Starting phenix.real_space_refine
on Mon Dec 30 10:17:52 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ip6_35633/12_2024/8ip6_35633.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ip6_35633/12_2024/8ip6_35633.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ip6_35633/12_2024/8ip6_35633.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ip6_35633/12_2024/8ip6_35633.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ip6_35633/12_2024/8ip6_35633.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ip6_35633/12_2024/8ip6_35633.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.047
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      65      5.16       5
     Cl      1      4.86       5
     C    8315      2.51       5
     N    2175      2.21       5
     O    2365      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 12921
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2584
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
      Conformer: "B"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
          bond proxies already assigned to first conformer: 2613
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
      Conformer: "B"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
          bond proxies already assigned to first conformer: 2613
    Chain: "C"
      Number of atoms: 2584
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
      Conformer: "B"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
          bond proxies already assigned to first conformer: 2613
    Chain: "D"
      Number of atoms: 2584
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
      Conformer: "B"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
          bond proxies already assigned to first conformer: 2613
    Chain: "E"
      Number of atoms: 2584
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
      Conformer: "B"
        Number of residues, atoms: 320, 2576
          Classifications: {'peptide': 320}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 8, 'TRANS': 311}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
          bond proxies already assigned to first conformer: 2613
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 13.29, per 1000 atoms: 1.03
  Number of scatterers: 12921
  At special positions: 0
  Unit cell: (112.554, 111.54, 141.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      65     16.00
     O    2365      8.00
     N    2175      7.00
     C    8315      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.16
  Conformation dependent library (CDL) restraints added in 3.0 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 5 sheets defined
      71.9% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 114 through 119
      removed outlier: 3.761A  pdb=" N   ARG A 119 " --> pdb=" O   ARG A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 172
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 183 through 219
      removed outlier: 3.693A  pdb=" N   ARG A 187 " --> pdb=" O   PRO A 183 " (cutoff:3.500A)
      Proline residue:  A 209  - end of helix
    Processing helix  chain 'A' and resid 227 through 261
      removed outlier: 3.528A  pdb=" N   ILE A 258 " --> pdb=" O   SER A 254 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLU A 261 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 269
      removed outlier: 3.668A  pdb=" N   LEU A 265 " --> pdb=" O   GLU A 261 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   CYS A 269 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 275
      removed outlier: 3.803A  pdb=" N   ASP A 275 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 283
      removed outlier: 4.103A  pdb=" N   LYS A 281 " --> pdb=" O   GLN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 360
      removed outlier: 4.184A  pdb=" N   MET A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLY A 356 " --> pdb=" O   PHE A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 401
    Processing helix  chain 'B' and resid 104 through 112
    Processing helix  chain 'B' and resid 114 through 119
      removed outlier: 3.761A  pdb=" N   ARG B 119 " --> pdb=" O   ARG B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 172
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 183 through 219
      removed outlier: 3.693A  pdb=" N   ARG B 187 " --> pdb=" O   PRO B 183 " (cutoff:3.500A)
      Proline residue:  B 209  - end of helix
    Processing helix  chain 'B' and resid 227 through 261
      removed outlier: 3.528A  pdb=" N   ILE B 258 " --> pdb=" O   SER B 254 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLU B 261 " --> pdb=" O   GLU B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 269
      removed outlier: 3.668A  pdb=" N   LEU B 265 " --> pdb=" O   GLU B 261 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   CYS B 269 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 275
      removed outlier: 3.802A  pdb=" N   ASP B 275 " --> pdb=" O   SER B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 283
      removed outlier: 4.101A  pdb=" N   LYS B 281 " --> pdb=" O   GLN B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 360
      removed outlier: 4.184A  pdb=" N   MET B 355 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLY B 356 " --> pdb=" O   PHE B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 401
    Processing helix  chain 'C' and resid 104 through 112
    Processing helix  chain 'C' and resid 114 through 119
      removed outlier: 3.761A  pdb=" N   ARG C 119 " --> pdb=" O   ARG C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 172
      Proline residue:  C 168  - end of helix
    Processing helix  chain 'C' and resid 183 through 219
      removed outlier: 3.693A  pdb=" N   ARG C 187 " --> pdb=" O   PRO C 183 " (cutoff:3.500A)
      Proline residue:  C 209  - end of helix
    Processing helix  chain 'C' and resid 227 through 261
      removed outlier: 3.528A  pdb=" N   ILE C 258 " --> pdb=" O   SER C 254 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLU C 261 " --> pdb=" O   GLU C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 269
      removed outlier: 3.668A  pdb=" N   LEU C 265 " --> pdb=" O   GLU C 261 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   CYS C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 275
      removed outlier: 3.803A  pdb=" N   ASP C 275 " --> pdb=" O   SER C 271 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 275 through 283
      removed outlier: 4.102A  pdb=" N   LYS C 281 " --> pdb=" O   GLN C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 360
      removed outlier: 4.184A  pdb=" N   MET C 355 " --> pdb=" O   LEU C 351 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLY C 356 " --> pdb=" O   PHE C 352 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 372 through 401
    Processing helix  chain 'D' and resid 104 through 112
    Processing helix  chain 'D' and resid 114 through 119
      removed outlier: 3.761A  pdb=" N   ARG D 119 " --> pdb=" O   ARG D 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 172
      Proline residue:  D 168  - end of helix
    Processing helix  chain 'D' and resid 183 through 219
      removed outlier: 3.693A  pdb=" N   ARG D 187 " --> pdb=" O   PRO D 183 " (cutoff:3.500A)
      Proline residue:  D 209  - end of helix
    Processing helix  chain 'D' and resid 227 through 261
      removed outlier: 3.528A  pdb=" N   ILE D 258 " --> pdb=" O   SER D 254 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLU D 261 " --> pdb=" O   GLU D 257 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 261 through 269
      removed outlier: 3.668A  pdb=" N   LEU D 265 " --> pdb=" O   GLU D 261 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   CYS D 269 " --> pdb=" O   LEU D 265 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 275
      removed outlier: 3.803A  pdb=" N   ASP D 275 " --> pdb=" O   SER D 271 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 283
      removed outlier: 4.102A  pdb=" N   LYS D 281 " --> pdb=" O   GLN D 277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 360
      removed outlier: 4.184A  pdb=" N   MET D 355 " --> pdb=" O   LEU D 351 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   GLY D 356 " --> pdb=" O   PHE D 352 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 372 through 401
    Processing helix  chain 'E' and resid 104 through 112
    Processing helix  chain 'E' and resid 114 through 119
      removed outlier: 3.762A  pdb=" N   ARG E 119 " --> pdb=" O   ARG E 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 159 through 172
      Proline residue:  E 168  - end of helix
    Processing helix  chain 'E' and resid 183 through 219
      removed outlier: 3.693A  pdb=" N   ARG E 187 " --> pdb=" O   PRO E 183 " (cutoff:3.500A)
      Proline residue:  E 209  - end of helix
    Processing helix  chain 'E' and resid 227 through 261
      removed outlier: 3.528A  pdb=" N   ILE E 258 " --> pdb=" O   SER E 254 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLU E 261 " --> pdb=" O   GLU E 257 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 261 through 269
      removed outlier: 3.668A  pdb=" N   LEU E 265 " --> pdb=" O   GLU E 261 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   CYS E 269 " --> pdb=" O   LEU E 265 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 275
      removed outlier: 3.802A  pdb=" N   ASP E 275 " --> pdb=" O   SER E 271 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 275 through 283
      removed outlier: 4.101A  pdb=" N   LYS E 281 " --> pdb=" O   GLN E 277 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 287 through 360
      removed outlier: 4.184A  pdb=" N   MET E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLY E 356 " --> pdb=" O   PHE E 352 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 372 through 401
    Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 103
      removed outlier: 4.220A  pdb=" N   LYS A 141 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 103
      removed outlier: 4.219A  pdb=" N   LYS B 141 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 103
      removed outlier: 4.219A  pdb=" N   LYS C 141 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 97 through 103
      removed outlier: 4.220A  pdb=" N   LYS D 141 " --> pdb=" O   LEU D 152 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 103
      removed outlier: 4.220A  pdb=" N   LYS E 141 " --> pdb=" O   LEU E 152 " (cutoff:3.500A)

    1000 hydrogen bonds defined for protein.
    2905 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.75

  Time building geometry restraints manager: 3.58 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4235
        1.34 -     1.46: 1965
        1.46 -     1.57: 6835
        1.57 -     1.69: 0
        1.69 -     1.80: 120
  Bond restraints: 13155
  Sorted by residual:
  bond pdb=" CA  VAL A  82 "
       pdb=" CB  VAL A  82 "
    ideal  model  delta    sigma   weight residual
    1.540  1.520  0.020 2.70e-02 1.37e+03 5.69e-01
  bond pdb=" CA  VAL D  82 "
       pdb=" CB  VAL D  82 "
    ideal  model  delta    sigma   weight residual
    1.540  1.520  0.020 2.70e-02 1.37e+03 5.54e-01
  bond pdb=" CA  VAL E  82 "
       pdb=" CB  VAL E  82 "
    ideal  model  delta    sigma   weight residual
    1.540  1.520  0.020 2.70e-02 1.37e+03 5.48e-01
  bond pdb=" CA  VAL C  82 "
       pdb=" CB  VAL C  82 "
    ideal  model  delta    sigma   weight residual
    1.540  1.520  0.020 2.70e-02 1.37e+03 5.48e-01
  bond pdb=" CA  VAL B  82 "
       pdb=" CB  VAL B  82 "
    ideal  model  delta    sigma   weight residual
    1.540  1.520  0.020 2.70e-02 1.37e+03 5.31e-01
  ... (remaining 13150 not shown)

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 3744
        2.83 -     3.35: 12582
        3.35 -     3.86: 20753
        3.86 -     4.38: 22868
        4.38 -     4.90: 41705
  Nonbonded interactions: 101652
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU D 185 "
            pdb=" OG  SER D 271 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" OE1 GLU C 185 "
            pdb=" OG  SER C 271 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OE1 GLU B 185 "
            pdb=" OG  SER B 271 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OE1 GLU E 185 "
            pdb=" OG  SER E 271 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OE1 GLU A 185 "
            pdb=" OG  SER A 271 "
     model   vdw
     2.310 3.040
  ... (remaining 101647 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.140
  Process input model:                     36.820
  Find NCS groups from input model:        0.630
  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:13.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020  13155  Z= 0.161
  Angle     :  0.427   4.812  17785  Z= 0.233
  Chirality :  0.036   0.130   2060
  Planarity :  0.003   0.028   2250
  Dihedral  : 13.001  87.474   4935
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.51 (0.22), residues: 1595
  helix:  4.02 (0.15), residues: 1040
  sheet:  3.02 (0.33), residues: 145
  loop : -0.04 (0.34), residues: 410

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

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

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 1.528 
Fit side-chains
REVERT: A  139 TYR cc_start: 0.9253 (p90) cc_final: 0.8948 (p90)
REVERT: A  257 GLU cc_start: 0.7899 (tt0) cc_final: 0.7659 (tp30)
REVERT: A  382 PHE cc_start: 0.8671 (m-80) cc_final: 0.8433 (m-80)
REVERT: A  383 MET cc_start: 0.5563 (mmp) cc_final: 0.5255 (mpp)
REVERT: B  383 MET cc_start: 0.5257 (mmp) cc_final: 0.4976 (mtm)
REVERT: B  391 ARG cc_start: 0.7934 (mtt180) cc_final: 0.7684 (tpt170)
REVERT: C  383 MET cc_start: 0.5609 (mmp) cc_final: 0.5337 (tpp)
REVERT: D  108 TYR cc_start: 0.8900 (m-10) cc_final: 0.8610 (m-80)
REVERT: D  139 TYR cc_start: 0.9319 (p90) cc_final: 0.9104 (p90)
REVERT: D  190 GLU cc_start: 0.8106 (tt0) cc_final: 0.7856 (tt0)
REVERT: D  257 GLU cc_start: 0.7945 (tt0) cc_final: 0.7643 (tp30)
REVERT: D  383 MET cc_start: 0.5076 (mmp) cc_final: 0.4771 (tpp)
REVERT: D  391 ARG cc_start: 0.7904 (mtt180) cc_final: 0.7516 (tpt170)
REVERT: E  190 GLU cc_start: 0.8239 (tt0) cc_final: 0.7715 (tt0)
REVERT: E  383 MET cc_start: 0.5298 (mmp) cc_final: 0.5051 (mpp)
REVERT: E  391 ARG cc_start: 0.7898 (mtt180) cc_final: 0.7647 (tpt170)
  outliers start: 0
  outliers final: 0
  residues processed: 269
  average time/residue: 1.4001
  time to fit residues: 406.5195
Evaluate side-chains
  178 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 135 optimal weight:    5.9990
   chunk 121 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 41 optimal weight:    0.3980
   chunk 81 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   chunk 125 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 93 optimal weight:    5.9990
   chunk 145 optimal weight:    3.9990
   overall best weight:    2.6788

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035  13155  Z= 0.371
  Angle     :  0.606   8.215  17785  Z= 0.308
  Chirality :  0.041   0.146   2060
  Planarity :  0.004   0.029   2250
  Dihedral  :  3.733  14.384   1740
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  :  8.73 %
    Favored  : 89.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.11 (0.21), residues: 1595
  helix:  3.41 (0.15), residues: 1105
  sheet:  2.94 (0.33), residues: 145
  loop :  0.07 (0.38), residues: 345

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

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

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 179
  time to evaluate  : 1.528 
Fit side-chains
REVERT: A  124 MET cc_start: 0.8394 (tpp) cc_final: 0.8155 (tpp)
REVERT: A  139 TYR cc_start: 0.9271 (p90) cc_final: 0.8966 (p90)
REVERT: A  257 GLU cc_start: 0.8036 (tt0) cc_final: 0.7794 (tp30)
REVERT: A  361 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8100 (ppp)
REVERT: A  382 PHE cc_start: 0.8757 (m-80) cc_final: 0.8309 (m-80)
REVERT: A  383 MET cc_start: 0.5669 (mmp) cc_final: 0.5375 (mpp)
REVERT: B  257 GLU cc_start: 0.7444 (tp30) cc_final: 0.7228 (tp30)
REVERT: B  261 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7143 (mp0)
REVERT: B  383 MET cc_start: 0.5017 (mmp) cc_final: 0.4739 (mtm)
REVERT: B  391 ARG cc_start: 0.7947 (mtt180) cc_final: 0.7717 (tpt170)
REVERT: C  383 MET cc_start: 0.5636 (mmp) cc_final: 0.5377 (tpp)
REVERT: C  391 ARG cc_start: 0.7557 (mtt180) cc_final: 0.7288 (tpt170)
REVERT: D  108 TYR cc_start: 0.8935 (m-10) cc_final: 0.8669 (m-80)
REVERT: D  139 TYR cc_start: 0.9335 (p90) cc_final: 0.9119 (p90)
REVERT: D  257 GLU cc_start: 0.7916 (tt0) cc_final: 0.7642 (tp30)
REVERT: D  383 MET cc_start: 0.5024 (mmp) cc_final: 0.4692 (tpp)
REVERT: D  391 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7528 (tpt170)
REVERT: E  190 GLU cc_start: 0.8276 (tt0) cc_final: 0.7835 (pt0)
REVERT: E  383 MET cc_start: 0.5523 (mmp) cc_final: 0.4871 (mpt)
REVERT: E  391 ARG cc_start: 0.7965 (mtt180) cc_final: 0.7668 (tpt170)
  outliers start: 27
  outliers final: 7
  residues processed: 192
  average time/residue: 1.4115
  time to fit residues: 293.7606
Evaluate side-chains
  169 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 160
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 ASP
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  385 SER
Chi-restraints excluded: chain C residue  385 SER
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 120 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 145 optimal weight:    0.8980
   chunk 157 optimal weight:   10.0000
   chunk 129 optimal weight:    3.9990
   chunk 144 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 116 optimal weight:    8.9990
   overall best weight:    0.9382

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13155  Z= 0.176
  Angle     :  0.514   9.259  17785  Z= 0.261
  Chirality :  0.037   0.130   2060
  Planarity :  0.003   0.032   2250
  Dihedral  :  3.524  14.386   1740
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  9.79 %
    Favored  : 88.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.40 (0.21), residues: 1595
  helix:  3.59 (0.15), residues: 1090
  sheet:  3.03 (0.33), residues: 145
  loop :  0.51 (0.38), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 162 
 HIS   0.002   0.000   HIS E 223 
 PHE   0.014   0.001   PHE C 352 
 TYR   0.026   0.002   TYR B 154 
 ARG   0.004   0.000   ARG B 228 

*********************** 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
  202 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 184
  time to evaluate  : 1.672 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9251 (p90) cc_final: 0.8929 (p90)
REVERT: A  257 GLU cc_start: 0.7951 (tt0) cc_final: 0.7692 (tp30)
REVERT: A  383 MET cc_start: 0.5641 (mmp) cc_final: 0.5372 (mpp)
REVERT: B  257 GLU cc_start: 0.7463 (tp30) cc_final: 0.7159 (tp30)
REVERT: B  261 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6826 (mp0)
REVERT: B  383 MET cc_start: 0.5105 (mmp) cc_final: 0.4805 (mtm)
REVERT: B  391 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7727 (tpt170)
REVERT: C  383 MET cc_start: 0.5553 (mmp) cc_final: 0.5285 (tpp)
REVERT: C  391 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7227 (tpt170)
REVERT: D  108 TYR cc_start: 0.8914 (m-10) cc_final: 0.8652 (m-80)
REVERT: D  190 GLU cc_start: 0.8164 (tt0) cc_final: 0.7855 (tt0)
REVERT: D  257 GLU cc_start: 0.7931 (tt0) cc_final: 0.7698 (tp30)
REVERT: D  383 MET cc_start: 0.4882 (mmp) cc_final: 0.4549 (tpp)
REVERT: D  391 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7518 (tpt170)
REVERT: E  266 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8149 (tp30)
REVERT: E  383 MET cc_start: 0.5394 (mmp) cc_final: 0.4740 (mpt)
REVERT: E  391 ARG cc_start: 0.8000 (mtt180) cc_final: 0.7707 (tpt170)
  outliers start: 18
  outliers final: 8
  residues processed: 193
  average time/residue: 1.3522
  time to fit residues: 283.2094
Evaluate side-chains
  177 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 168
  time to evaluate  : 1.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  385 SER
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain D residue  338 LEU
Chi-restraints excluded: chain D residue  359 PHE
Chi-restraints excluded: chain E residue  349 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 143 optimal weight:    0.9980
   chunk 109 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 146 optimal weight:    3.9990
   chunk 154 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 138 optimal weight:    0.0770
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.8142

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  13155  Z= 0.160
  Angle     :  0.497   9.698  17785  Z= 0.251
  Chirality :  0.037   0.130   2060
  Planarity :  0.003   0.033   2250
  Dihedral  :  3.445  13.954   1740
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.48 %
    Favored  : 87.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.42 (0.21), residues: 1595
  helix:  3.63 (0.15), residues: 1085
  sheet:  3.11 (0.33), residues: 145
  loop :  0.44 (0.38), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 162 
 HIS   0.002   0.000   HIS B 223 
 PHE   0.018   0.001   PHE A 352 
 TYR   0.028   0.002   TYR C 154 
 ARG   0.006   0.000   ARG B 228 

*********************** 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
  197 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 181
  time to evaluate  : 1.489 
Fit side-chains
REVERT: A  139 TYR cc_start: 0.9258 (p90) cc_final: 0.8910 (p90)
REVERT: A  257 GLU cc_start: 0.7979 (tt0) cc_final: 0.7714 (tp30)
REVERT: A  361 MET cc_start: 0.8643 (ptp) cc_final: 0.8156 (ppp)
REVERT: A  383 MET cc_start: 0.5544 (mmp) cc_final: 0.5243 (mpp)
REVERT: B  257 GLU cc_start: 0.7409 (tp30) cc_final: 0.6245 (tp30)
REVERT: B  261 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6039 (mp0)
REVERT: B  383 MET cc_start: 0.4764 (mmp) cc_final: 0.4427 (mtm)
REVERT: B  391 ARG cc_start: 0.7923 (mtt180) cc_final: 0.7673 (tpt170)
REVERT: C  109 GLN cc_start: 0.8333 (tp40) cc_final: 0.8084 (tp40)
REVERT: C  359 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7334 (m-80)
REVERT: C  383 MET cc_start: 0.5422 (mmp) cc_final: 0.5164 (tpp)
REVERT: C  391 ARG cc_start: 0.7511 (mtt180) cc_final: 0.7211 (tpt170)
REVERT: D  108 TYR cc_start: 0.8910 (m-10) cc_final: 0.8656 (m-80)
REVERT: D  137 MET cc_start: 0.8916 (mtm) cc_final: 0.8662 (mtt)
REVERT: D  257 GLU cc_start: 0.7890 (tt0) cc_final: 0.7675 (tp30)
REVERT: D  383 MET cc_start: 0.4900 (mmp) cc_final: 0.4604 (mpp)
REVERT: D  391 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7514 (tpt170)
REVERT: E  190 GLU cc_start: 0.8230 (tt0) cc_final: 0.7840 (tt0)
REVERT: E  383 MET cc_start: 0.5165 (mmp) cc_final: 0.4537 (mpt)
REVERT: E  391 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7689 (tpt170)
  outliers start: 16
  outliers final: 6
  residues processed: 189
  average time/residue: 1.3214
  time to fit residues: 271.3895
Evaluate side-chains
  176 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 168
  time to evaluate  : 1.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  385 SER
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain C residue  385 SER
Chi-restraints excluded: chain D residue  359 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 128 optimal weight:    6.9990
   chunk 87 optimal weight:    0.6980
   chunk 2 optimal weight:    4.9990
   chunk 115 optimal weight:    0.0010
   chunk 63 optimal weight:   10.0000
   chunk 131 optimal weight:    3.9990
   chunk 106 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 78 optimal weight:    6.9990
   chunk 138 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    1.9392

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13155  Z= 0.280
  Angle     :  0.560  10.429  17785  Z= 0.282
  Chirality :  0.039   0.134   2060
  Planarity :  0.004   0.032   2250
  Dihedral  :  3.647  14.564   1740
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 12.18 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.18 (0.21), residues: 1595
  helix:  3.41 (0.15), residues: 1105
  sheet:  3.11 (0.33), residues: 145
  loop :  0.24 (0.39), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 162 
 HIS   0.002   0.001   HIS E 288 
 PHE   0.017   0.002   PHE E  86 
 TYR   0.027   0.002   TYR C 154 
 ARG   0.005   0.000   ARG E 301 

*********************** 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
  183 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 169
  time to evaluate  : 1.685 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9256 (p90) cc_final: 0.8987 (p90)
REVERT: A  257 GLU cc_start: 0.7979 (tt0) cc_final: 0.7715 (tp30)
REVERT: A  361 MET cc_start: 0.8638 (ptp) cc_final: 0.8182 (ppp)
REVERT: A  383 MET cc_start: 0.5525 (mmp) cc_final: 0.5185 (mpp)
REVERT: B  190 GLU cc_start: 0.8126 (tt0) cc_final: 0.7695 (pt0)
REVERT: B  257 GLU cc_start: 0.7423 (tp30) cc_final: 0.6567 (tp30)
REVERT: B  261 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6558 (mp0)
REVERT: B  383 MET cc_start: 0.4554 (mmp) cc_final: 0.4234 (mtm)
REVERT: B  391 ARG cc_start: 0.7906 (mtt180) cc_final: 0.7621 (tpt170)
REVERT: C  383 MET cc_start: 0.5445 (mmp) cc_final: 0.5173 (tpp)
REVERT: C  391 ARG cc_start: 0.7517 (mtt180) cc_final: 0.7208 (tpt170)
REVERT: D  108 TYR cc_start: 0.8940 (m-10) cc_final: 0.8697 (m-80)
REVERT: D  137 MET cc_start: 0.9001 (mtm) cc_final: 0.8800 (mtm)
REVERT: D  257 GLU cc_start: 0.7911 (tt0) cc_final: 0.7701 (tp30)
REVERT: D  383 MET cc_start: 0.4895 (mmp) cc_final: 0.4593 (mpp)
REVERT: D  391 ARG cc_start: 0.7955 (mtt180) cc_final: 0.7526 (tpt170)
REVERT: E  383 MET cc_start: 0.5238 (mmp) cc_final: 0.4618 (mpt)
REVERT: E  391 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7734 (tpt-90)
  outliers start: 14
  outliers final: 7
  residues processed: 181
  average time/residue: 1.3501
  time to fit residues: 266.8132
Evaluate side-chains
  170 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 162
  time to evaluate  : 1.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  385 SER
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  385 SER
Chi-restraints excluded: chain E residue  385 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 52 optimal weight:    9.9990
   chunk 139 optimal weight:    0.9990
   chunk 30 optimal weight:    8.9990
   chunk 90 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 154 optimal weight:    0.8980
   chunk 128 optimal weight:    6.9990
   chunk 71 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    1.7788

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  13155  Z= 0.259
  Angle     :  0.548  10.934  17785  Z= 0.277
  Chirality :  0.038   0.181   2060
  Planarity :  0.003   0.033   2250
  Dihedral  :  3.646  14.967   1740
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 12.96 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.12 (0.21), residues: 1595
  helix:  3.38 (0.15), residues: 1105
  sheet:  2.99 (0.34), residues: 145
  loop :  0.22 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 196 
 HIS   0.002   0.001   HIS B 223 
 PHE   0.019   0.001   PHE A 352 
 TYR   0.029   0.002   TYR B 108 
 ARG   0.005   0.000   ARG E 301 

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

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

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

  3190 Ramachandran restraints generated.
    1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 169
  time to evaluate  : 1.551 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9262 (p90) cc_final: 0.8997 (p90)
REVERT: A  257 GLU cc_start: 0.8038 (tt0) cc_final: 0.7765 (tp30)
REVERT: A  361 MET cc_start: 0.8623 (ptp) cc_final: 0.8156 (ppp)
REVERT: A  383 MET cc_start: 0.5553 (mmp) cc_final: 0.5238 (mpp)
REVERT: B  257 GLU cc_start: 0.7432 (tp30) cc_final: 0.6513 (tp30)
REVERT: B  261 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6494 (mp0)
REVERT: B  383 MET cc_start: 0.4448 (mmp) cc_final: 0.4141 (mtm)
REVERT: B  391 ARG cc_start: 0.7904 (mtt180) cc_final: 0.7612 (tpt170)
REVERT: C  383 MET cc_start: 0.5491 (mmp) cc_final: 0.5234 (tpp)
REVERT: C  391 ARG cc_start: 0.7417 (mtt180) cc_final: 0.7101 (tpt170)
REVERT: D  108 TYR cc_start: 0.8940 (m-10) cc_final: 0.8700 (m-80)
REVERT: D  257 GLU cc_start: 0.7918 (tt0) cc_final: 0.7699 (tp30)
REVERT: D  391 ARG cc_start: 0.7776 (mtt180) cc_final: 0.7458 (tpt170)
REVERT: E  383 MET cc_start: 0.5308 (mmp) cc_final: 0.4680 (mpt)
REVERT: E  391 ARG cc_start: 0.8041 (mtt180) cc_final: 0.7748 (tpt-90)
  outliers start: 10
  outliers final: 7
  residues processed: 177
  average time/residue: 1.3239
  time to fit residues: 254.6053
Evaluate side-chains
  168 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 160
  time to evaluate  : 1.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  385 SER
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  385 SER
Chi-restraints excluded: chain E residue  385 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 149 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 130 optimal weight:    0.6980
   chunk 86 optimal weight:    4.9990
   chunk 154 optimal weight:    4.9990
   chunk 96 optimal weight:    6.9990
   chunk 94 optimal weight:    4.9990
   chunk 71 optimal weight:    0.4980
   overall best weight:    1.8384

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13155  Z= 0.268
  Angle     :  0.567  11.864  17785  Z= 0.283
  Chirality :  0.039   0.168   2060
  Planarity :  0.004   0.032   2250
  Dihedral  :  3.661  15.256   1740
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 12.96 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.12 (0.22), residues: 1595
  helix:  3.38 (0.15), residues: 1105
  sheet:  2.90 (0.34), residues: 145
  loop :  0.26 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 273 
 HIS   0.002   0.001   HIS B 223 
 PHE   0.018   0.002   PHE E 352 
 TYR   0.030   0.003   TYR B 108 
 ARG   0.005   0.000   ARG E 337 

*********************** 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
  182 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 169
  time to evaluate  : 1.554 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9266 (p90) cc_final: 0.8946 (p90)
REVERT: A  257 GLU cc_start: 0.8035 (tt0) cc_final: 0.7761 (tp30)
REVERT: A  383 MET cc_start: 0.5502 (mmp) cc_final: 0.5161 (mpp)
REVERT: B  257 GLU cc_start: 0.7446 (tp30) cc_final: 0.6536 (tp30)
REVERT: B  261 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6505 (mp0)
REVERT: B  383 MET cc_start: 0.4507 (mmp) cc_final: 0.4213 (mtm)
REVERT: B  391 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7652 (tpt170)
REVERT: C  383 MET cc_start: 0.5486 (mmp) cc_final: 0.5232 (tpp)
REVERT: C  391 ARG cc_start: 0.7399 (mtt180) cc_final: 0.6995 (tpt170)
REVERT: D  108 TYR cc_start: 0.8945 (m-10) cc_final: 0.8705 (m-80)
REVERT: D  257 GLU cc_start: 0.7921 (tt0) cc_final: 0.7706 (tp30)
REVERT: D  391 ARG cc_start: 0.7896 (mtt180) cc_final: 0.7522 (tpt170)
REVERT: E  383 MET cc_start: 0.5227 (mmp) cc_final: 0.4588 (mpt)
REVERT: E  391 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7747 (tpt-90)
  outliers start: 13
  outliers final: 10
  residues processed: 179
  average time/residue: 1.3336
  time to fit residues: 260.0177
Evaluate side-chains
  174 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 163
  time to evaluate  : 1.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain C residue  385 SER
Chi-restraints excluded: chain E residue  350 SER
Chi-restraints excluded: chain E residue  385 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 92 optimal weight:    9.9990
   chunk 46 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 98 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 121 optimal weight:    2.9990
   overall best weight:    2.3588

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030  13155  Z= 0.329
  Angle     :  0.592  12.448  17785  Z= 0.296
  Chirality :  0.040   0.159   2060
  Planarity :  0.004   0.032   2250
  Dihedral  :  3.761  15.607   1740
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 13.45 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.97 (0.21), residues: 1595
  helix:  3.27 (0.15), residues: 1105
  sheet:  2.80 (0.35), residues: 145
  loop :  0.22 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 273 
 HIS   0.002   0.001   HIS A 288 
 PHE   0.015   0.002   PHE A  86 
 TYR   0.032   0.003   TYR B 108 
 ARG   0.005   0.000   ARG E 337 

*********************** 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
  184 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 170
  time to evaluate  : 1.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9266 (p90) cc_final: 0.9001 (p90)
REVERT: A  257 GLU cc_start: 0.8035 (tt0) cc_final: 0.7765 (tp30)
REVERT: A  361 MET cc_start: 0.8614 (ptp) cc_final: 0.8187 (ppp)
REVERT: A  382 PHE cc_start: 0.8684 (m-80) cc_final: 0.8418 (m-80)
REVERT: A  383 MET cc_start: 0.5587 (mmp) cc_final: 0.5245 (mpp)
REVERT: B  257 GLU cc_start: 0.7464 (tp30) cc_final: 0.7186 (tp30)
REVERT: B  383 MET cc_start: 0.4580 (mmp) cc_final: 0.4266 (mtm)
REVERT: C  383 MET cc_start: 0.5567 (mmp) cc_final: 0.5330 (tpp)
REVERT: C  391 ARG cc_start: 0.7509 (mtt180) cc_final: 0.7252 (tpt170)
REVERT: D  108 TYR cc_start: 0.8951 (m-10) cc_final: 0.8708 (m-80)
REVERT: D  257 GLU cc_start: 0.7913 (tt0) cc_final: 0.7633 (tp30)
REVERT: D  352 PHE cc_start: 0.8665 (m-80) cc_final: 0.8399 (m-80)
REVERT: D  391 ARG cc_start: 0.7997 (mtt180) cc_final: 0.7541 (tpt170)
REVERT: E  391 ARG cc_start: 0.8075 (mtt180) cc_final: 0.7754 (tpt-90)
  outliers start: 14
  outliers final: 12
  residues processed: 183
  average time/residue: 1.3522
  time to fit residues: 268.4467
Evaluate side-chains
  171 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 159
  time to evaluate  : 1.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  385 SER
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  385 SER
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  350 SER
Chi-restraints excluded: chain E residue  385 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 140 optimal weight:    0.5980
   chunk 147 optimal weight:    2.9990
   chunk 134 optimal weight:    1.9990
   chunk 143 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 62 optimal weight:    8.9990
   chunk 112 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 129 optimal weight:    0.9990
   chunk 135 optimal weight:    0.9980
   chunk 94 optimal weight:   10.0000
   overall best weight:    1.1186

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13155  Z= 0.193
  Angle     :  0.546  12.864  17785  Z= 0.270
  Chirality :  0.037   0.166   2060
  Planarity :  0.003   0.033   2250
  Dihedral  :  3.577  15.106   1740
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 13.31 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.18 (0.22), residues: 1595
  helix:  3.42 (0.15), residues: 1105
  sheet:  2.93 (0.34), residues: 145
  loop :  0.29 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 162 
 HIS   0.001   0.000   HIS E 223 
 PHE   0.017   0.001   PHE A 352 
 TYR   0.030   0.002   TYR B 108 
 ARG   0.005   0.000   ARG E 337 

*********************** 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
  189 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 174
  time to evaluate  : 1.608 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9254 (p90) cc_final: 0.8932 (p90)
REVERT: A  257 GLU cc_start: 0.8055 (tt0) cc_final: 0.7785 (tp30)
REVERT: A  382 PHE cc_start: 0.8635 (m-80) cc_final: 0.8365 (m-80)
REVERT: A  383 MET cc_start: 0.5465 (mmp) cc_final: 0.5133 (mpp)
REVERT: B  257 GLU cc_start: 0.7430 (tp30) cc_final: 0.7199 (tp30)
REVERT: B  383 MET cc_start: 0.4432 (mmp) cc_final: 0.4125 (mtm)
REVERT: C  383 MET cc_start: 0.5485 (mmp) cc_final: 0.5240 (tpp)
REVERT: D  108 TYR cc_start: 0.8928 (m-10) cc_final: 0.8692 (m-80)
REVERT: D  257 GLU cc_start: 0.7946 (tt0) cc_final: 0.7686 (tp30)
REVERT: D  352 PHE cc_start: 0.8647 (m-80) cc_final: 0.8375 (m-80)
REVERT: E  190 GLU cc_start: 0.8267 (tt0) cc_final: 0.7921 (tt0)
REVERT: E  391 ARG cc_start: 0.8041 (mtt180) cc_final: 0.7741 (tpt-90)
  outliers start: 15
  outliers final: 12
  residues processed: 184
  average time/residue: 1.2984
  time to fit residues: 260.0277
Evaluate side-chains
  178 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 166
  time to evaluate  : 1.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  385 SER
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  349 LEU
Chi-restraints excluded: chain E residue  350 SER
Chi-restraints excluded: chain E residue  385 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 151 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 105 optimal weight:    7.9990
   chunk 159 optimal weight:    0.0870
   chunk 146 optimal weight:    0.9980
   chunk 126 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    0.8162

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13155  Z= 0.165
  Angle     :  0.547  13.264  17785  Z= 0.269
  Chirality :  0.038   0.273   2060
  Planarity :  0.003   0.033   2250
  Dihedral  :  3.512  14.764   1740
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 14.01 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.23 (0.22), residues: 1595
  helix:  3.45 (0.15), residues: 1105
  sheet:  2.99 (0.34), residues: 145
  loop :  0.34 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 162 
 HIS   0.002   0.000   HIS E 223 
 PHE   0.017   0.001   PHE E 352 
 TYR   0.029   0.002   TYR B 108 
 ARG   0.006   0.000   ARG E 301 

********************** 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
  184 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 172
  time to evaluate  : 1.525 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.9254 (p90) cc_final: 0.8931 (p90)
REVERT: A  257 GLU cc_start: 0.8052 (tt0) cc_final: 0.7786 (tp30)
REVERT: A  361 MET cc_start: 0.8628 (ptp) cc_final: 0.8110 (ppp)
REVERT: A  383 MET cc_start: 0.5457 (mmp) cc_final: 0.5131 (mpp)
REVERT: B  257 GLU cc_start: 0.7327 (tp30) cc_final: 0.7080 (tp30)
REVERT: B  355 MET cc_start: 0.8294 (ttm) cc_final: 0.8026 (ttp)
REVERT: B  383 MET cc_start: 0.4471 (mmp) cc_final: 0.4129 (mtm)
REVERT: B  391 ARG cc_start: 0.7697 (tpt170) cc_final: 0.7435 (tpt170)
REVERT: C  359 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7424 (m-80)
REVERT: C  383 MET cc_start: 0.5489 (mmp) cc_final: 0.5227 (tpp)
REVERT: C  391 ARG cc_start: 0.7513 (tpt170) cc_final: 0.7307 (tpt170)
REVERT: D  108 TYR cc_start: 0.8939 (m-10) cc_final: 0.8706 (m-80)
REVERT: D  257 GLU cc_start: 0.7953 (tt0) cc_final: 0.7682 (tp30)
REVERT: D  391 ARG cc_start: 0.7911 (mtt180) cc_final: 0.7541 (tpt170)
REVERT: E  190 GLU cc_start: 0.8248 (tt0) cc_final: 0.7899 (tt0)
REVERT: E  391 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7733 (tpt-90)
  outliers start: 12
  outliers final: 11
  residues processed: 181
  average time/residue: 1.3951
  time to fit residues: 273.6129
Evaluate side-chains
  179 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 167
  time to evaluate  : 1.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  385 SER
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  349 LEU
Chi-restraints excluded: chain E residue  350 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 135 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 127 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 130 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 111 optimal weight:    4.9990
   overall best weight:    0.8984

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.114820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.082612 restraints weight = 65310.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 4.42
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3088
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3088
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13155  Z= 0.174
  Angle     :  0.552  13.213  17785  Z= 0.272
  Chirality :  0.037   0.213   2060
  Planarity :  0.003   0.033   2250
  Dihedral  :  3.488  14.527   1740
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 13.94 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.26 (0.22), residues: 1595
  helix:  3.47 (0.15), residues: 1105
  sheet:  2.98 (0.34), residues: 145
  loop :  0.34 (0.40), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 162 
 HIS   0.002   0.000   HIS E 223 
 PHE   0.016   0.001   PHE A 352 
 TYR   0.029   0.002   TYR B 108 
 ARG   0.007   0.000   ARG E 301 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4521.02 seconds
wall clock time: 81 minutes 55.41 seconds (4915.41 seconds total)