdb=" N   ASP D 275 " --> pdb=" O   SER D 271 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 283
      removed outlier: 4.122A  pdb=" N   LYS D 281 " --> pdb=" O   GLN D 277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 359
      removed outlier: 3.851A  pdb=" N   PHE D 359 " --> pdb=" O   MET D 355 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 371 through 401
      removed outlier: 4.548A  pdb=" N   TRP D 375 " --> pdb=" O   HIS D 371 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 104 through 112
    Processing helix  chain 'E' and resid 114 through 119
      removed outlier: 3.642A  pdb=" N   ARG E 119 " --> pdb=" O   ARG E 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 159 through 173
      removed outlier: 4.238A  pdb=" N   LEU E 167 " --> pdb=" O   LEU E 163 " (cutoff:3.500A)
      Proline residue:  E 168  - end of helix
    Processing helix  chain 'E' and resid 183 through 219
      removed outlier: 3.645A  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: 3.865A  pdb=" N   GLU E 261 " --> pdb=" O   GLU E 257 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 261 through 269
      removed outlier: 3.552A  pdb=" N   LEU E 265 " --> pdb=" O   GLU E 261 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   CYS E 269 " --> pdb=" O   LEU E 265 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 275
      removed outlier: 3.867A  pdb=" N   ASP E 275 " --> pdb=" O   SER E 271 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 275 through 283
      removed outlier: 4.123A  pdb=" N   LYS E 281 " --> pdb=" O   GLN E 277 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 287 through 359
      removed outlier: 3.851A  pdb=" N   PHE E 359 " --> pdb=" O   MET E 355 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 371 through 401
      removed outlier: 4.549A  pdb=" N   TRP E 375 " --> pdb=" O   HIS E 371 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 103
      removed outlier: 4.137A  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: 4.137A  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: 4.138A  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: 4.138A  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: 4.138A  pdb=" N   LYS E 141 " --> pdb=" O   LEU E 152 " (cutoff:3.500A)

    1005 hydrogen bonds defined for protein.
    2935 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.87

  Time building geometry restraints manager: 3.71 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.34: 4235
        1.34 -     1.46: 2050
        1.46 -     1.57: 6750
        1.57 -     1.69: 0
        1.69 -     1.81: 120
  Bond restraints: 13155
  Sorted by residual:
  bond pdb=" N   GLY C 353 "
       pdb=" CA  GLY C 353 "
    ideal  model  delta    sigma   weight residual
    1.453  1.444  0.009 1.24e-02 6.50e+03 5.37e-01
  bond pdb=" CA  VAL B  82 "
       pdb=" CB  VAL B  82 "
    ideal  model  delta    sigma   weight residual
    1.540  1.521  0.019 2.70e-02 1.37e+03 5.17e-01
  bond pdb=" CB  MET B 344 "
       pdb=" CG  MET B 344 "
    ideal  model  delta    sigma   weight residual
    1.520  1.498  0.022 3.00e-02 1.11e+03 5.16e-01
  bond pdb=" CB  MET C 344 "
       pdb=" CG  MET C 344 "
    ideal  model  delta    sigma   weight residual
    1.520  1.499  0.021 3.00e-02 1.11e+03 5.09e-01
  bond pdb=" CB  MET D 344 "
       pdb=" CG  MET D 344 "
    ideal  model  delta    sigma   weight residual
    1.520  1.499  0.021 3.00e-02 1.11e+03 5.09e-01
  ... (remaining 13150 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.00: 17221
        1.00 -     1.99: 446
        1.99 -     2.99: 69
        2.99 -     3.98: 34
        3.98 -     4.98: 15
  Bond angle restraints: 17785
  Sorted by residual:
  angle pdb=" N   LEU B 354 "
        pdb=" CA  LEU B 354 "
        pdb=" C   LEU B 354 "
      ideal   model   delta    sigma   weight residual
     111.28  109.20    2.08 1.09e+00 8.42e-01 3.63e+00
  angle pdb=" N   LEU E 354 "
        pdb=" CA  LEU E 354 "
        pdb=" C   LEU E 354 "
      ideal   model   delta    sigma   weight residual
     111.28  109.21    2.07 1.09e+00 8.42e-01 3.59e+00
  angle pdb=" N   LEU D 354 "
        pdb=" CA  LEU D 354 "
        pdb=" C   LEU D 354 "
      ideal   model   delta    sigma   weight residual
     111.28  109.25    2.03 1.09e+00 8.42e-01 3.48e+00
  angle pdb=" N   LEU A 354 "
        pdb=" CA  LEU A 354 "
        pdb=" C   LEU A 354 "
      ideal   model   delta    sigma   weight residual
     111.28  109.25    2.03 1.09e+00 8.42e-01 3.46e+00
  angle pdb=" N   LEU C 354 "
        pdb=" CA  LEU C 354 "
        pdb=" C   LEU C 354 "
      ideal   model   delta    sigma   weight residual
     111.28  109.26    2.02 1.09e+00 8.42e-01 3.45e+00
  ... (remaining 17780 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 7325
       17.43 -    34.86: 580
       34.86 -    52.30: 70
       52.30 -    69.73: 10
       69.73 -    87.16: 10
  Dihedral angle restraints: 7995
    sinusoidal: 3295
      harmonic: 4700
  Sorted by residual:
  dihedral pdb=" CB  GLU E 147 "
           pdb=" CG  GLU E 147 "
           pdb=" CD  GLU E 147 "
           pdb=" OE1 GLU E 147 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.16  -87.16     1      3.00e+01 1.11e-03 1.01e+01
  dihedral pdb=" CB  GLU B 147 "
           pdb=" CG  GLU B 147 "
           pdb=" CD  GLU B 147 "
           pdb=" OE1 GLU B 147 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.14  -87.14     1      3.00e+01 1.11e-03 1.01e+01
  dihedral pdb=" CB  GLU C 147 "
           pdb=" CG  GLU C 147 "
           pdb=" CD  GLU C 147 "
           pdb=" OE1 GLU C 147 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.07  -87.07     1      3.00e+01 1.11e-03 1.01e+01
  ... (remaining 7992 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 1289
       0.025 -    0.050: 446
       0.050 -    0.074: 218
       0.074 -    0.099: 54
       0.099 -    0.124: 53
  Chirality restraints: 2060
  Sorted by residual:
  chirality pdb=" CA  LEU B 167 "
            pdb=" N   LEU B 167 "
            pdb=" C   LEU B 167 "
            pdb=" CB  LEU B 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.84e-01
  chirality pdb=" CA  LEU E 167 "
            pdb=" N   LEU E 167 "
            pdb=" C   LEU E 167 "
            pdb=" CB  LEU E 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.79e-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    2.39    0.12 2.00e-01 2.50e+01 3.72e-01
  ... (remaining 2057 not shown)

  Planarity restraints: 2250
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 182 "   -0.017 5.00e-02 4.00e+02   2.64e-02 1.12e+00
        pdb=" N   PRO A 183 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO A 183 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 183 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 182 "   -0.017 5.00e-02 4.00e+02   2.64e-02 1.11e+00
        pdb=" N   PRO C 183 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO C 183 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO C 183 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 182 "   -0.017 5.00e-02 4.00e+02   2.63e-02 1.11e+00
        pdb=" N   PRO D 183 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO D 183 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO D 183 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 2247 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2121
        2.77 -     3.30: 12626
        3.30 -     3.83: 22547
        3.83 -     4.37: 25128
        4.37 -     4.90: 45168
  Nonbonded interactions: 107590
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 179 "
            pdb=" OE1 GLU B 190 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OG1 THR E 179 "
            pdb=" OE1 GLU E 190 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OG1 THR A 179 "
            pdb=" OE1 GLU A 190 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OG1 THR C 179 "
            pdb=" OE1 GLU C 190 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OG1 THR D 179 "
            pdb=" OE1 GLU D 190 "
     model   vdw
     2.236 3.040
  ... (remaining 107585 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.770
  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:          0.530
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     38.980
  Find NCS groups from input model:        0.580
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
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  13155  Z= 0.112
  Angle     :  0.434   4.981  17785  Z= 0.241
  Chirality :  0.036   0.124   2060
  Planarity :  0.003   0.026   2250
  Dihedral  : 12.761  87.159   4935
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.88 (0.21), residues: 1595
  helix:  3.36 (0.15), residues: 1070
  sheet:  2.09 (0.37), residues: 145
  loop :  0.28 (0.35), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 196 
 HIS   0.002   0.000   HIS B 122 
 PHE   0.014   0.001   PHE A 352 
 TYR   0.012   0.001   TYR A 299 
 ARG   0.002   0.000   ARG B 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08422 ( 1005)
  hydrogen bonds       : angle       4.33404 ( 2935)
  covalent geometry    : bond        0.00211 (13155)
  covalent geometry    : angle       0.43424 (17785)

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

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 274
  time to evaluate  : 1.516 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8052 (mm-30)
REVERT: A  286 ILE cc_start: 0.8478 (mt) cc_final: 0.8115 (mp)
REVERT: A  344 MET cc_start: 0.8824 (mtt) cc_final: 0.8570 (mtt)
REVERT: A  390 ARG cc_start: 0.7591 (mtt180) cc_final: 0.7371 (mpt180)
REVERT: B  286 ILE cc_start: 0.8474 (mt) cc_final: 0.8115 (mp)
REVERT: C  103 LYS cc_start: 0.8760 (mttm) cc_final: 0.8526 (mmmm)
REVERT: C  138 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8010 (mm-30)
REVERT: C  368 GLU cc_start: 0.7688 (mp0) cc_final: 0.7470 (mp0)
REVERT: D  109 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8320 (tm-30)
REVERT: D  138 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8047 (mm-30)
REVERT: D  286 ILE cc_start: 0.8508 (mt) cc_final: 0.8154 (mp)
REVERT: E  138 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8026 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 274
  average time/residue: 1.5134
  time to fit residues: 445.2419
Evaluate side-chains
  182 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 135 optimal weight:    1.9990
   chunk 121 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 41 optimal weight:    9.9990
   chunk 81 optimal weight:    2.9990
   chunk 64 optimal weight:    7.9990
   chunk 125 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 145 optimal weight:    4.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 121 GLN
C 121 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.100327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.071715 restraints weight = 52798.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.2931 rms_B_bonded: 4.06
r_work: 0.2719 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2717
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2717 r_free = 0.2717    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 = 0.2717 r_free = 0.2717    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2717
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040  13155  Z= 0.272
  Angle     :  0.614   9.580  17785  Z= 0.306
  Chirality :  0.044   0.229   2060
  Planarity :  0.004   0.038   2250
  Dihedral  :  4.046  15.753   1740
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  8.80 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.40 (0.21), residues: 1595
  helix:  2.85 (0.15), residues: 1080
  sheet:  2.14 (0.37), residues: 145
  loop :  0.43 (0.37), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 162 
 HIS   0.002   0.001   HIS C 331 
 PHE   0.026   0.002   PHE A  86 
 TYR   0.025   0.002   TYR D 299 
 ARG   0.011   0.001   ARG A 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05444 ( 1005)
  hydrogen bonds       : angle       4.06491 ( 2935)
  covalent geometry    : bond        0.00637 (13155)
  covalent geometry    : angle       0.61376 (17785)

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

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 163
  time to evaluate  : 1.544 
Fit side-chains
REVERT: A  286 ILE cc_start: 0.8590 (mt) cc_final: 0.8198 (mp)
REVERT: A  344 MET cc_start: 0.9064 (mtt) cc_final: 0.8820 (mtt)
REVERT: A  368 GLU cc_start: 0.7973 (mp0) cc_final: 0.7602 (mp0)
REVERT: A  390 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7437 (mpt180)
REVERT: B  286 ILE cc_start: 0.8493 (mt) cc_final: 0.8088 (mp)
REVERT: C  368 GLU cc_start: 0.7914 (mp0) cc_final: 0.7479 (mp0)
REVERT: D  109 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8582 (tm-30)
REVERT: D  286 ILE cc_start: 0.8581 (mt) cc_final: 0.8157 (mp)
REVERT: D  391 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6855 (ttp-170)
REVERT: E  124 MET cc_start: 0.9006 (tpt) cc_final: 0.8672 (tpp)
REVERT: E  190 GLU cc_start: 0.8822 (tt0) cc_final: 0.8456 (tt0)
  outliers start: 17
  outliers final: 0
  residues processed: 168
  average time/residue: 1.5367
  time to fit residues: 277.7061
Evaluate side-chains
  143 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 1.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  391 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 101 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 146 optimal weight:    0.7980
   chunk 136 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3448 r_free = 0.3448 target = 0.106431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.079482 restraints weight = 42365.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 3.58
r_work: 0.2857 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2849
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2849
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  13155  Z= 0.123
  Angle     :  0.480   9.595  17785  Z= 0.247
  Chirality :  0.039   0.215   2060
  Planarity :  0.003   0.029   2250
  Dihedral  :  3.862  14.705   1740
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  9.23 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.56 (0.21), residues: 1595
  helix:  3.08 (0.15), residues: 1050
  sheet:  2.13 (0.37), residues: 145
  loop :  0.40 (0.35), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 162 
 HIS   0.001   0.000   HIS D 371 
 PHE   0.015   0.001   PHE A 352 
 TYR   0.017   0.002   TYR A 154 
 ARG   0.008   0.001   ARG C 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04689 ( 1005)
  hydrogen bonds       : angle       3.79749 ( 2935)
  covalent geometry    : bond        0.00264 (13155)
  covalent geometry    : angle       0.48028 (17785)

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

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 171
  time to evaluate  : 1.657 
Fit side-chains
REVERT: A  137 MET cc_start: 0.9338 (mpp) cc_final: 0.8981 (mtt)
REVERT: A  138 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8522 (mm-30)
REVERT: A  286 ILE cc_start: 0.8620 (mt) cc_final: 0.8235 (mp)
REVERT: A  344 MET cc_start: 0.9051 (mtt) cc_final: 0.8804 (mtt)
REVERT: A  368 GLU cc_start: 0.7889 (mp0) cc_final: 0.7499 (mp0)
REVERT: A  390 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7416 (mpt180)
REVERT: B  286 ILE cc_start: 0.8546 (mt) cc_final: 0.8151 (mp)
REVERT: C  138 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8501 (mm-30)
REVERT: C  368 GLU cc_start: 0.7877 (mp0) cc_final: 0.7460 (mp0)
REVERT: D  109 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8540 (tm-30)
REVERT: D  286 ILE cc_start: 0.8611 (mt) cc_final: 0.8203 (mp)
REVERT: D  337 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8206 (ttm-80)
REVERT: D  391 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6792 (ttp-170)
REVERT: E  138 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8498 (mm-30)
REVERT: E  368 GLU cc_start: 0.7817 (mp0) cc_final: 0.7499 (mp0)
REVERT: E  391 ARG cc_start: 0.7278 (ttt180) cc_final: 0.6979 (mmm160)
  outliers start: 11
  outliers final: 1
  residues processed: 175
  average time/residue: 1.6234
  time to fit residues: 306.2462
Evaluate side-chains
  168 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 165
  time to evaluate  : 1.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain D residue  337 ARG
Chi-restraints excluded: chain D residue  391 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 129 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 125 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 70 optimal weight:    0.8980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.106639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.078997 restraints weight = 53900.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 3.94
r_work: 0.2820 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2822
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13155  Z= 0.141
  Angle     :  0.501   9.260  17785  Z= 0.252
  Chirality :  0.039   0.208   2060
  Planarity :  0.003   0.028   2250
  Dihedral  :  3.842  14.281   1740
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 10.07 %
    Favored  : 89.08 %
  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:  3.62 (0.21), residues: 1595
  helix:  3.10 (0.15), residues: 1050
  sheet:  2.23 (0.37), residues: 145
  loop :  0.46 (0.35), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 162 
 HIS   0.001   0.000   HIS D 371 
 PHE   0.016   0.001   PHE A  86 
 TYR   0.019   0.002   TYR B 299 
 ARG   0.006   0.001   ARG C 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04749 ( 1005)
  hydrogen bonds       : angle       3.79986 ( 2935)
  covalent geometry    : bond        0.00313 (13155)
  covalent geometry    : angle       0.50128 (17785)

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

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 170
  time to evaluate  : 2.784 
Fit side-chains
REVERT: A  137 MET cc_start: 0.9349 (mpp) cc_final: 0.9046 (mtt)
REVERT: A  138 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8549 (mm-30)
REVERT: A  286 ILE cc_start: 0.8622 (mt) cc_final: 0.8235 (mp)
REVERT: A  344 MET cc_start: 0.9101 (mtt) cc_final: 0.8871 (mtt)
REVERT: A  368 GLU cc_start: 0.7936 (mp0) cc_final: 0.7523 (mp0)
REVERT: A  390 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7455 (mpt180)
REVERT: B  138 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8580 (mm-30)
REVERT: B  286 ILE cc_start: 0.8576 (mt) cc_final: 0.8181 (mp)
REVERT: C  138 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8530 (mm-30)
REVERT: C  368 GLU cc_start: 0.7927 (mp0) cc_final: 0.7477 (mp0)
REVERT: D  109 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8552 (tm-30)
REVERT: D  286 ILE cc_start: 0.8639 (mt) cc_final: 0.8223 (mp)
REVERT: D  337 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8247 (ttm-80)
REVERT: D  391 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6830 (ttp-170)
REVERT: E  138 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8538 (mm-30)
REVERT: E  297 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8134 (tt0)
REVERT: E  368 GLU cc_start: 0.7870 (mp0) cc_final: 0.7507 (mp0)
  outliers start: 12
  outliers final: 3
  residues processed: 174
  average time/residue: 1.8449
  time to fit residues: 349.5211
Evaluate side-chains
  166 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 160
  time to evaluate  : 1.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain C residue  314 ARG
Chi-restraints excluded: chain D residue  337 ARG
Chi-restraints excluded: chain D residue  373 ILE
Chi-restraints excluded: chain D residue  391 ARG
Chi-restraints excluded: chain E residue  297 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 157 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 48 optimal weight:    2.9990
   chunk 98 optimal weight:    5.9990
   chunk 79 optimal weight:    3.9990
   chunk 70 optimal weight:    0.6980
   chunk 71 optimal weight:    0.6980
   chunk 76 optimal weight:    0.5980
   chunk 132 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   overall best weight:    1.7984

-------------------------------------------------------------------------------
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 = 0.3423 r_free = 0.3423 target = 0.104792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.077190 restraints weight = 48105.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 3.76
r_work: 0.2820 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2811
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2811
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  13155  Z= 0.198
  Angle     :  0.529   8.569  17785  Z= 0.268
  Chirality :  0.040   0.230   2060
  Planarity :  0.003   0.028   2250
  Dihedral  :  3.985  14.804   1740
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 10.28 %
    Favored  : 88.66 %
  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:  3.59 (0.21), residues: 1595
  helix:  3.12 (0.15), residues: 1040
  sheet:  2.27 (0.38), residues: 145
  loop :  0.38 (0.34), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 162 
 HIS   0.002   0.001   HIS D 371 
 PHE   0.020   0.002   PHE A  86 
 TYR   0.022   0.002   TYR B 299 
 ARG   0.006   0.001   ARG D 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05093 ( 1005)
  hydrogen bonds       : angle       3.91453 ( 2935)
  covalent geometry    : bond        0.00461 (13155)
  covalent geometry    : angle       0.52889 (17785)

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

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 1.507 
Fit side-chains
REVERT: A  137 MET cc_start: 0.9328 (mpp) cc_final: 0.9045 (mtt)
REVERT: A  138 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8499 (mm-30)
REVERT: A  190 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8306 (tp30)
REVERT: A  286 ILE cc_start: 0.8626 (mt) cc_final: 0.8242 (mp)
REVERT: A  344 MET cc_start: 0.9065 (mtt) cc_final: 0.8822 (mtt)
REVERT: A  368 GLU cc_start: 0.7966 (mp0) cc_final: 0.7548 (mp0)
REVERT: A  390 ARG cc_start: 0.8050 (mtt180) cc_final: 0.7386 (mpt180)
REVERT: B  286 ILE cc_start: 0.8521 (mt) cc_final: 0.8128 (mp)
REVERT: C  368 GLU cc_start: 0.7958 (mp0) cc_final: 0.7476 (mp0)
REVERT: D  109 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8558 (tm-30)
REVERT: D  286 ILE cc_start: 0.8592 (mt) cc_final: 0.8172 (mp)
REVERT: D  391 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6806 (ttp-170)
REVERT: E  124 MET cc_start: 0.8870 (tpt) cc_final: 0.8550 (tpp)
REVERT: E  138 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8534 (mm-30)
REVERT: E  297 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8187 (tt0)
  outliers start: 15
  outliers final: 3
  residues processed: 163
  average time/residue: 1.5119
  time to fit residues: 265.4024
Evaluate side-chains
  160 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 154
  time to evaluate  : 1.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 GLU
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain C residue  314 ARG
Chi-restraints excluded: chain D residue  391 ARG
Chi-restraints excluded: chain E residue  297 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 109 optimal weight:    0.9990
   chunk 122 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 137 optimal weight:   10.0000
   chunk 157 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 148 optimal weight:    5.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3456 r_free = 0.3456 target = 0.106857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.079149 restraints weight = 53618.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 3.93
r_work: 0.2832 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2836
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2836
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  13155  Z= 0.127
  Angle     :  0.481   9.530  17785  Z= 0.244
  Chirality :  0.039   0.218   2060
  Planarity :  0.003   0.030   2250
  Dihedral  :  3.851  15.115   1740
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 11.20 %
    Favored  : 88.17 %
  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:  3.63 (0.21), residues: 1595
  helix:  3.10 (0.15), residues: 1050
  sheet:  2.25 (0.37), residues: 145
  loop :  0.49 (0.35), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 196 
 HIS   0.001   0.000   HIS C 371 
 PHE   0.017   0.001   PHE A 352 
 TYR   0.020   0.002   TYR B 299 
 ARG   0.007   0.001   ARG D 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04678 ( 1005)
  hydrogen bonds       : angle       3.78391 ( 2935)
  covalent geometry    : bond        0.00276 (13155)
  covalent geometry    : angle       0.48078 (17785)

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

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 167
  time to evaluate  : 1.679 
Fit side-chains
REVERT: A  137 MET cc_start: 0.9326 (mpp) cc_final: 0.9030 (mtt)
REVERT: A  138 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8559 (mm-30)
REVERT: A  190 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8329 (tp30)
REVERT: A  286 ILE cc_start: 0.8633 (mt) cc_final: 0.8239 (mp)
REVERT: A  344 MET cc_start: 0.9105 (mtt) cc_final: 0.8869 (mtt)
REVERT: A  368 GLU cc_start: 0.7950 (mp0) cc_final: 0.7540 (mp0)
REVERT: A  390 ARG cc_start: 0.8085 (mtt180) cc_final: 0.7441 (mpt180)
REVERT: B  286 ILE cc_start: 0.8561 (mt) cc_final: 0.8173 (mp)
REVERT: C  138 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8518 (mm-30)
REVERT: C  368 GLU cc_start: 0.7948 (mp0) cc_final: 0.7458 (mp0)
REVERT: D  109 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8545 (tm-30)
REVERT: D  286 ILE cc_start: 0.8636 (mt) cc_final: 0.8208 (mp)
REVERT: D  391 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6828 (ttp-170)
REVERT: E  138 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8575 (mm-30)
REVERT: E  297 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8088 (tt0)
REVERT: E  368 GLU cc_start: 0.7934 (mp0) cc_final: 0.7561 (mp0)
  outliers start: 9
  outliers final: 2
  residues processed: 172
  average time/residue: 1.5572
  time to fit residues: 290.7825
Evaluate side-chains
  169 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 164
  time to evaluate  : 1.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 GLU
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain D residue  391 ARG
Chi-restraints excluded: chain E residue  297 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 64 optimal weight:    7.9990
   chunk 79 optimal weight:    4.9990
   chunk 127 optimal weight:    2.9990
   chunk 141 optimal weight:    4.9990
   chunk 121 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 85 optimal weight:    3.9990
   chunk 131 optimal weight:    0.7980
   chunk 155 optimal weight:    0.9980
   chunk 80 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   overall best weight:    1.7584

-------------------------------------------------------------------------------
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 = 0.3421 r_free = 0.3421 target = 0.104664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.076513 restraints weight = 60718.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 4.14
r_work: 0.2760 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2775
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2775 r_free = 0.2775    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2775 r_free = 0.2775    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2775
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  13155  Z= 0.195
  Angle     :  0.536  10.014  17785  Z= 0.269
  Chirality :  0.040   0.235   2060
  Planarity :  0.003   0.029   2250
  Dihedral  :  3.998  14.937   1740
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 11.41 %
    Favored  : 87.89 %
  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:  3.42 (0.21), residues: 1595
  helix:  2.91 (0.15), residues: 1070
  sheet:  2.27 (0.38), residues: 145
  loop :  0.31 (0.36), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 196 
 HIS   0.002   0.001   HIS A 371 
 PHE   0.019   0.002   PHE A  86 
 TYR   0.024   0.002   TYR B 299 
 ARG   0.008   0.001   ARG D 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05067 ( 1005)
  hydrogen bonds       : angle       3.90797 ( 2935)
  covalent geometry    : bond        0.00452 (13155)
  covalent geometry    : angle       0.53609 (17785)

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

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 158
  time to evaluate  : 1.509 
Fit side-chains
REVERT: A  137 MET cc_start: 0.9356 (mpp) cc_final: 0.9027 (mtt)
REVERT: A  138 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8542 (mm-30)
REVERT: A  190 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8334 (tp30)
REVERT: A  286 ILE cc_start: 0.8640 (mt) cc_final: 0.8244 (mp)
REVERT: A  344 MET cc_start: 0.9127 (mtt) cc_final: 0.8902 (mtt)
REVERT: A  368 GLU cc_start: 0.8002 (mp0) cc_final: 0.7551 (mp0)
REVERT: A  390 ARG cc_start: 0.8108 (mtt180) cc_final: 0.7455 (mpt180)
REVERT: B  286 ILE cc_start: 0.8559 (mt) cc_final: 0.8168 (mp)
REVERT: C  138 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8535 (mm-30)
REVERT: C  368 GLU cc_start: 0.8029 (mp0) cc_final: 0.7515 (mp0)
REVERT: D  109 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8606 (tm-30)
REVERT: D  286 ILE cc_start: 0.8624 (mt) cc_final: 0.8193 (mp)
REVERT: D  391 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6882 (ttp-170)
REVERT: E  124 MET cc_start: 0.8917 (tpt) cc_final: 0.8598 (tpp)
REVERT: E  138 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8581 (mm-30)
REVERT: E  297 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8247 (tt0)
  outliers start: 10
  outliers final: 1
  residues processed: 163
  average time/residue: 1.4368
  time to fit residues: 252.4832
Evaluate side-chains
  161 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 157
  time to evaluate  : 1.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 GLU
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain D residue  391 ARG
Chi-restraints excluded: chain E residue  297 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 141 optimal weight:    0.9990
   chunk 118 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 146 optimal weight:    0.7980
   chunk 113 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3450 r_free = 0.3450 target = 0.106420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.078559 restraints weight = 58220.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 4.07
r_work: 0.2809 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2816
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2816 r_free = 0.2816    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2816 r_free = 0.2816    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2816
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13155  Z= 0.132
  Angle     :  0.495   9.317  17785  Z= 0.249
  Chirality :  0.039   0.234   2060
  Planarity :  0.003   0.030   2250
  Dihedral  :  3.897  18.323   1740
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 11.97 %
    Favored  : 87.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.52 (0.21), residues: 1595
  helix:  3.00 (0.15), residues: 1070
  sheet:  2.23 (0.38), residues: 145
  loop :  0.32 (0.36), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 196 
 HIS   0.001   0.000   HIS C 371 
 PHE   0.016   0.001   PHE A 352 
 TYR   0.021   0.002   TYR B 299 
 ARG   0.008   0.001   ARG D 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04715 ( 1005)
  hydrogen bonds       : angle       3.80536 ( 2935)
  covalent geometry    : bond        0.00288 (13155)
  covalent geometry    : angle       0.49531 (17785)

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

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 168
  time to evaluate  : 1.500 
Fit side-chains
REVERT: A  137 MET cc_start: 0.9331 (mpp) cc_final: 0.9012 (mtt)
REVERT: A  138 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8579 (mm-30)
REVERT: A  190 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8335 (tp30)
REVERT: A  286 ILE cc_start: 0.8654 (mt) cc_final: 0.8256 (mp)
REVERT: A  344 MET cc_start: 0.9131 (mtt) cc_final: 0.8900 (mtt)
REVERT: A  368 GLU cc_start: 0.7975 (mp0) cc_final: 0.7514 (mp0)
REVERT: A  390 ARG cc_start: 0.8084 (mtt180) cc_final: 0.7428 (mpt180)
REVERT: B  138 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8545 (mm-30)
REVERT: B  286 ILE cc_start: 0.8578 (mt) cc_final: 0.8191 (mp)
REVERT: C  138 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8530 (mm-30)
REVERT: C  368 GLU cc_start: 0.8009 (mp0) cc_final: 0.7501 (mp0)
REVERT: D  109 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8554 (tm-30)
REVERT: D  286 ILE cc_start: 0.8643 (mt) cc_final: 0.8211 (mp)
REVERT: D  391 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6839 (ttp-170)
REVERT: E  138 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8596 (mm-30)
REVERT: E  297 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8112 (tt0)
REVERT: E  368 GLU cc_start: 0.7920 (mp0) cc_final: 0.7551 (mp0)
  outliers start: 7
  outliers final: 1
  residues processed: 171
  average time/residue: 1.3899
  time to fit residues: 256.7652
Evaluate side-chains
  166 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 162
  time to evaluate  : 1.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 GLU
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain D residue  391 ARG
Chi-restraints excluded: chain E residue  297 GLU
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 84 optimal weight:    4.9990
   chunk 131 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 143 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 20 optimal weight:    9.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.3447 r_free = 0.3447 target = 0.106467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.077835 restraints weight = 59471.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 4.26
r_work: 0.2784 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2801
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2801 r_free = 0.2801    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2801 r_free = 0.2801    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2801
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13155  Z= 0.140
  Angle     :  0.500   9.210  17785  Z= 0.252
  Chirality :  0.039   0.238   2060
  Planarity :  0.003   0.033   2250
  Dihedral  :  3.895  15.290   1740
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 11.69 %
    Favored  : 87.89 %
  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:  3.53 (0.21), residues: 1595
  helix:  3.01 (0.15), residues: 1070
  sheet:  2.20 (0.38), residues: 145
  loop :  0.35 (0.36), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 196 
 HIS   0.001   0.000   HIS C 371 
 PHE   0.017   0.001   PHE A 352 
 TYR   0.022   0.002   TYR B 299 
 ARG   0.008   0.001   ARG E 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04746 ( 1005)
  hydrogen bonds       : angle       3.79756 ( 2935)
  covalent geometry    : bond        0.00311 (13155)
  covalent geometry    : angle       0.50001 (17785)

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

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 165
  time to evaluate  : 1.685 
Fit side-chains
REVERT: A  137 MET cc_start: 0.9346 (mpp) cc_final: 0.8979 (mtt)
REVERT: A  138 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8574 (mm-30)
REVERT: A  190 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8342 (tp30)
REVERT: A  286 ILE cc_start: 0.8623 (mt) cc_final: 0.8221 (mp)
REVERT: A  344 MET cc_start: 0.9120 (mtt) cc_final: 0.8890 (mtt)
REVERT: A  368 GLU cc_start: 0.7981 (mp0) cc_final: 0.7514 (mp0)
REVERT: A  390 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7402 (mpt180)
REVERT: B  286 ILE cc_start: 0.8575 (mt) cc_final: 0.8183 (mp)
REVERT: C  138 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8521 (mm-30)
REVERT: C  368 GLU cc_start: 0.8016 (mp0) cc_final: 0.7520 (mp0)
REVERT: D  109 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8590 (tm-30)
REVERT: D  286 ILE cc_start: 0.8634 (mt) cc_final: 0.8197 (mp)
REVERT: D  372 ARG cc_start: 0.8314 (mpp80) cc_final: 0.7124 (mmm160)
REVERT: D  391 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6840 (ttp-170)
REVERT: E  138 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8586 (mm-30)
REVERT: E  297 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8118 (tt0)
REVERT: E  368 GLU cc_start: 0.7891 (mp0) cc_final: 0.7515 (mp0)
  outliers start: 6
  outliers final: 1
  residues processed: 168
  average time/residue: 1.5013
  time to fit residues: 272.1246
Evaluate side-chains
  168 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 164
  time to evaluate  : 1.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 GLU
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain D residue  391 ARG
Chi-restraints excluded: chain E residue  297 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 41 optimal weight:    9.9990
   chunk 113 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 120 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0170
   chunk 79 optimal weight:    1.9990
   chunk 51 optimal weight:    0.1980
   chunk 44 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.6422

-------------------------------------------------------------------------------
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 = 0.3468 r_free = 0.3468 target = 0.107689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.080749 restraints weight = 41804.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 3.55
r_work: 0.2869 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2870
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2870 r_free = 0.2870    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2870 r_free = 0.2870    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2870
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  13155  Z= 0.114
  Angle     :  0.484  10.145  17785  Z= 0.243
  Chirality :  0.039   0.229   2060
  Planarity :  0.003   0.033   2250
  Dihedral  :  3.816  14.634   1740
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 11.90 %
    Favored  : 87.89 %
  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:  3.69 (0.21), residues: 1595
  helix:  3.16 (0.15), residues: 1050
  sheet:  2.17 (0.38), residues: 145
  loop :  0.53 (0.35), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 196 
 HIS   0.001   0.000   HIS B 371 
 PHE   0.016   0.001   PHE D 352 
 TYR   0.021   0.002   TYR B 299 
 ARG   0.008   0.001   ARG E 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04543 ( 1005)
  hydrogen bonds       : angle       3.72352 ( 2935)
  covalent geometry    : bond        0.00238 (13155)
  covalent geometry    : angle       0.48439 (17785)

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

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 171
  time to evaluate  : 1.551 
Fit side-chains
REVERT: A  137 MET cc_start: 0.9307 (mpp) cc_final: 0.8874 (mtt)
REVERT: A  138 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8580 (mm-30)
REVERT: A  190 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8300 (tp30)
REVERT: A  286 ILE cc_start: 0.8632 (mt) cc_final: 0.8246 (mp)
REVERT: A  344 MET cc_start: 0.9115 (mtt) cc_final: 0.8895 (mtt)
REVERT: A  368 GLU cc_start: 0.7943 (mp0) cc_final: 0.7481 (mp0)
REVERT: A  390 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7419 (mpt180)
REVERT: B  286 ILE cc_start: 0.8594 (mt) cc_final: 0.8213 (mp)
REVERT: C  138 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8471 (mm-30)
REVERT: C  368 GLU cc_start: 0.7984 (mp0) cc_final: 0.7482 (mp0)
REVERT: D  109 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8568 (tm-30)
REVERT: D  286 ILE cc_start: 0.8641 (mt) cc_final: 0.8215 (mp)
REVERT: D  372 ARG cc_start: 0.8324 (mpp80) cc_final: 0.7118 (mmm160)
REVERT: D  398 ARG cc_start: 0.8027 (ttp-110) cc_final: 0.7669 (mtp85)
REVERT: E  138 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8561 (mm-30)
REVERT: E  297 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8030 (tt0)
REVERT: E  368 GLU cc_start: 0.7863 (mp0) cc_final: 0.7520 (mp0)
REVERT: E  398 ARG cc_start: 0.8026 (ttp-110) cc_final: 0.7774 (mtm110)
  outliers start: 3
  outliers final: 0
  residues processed: 174
  average time/residue: 1.4725
  time to fit residues: 277.1356
Evaluate side-chains
  167 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 165
  time to evaluate  : 1.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 GLU
Chi-restraints excluded: chain E residue  297 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 52 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 139 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 100 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 135 optimal weight:    0.6980
   chunk 93 optimal weight:    0.4980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3472 r_free = 0.3472 target = 0.107945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.079858 restraints weight = 71749.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 4.40
r_work: 0.2833 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2822
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  13155  Z= 0.114
  Angle     :  0.479   9.646  17785  Z= 0.242
  Chirality :  0.038   0.234   2060
  Planarity :  0.003   0.034   2250
  Dihedral  :  3.789  15.623   1740
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 11.90 %
    Favored  : 87.96 %
  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:  3.74 (0.21), residues: 1595
  helix:  3.18 (0.15), residues: 1050
  sheet:  2.19 (0.37), residues: 145
  loop :  0.58 (0.36), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 196 
 HIS   0.001   0.000   HIS B 371 
 PHE   0.016   0.001   PHE A 352 
 TYR   0.022   0.002   TYR B 299 
 ARG   0.008   0.001   ARG D 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04522 ( 1005)
  hydrogen bonds       : angle       3.70141 ( 2935)
  covalent geometry    : bond        0.00237 (13155)
  covalent geometry    : angle       0.47896 (17785)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11474.66 seconds
wall clock time: 196 minutes 39.28 seconds (11799.28 seconds total)