Starting phenix.real_space_refine
on Fri Aug 22 20:24:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fgv_50430/08_2025/9fgv_50430.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fgv_50430/08_2025/9fgv_50430.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fgv_50430/08_2025/9fgv_50430.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fgv_50430/08_2025/9fgv_50430.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fgv_50430/08_2025/9fgv_50430.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fgv_50430/08_2025/9fgv_50430.map"
  }
  resolution = 3.39
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.014
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: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    4934      2.51       5
     N    1252      2.21       5
     O    1475      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7685
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2870
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 366, 2842
          Classifications: {'peptide': 366}
          Link IDs: {'PTRANS': 21, 'TRANS': 344}
      Conformer: "B"
        Number of residues, atoms: 366, 2842
          Classifications: {'peptide': 366}
          Link IDs: {'PTRANS': 21, 'TRANS': 344}
          bond proxies already assigned to first conformer: 2877
    Chain: "B"
      Number of atoms: 969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 969
          Classifications: {'peptide': 125}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "C"
      Number of atoms: 2870
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 366, 2842
          Classifications: {'peptide': 366}
          Link IDs: {'PTRANS': 21, 'TRANS': 344}
      Conformer: "B"
        Number of residues, atoms: 366, 2842
          Classifications: {'peptide': 366}
          Link IDs: {'PTRANS': 21, 'TRANS': 344}
          bond proxies already assigned to first conformer: 2877
    Chain: "D"
      Number of atoms: 976
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 125, 970
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 3, 'TRANS': 121}
      Conformer: "B"
        Number of residues, atoms: 125, 970
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 3, 'TRANS': 121}
          bond proxies already assigned to first conformer: 985
  Time building chain proxies: 3.37, per 1000 atoms: 0.44
  Number of scatterers: 7685
  At special positions: 0
  Unit cell: (82.49, 124.83, 72.27, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O    1475      8.00
     N    1252      7.00
     C    4934      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  11 " - pdb=" SG  CYS D  11 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03

  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: 0.70
  Conformation dependent library (CDL) restraints added in 698.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1820

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 16 sheets defined
      42.0% alpha, 25.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 32
    Processing helix  chain 'A' and resid 42 through 52
      Proline residue:  A  48  - end of helix
    Processing helix  chain 'A' and resid 64 through 73
      removed outlier: 3.554A  pdb=" N   GLY A  68 " --> pdb=" O   HIS A  64 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   GLY A  69 " --> pdb=" O   ASP A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 87
    Processing helix  chain 'A' and resid 90 through 97
      removed outlier: 3.711A  pdb=" N   VAL A  97 " --> pdb=" O   THR A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 141
      removed outlier: 4.638A  pdb=" N   ALA A 134 " --> pdb=" O   GLU A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 162
      Proline residue:  A 159  - end of helix
    Processing helix  chain 'A' and resid 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 185 through 201
    Processing helix  chain 'A' and resid 209 through 219
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 231 through 239
    Processing helix  chain 'A' and resid 272 through 283
    Processing helix  chain 'A' and resid 286 through 297
    Processing helix  chain 'A' and resid 304 through 312
      removed outlier: 4.215A  pdb=" N   GLU A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 327
    Processing helix  chain 'A' and resid 335 through 353
    Processing helix  chain 'A' and resid 356 through 366
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 3.543A  pdb=" N   THR B  91 " --> pdb=" O   PRO B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 112
    Processing helix  chain 'C' and resid 16 through 32
    Processing helix  chain 'C' and resid 42 through 52
      Proline residue:  C  48  - end of helix
    Processing helix  chain 'C' and resid 64 through 73
      removed outlier: 3.675A  pdb=" N   GLY C  68 " --> pdb=" O   HIS C  64 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   GLY C  69 " --> pdb=" O   ASP C  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 87
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.582A  pdb=" N   VAL C  97 " --> pdb=" O   THR C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 141
      removed outlier: 4.628A  pdb=" N   ALA C 134 " --> pdb=" O   GLU C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 162
      Proline residue:  C 159  - end of helix
    Processing helix  chain 'C' and resid 163 through 165
      No H-bonds generated for 'chain 'C' and resid 163 through 165'
    Processing helix  chain 'C' and resid 185 through 201
    Processing helix  chain 'C' and resid 209 through 219
    Processing helix  chain 'C' and resid 228 through 230
      No H-bonds generated for 'chain 'C' and resid 228 through 230'
    Processing helix  chain 'C' and resid 231 through 239
    Processing helix  chain 'C' and resid 272 through 283
    Processing helix  chain 'C' and resid 286 through 297
      removed outlier: 3.509A  pdb=" N   ASP C 296 " --> pdb=" O   ALA C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 304 through 312
      removed outlier: 4.169A  pdb=" N   GLU C 310 " --> pdb=" O   SER C 306 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 314 through 327
    Processing helix  chain 'C' and resid 335 through 353
    Processing helix  chain 'C' and resid 356 through 366
    Processing helix  chain 'D' and resid 62 through 65
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 3.543A  pdb=" N   THR D  91 " --> pdb=" O   PRO D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 108 through 112
      removed outlier: 3.528A  pdb=" N   TYR D 112 " --> pdb=" O   GLN D 109 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 38
      removed outlier: 6.601A  pdb=" N   LEU A   7 " --> pdb=" O   THR A  36 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   GLU A  38 " --> pdb=" O   LEU A   7 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ILE A   9 " --> pdb=" O   GLU A  38 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   VAL A   8 " --> pdb=" O   ILE A  59 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   PHE A  61 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   TRP A  10 " --> pdb=" O   PHE A  61 " (cutoff:3.500A)
      removed outlier: 9.159A  pdb=" N   ALA A  63 " --> pdb=" O   TRP A  10 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   PHE A 258 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   ALA A 112 " --> pdb=" O   PHE A 258 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   GLY A 260 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   VAL A 110 " --> pdb=" O   GLY A 260 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   LEU A 262 " --> pdb=" O   ILE A 108 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ALA A 301 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 38
      removed outlier: 6.601A  pdb=" N   LEU A   7 " --> pdb=" O   THR A  36 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   GLU A  38 " --> pdb=" O   LEU A   7 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ILE A   9 " --> pdb=" O   GLU A  38 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   VAL A   8 " --> pdb=" O   ILE A  59 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   PHE A  61 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   TRP A  10 " --> pdb=" O   PHE A  61 " (cutoff:3.500A)
      removed outlier: 9.159A  pdb=" N   ALA A  63 " --> pdb=" O   TRP A  10 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99
    Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 147
      removed outlier: 6.244A  pdb=" N   ALA A 146 " --> pdb=" O   MET A 224 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   ILE A 226 " --> pdb=" O   ALA A 146 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   ALA A 223 " --> pdb=" O   ASN A 118 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 172
      removed outlier: 3.794A  pdb=" N   LYS A 170 " --> pdb=" O   ASP A 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 7
    Processing sheet with id=AA7, first strand: chain 'B' and resid 11 through 12
      removed outlier: 6.256A  pdb=" N   ARG B  38 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 5.347A  pdb=" N   GLY B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 11 through 12
    Processing sheet with id=AA9, first strand: chain 'C' and resid 35 through 38
      removed outlier: 6.620A  pdb=" N   LEU C   7 " --> pdb=" O   THR C  36 " (cutoff:3.500A)
      removed outlier: 7.947A  pdb=" N   GLU C  38 " --> pdb=" O   LEU C   7 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   ILE C   9 " --> pdb=" O   GLU C  38 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   VAL C   8 " --> pdb=" O   ILE C  59 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   PHE C  61 " --> pdb=" O   VAL C   8 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   TRP C  10 " --> pdb=" O   PHE C  61 " (cutoff:3.500A)
      removed outlier: 9.173A  pdb=" N   ALA C  63 " --> pdb=" O   TRP C  10 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   PHE C 258 " --> pdb=" O   ALA C 112 " (cutoff:3.500A)
      removed outlier: 4.939A  pdb=" N   ALA C 112 " --> pdb=" O   PHE C 258 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   GLY C 260 " --> pdb=" O   VAL C 110 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   VAL C 110 " --> pdb=" O   GLY C 260 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   LEU C 262 " --> pdb=" O   ILE C 108 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA C 301 " --> pdb=" O   VAL C 110 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 38
      removed outlier: 6.620A  pdb=" N   LEU C   7 " --> pdb=" O   THR C  36 " (cutoff:3.500A)
      removed outlier: 7.947A  pdb=" N   GLU C  38 " --> pdb=" O   LEU C   7 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   ILE C   9 " --> pdb=" O   GLU C  38 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   VAL C   8 " --> pdb=" O   ILE C  59 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   PHE C  61 " --> pdb=" O   VAL C   8 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   TRP C  10 " --> pdb=" O   PHE C  61 " (cutoff:3.500A)
      removed outlier: 9.173A  pdb=" N   ALA C  63 " --> pdb=" O   TRP C  10 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 99
    Processing sheet with id=AB3, first strand: chain 'C' and resid 145 through 147
      removed outlier: 6.249A  pdb=" N   ALA C 146 " --> pdb=" O   MET C 224 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   ILE C 226 " --> pdb=" O   ALA C 146 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   ALA C 223 " --> pdb=" O   ASN C 118 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 170 through 172
      removed outlier: 3.788A  pdb=" N   LYS C 170 " --> pdb=" O   ASP C 177 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AB6, first strand: chain 'D' and resid 11 through 12
      removed outlier: 6.280A  pdb=" N   ARG D  38 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 5.337A  pdb=" N   GLY D  47 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 11 through 12

    373 hydrogen bonds defined for protein.
    1023 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: 1.33

  Time building geometry restraints manager: 0.97 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: 2456
        1.34 -     1.46: 1644
        1.46 -     1.58: 3741
        1.58 -     1.69: 0
        1.69 -     1.81: 42
  Bond restraints: 7883
  Sorted by residual:
  bond pdb=" CB  LYS A 137 "
       pdb=" CG  LYS A 137 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.19e+00
  bond pdb=" CG  LYS A 137 "
       pdb=" CD  LYS A 137 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.14e+00
  bond pdb=" CA  GLY A 260 "
       pdb=" C   GLY A 260 "
    ideal  model  delta    sigma   weight residual
    1.520  1.513  0.008 7.30e-03 1.88e+04 1.07e+00
  bond pdb=" CA  GLY C 260 "
       pdb=" C   GLY C 260 "
    ideal  model  delta    sigma   weight residual
    1.520  1.513  0.007 7.30e-03 1.88e+04 9.07e-01
  bond pdb=" CA  LYS C 239 "
       pdb=" CB  LYS C 239 "
    ideal  model  delta    sigma   weight residual
    1.529  1.543 -0.014 1.62e-02 3.81e+03 7.32e-01
  ... (remaining 7878 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 10573
        1.60 -     3.20: 126
        3.20 -     4.80: 17
        4.80 -     6.40: 2
        6.40 -     8.00: 1
  Bond angle restraints: 10719
  Sorted by residual:
  angle pdb=" CB  LYS A 137 "
        pdb=" CG  LYS A 137 "
        pdb=" CD  LYS A 137 "
      ideal   model   delta    sigma   weight residual
     111.30  119.30   -8.00 2.30e+00 1.89e-01 1.21e+01
  angle pdb=" CA  LYS C 239 "
        pdb=" CB  LYS C 239 "
        pdb=" CG  LYS C 239 "
      ideal   model   delta    sigma   weight residual
     114.10  118.71   -4.61 2.00e+00 2.50e-01 5.32e+00
  angle pdb=" CA  MET A 336 "
        pdb=" CB  MET A 336 "
        pdb=" CG  MET A 336 "
      ideal   model   delta    sigma   weight residual
     114.10  109.50    4.60 2.00e+00 2.50e-01 5.28e+00
  angle pdb=" N   ASN C 332 "
        pdb=" CA  ASN C 332 "
        pdb=" C   ASN C 332 "
      ideal   model   delta    sigma   weight residual
     110.44  113.15   -2.71 1.20e+00 6.94e-01 5.12e+00
  angle pdb=" C   SER C 238 "
        pdb=" N   LYS C 239 "
        pdb=" CA  LYS C 239 "
      ideal   model   delta    sigma   weight residual
     122.07  125.27   -3.20 1.43e+00 4.89e-01 5.00e+00
  ... (remaining 10714 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.29: 4335
       17.29 -    34.58: 300
       34.58 -    51.86: 66
       51.86 -    69.15: 8
       69.15 -    86.44: 3
  Dihedral angle restraints: 4712
    sinusoidal: 1836
      harmonic: 2876
  Sorted by residual:
  dihedral pdb=" CB  CYS B  11 "
           pdb=" SG  CYS B  11 "
           pdb=" SG  CYS D  11 "
           pdb=" CB  CYS D  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -34.95  -51.05     1      1.00e+01 1.00e-02 3.56e+01
  dihedral pdb=" CA  MET C 336 "
           pdb=" C   MET C 336 "
           pdb=" N   SER C 337 "
           pdb=" CA  SER C 337 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.65   19.35     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  MET A 336 "
           pdb=" C   MET A 336 "
           pdb=" N   SER A 337 "
           pdb=" CA  SER A 337 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.68   19.32     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 4709 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 874
       0.039 -    0.079: 178
       0.079 -    0.118: 94
       0.118 -    0.158: 4
       0.158 -    0.197: 2
  Chirality restraints: 1152
  Sorted by residual:
  chirality pdb=" CA  MET C 336 "
            pdb=" N   MET C 336 "
            pdb=" C   MET C 336 "
            pdb=" CB  MET C 336 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.71e-01
  chirality pdb=" CA  MET A 336 "
            pdb=" N   MET A 336 "
            pdb=" C   MET A 336 "
            pdb=" CB  MET A 336 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.43e-01
  chirality pdb=" CB  ILE A 329 "
            pdb=" CA  ILE A 329 "
            pdb=" CG1 ILE A 329 "
            pdb=" CG2 ILE A 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.51e-01
  ... (remaining 1149 not shown)

  Planarity restraints: 1388
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 330 "    0.040 5.00e-02 4.00e+02   6.11e-02 5.98e+00
        pdb=" N   PRO A 331 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO A 331 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 331 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET C 330 "   -0.035 5.00e-02 4.00e+02   5.35e-02 4.57e+00
        pdb=" N   PRO C 331 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO C 331 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 331 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 333 "   -0.022 5.00e-02 4.00e+02   3.35e-02 1.79e+00
        pdb=" N   PRO A 334 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 334 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 334 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1385 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 841
        2.75 -     3.29: 7435
        3.29 -     3.83: 13115
        3.83 -     4.36: 15727
        4.36 -     4.90: 27034
  Nonbonded interactions: 64152
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 214 "
            pdb=" ND2 ASN A 218 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" NE2 HIS C  64 "
            pdb=" O   MET C 330 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" OE1 GLN A  72 "
            pdb=" OH  TYR A  99 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" NE2 HIS A  64 "
            pdb=" O   MET A 330 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" O   TYR C  90 "
            pdb=" OG1 THR C  93 "
     model   vdw
     2.308 3.040
  ... (remaining 64147 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 1 through 21 or resid 23 through 81 or resid 83 through 21 \ 
0 or resid 212 through 237 or resid 239 through 277 or resid 279 through 329 or  \ 
resid 331 through 366))
  selection = (chain 'C' and (resid 1 through 21 or resid 23 through 81 or resid 83 through 21 \ 
0 or resid 212 through 237 or resid 239 through 277 or resid 279 through 329 or  \ 
resid 331 through 366))
}
ncs_group {
  reference = (chain 'B' and (resid 0 through 16 or resid 18 through 31 or resid 33 through 12 \ 
4))
  selection = (chain 'D' and (resid 0 through 16 or resid 18 through 31 or resid 33 through 12 \ 
4))
}

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=0.00 max=1.00 mean=0.99
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:             4.380
  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:          0.210
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.060
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  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:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
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   0.033   7886  Z= 0.095
  Angle     :  0.454   8.001  10725  Z= 0.244
  Chirality :  0.041   0.197   1152
  Planarity :  0.004   0.061   1388
  Dihedral  : 12.655  86.437   2883
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.27), residues: 988
  helix:  1.65 (0.28), residues: 352
  sheet:  1.28 (0.37), residues: 188
  loop :  1.12 (0.32), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  98 
 TYR   0.009   0.001   TYR C 242 
 PHE   0.008   0.001   PHE C 149 
 TRP   0.007   0.001   TRP C  62 
 HIS   0.008   0.002   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00193 ( 7883)
  covalent geometry    : angle       0.45351 (10719)
  SS BOND              : bond        0.00135 (    3)
  SS BOND              : angle       1.15153 (    6)
  hydrogen bonds       : bond        0.17306 (  355)
  hydrogen bonds       : angle       7.03074 ( 1023)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.284 
Fit side-chains
REVERT: B   28 ILE cc_start: 0.6165 (pt) cc_final: 0.5744 (mm)
REVERT: C  102 LYS cc_start: 0.7441 (mttm) cc_final: 0.7167 (pttt)
REVERT: C  218 ASN cc_start: 0.8216 (m-40) cc_final: 0.7738 (m110)
REVERT: C  239 LYS cc_start: 0.6095 (ptmm) cc_final: 0.5802 (ptpp)
REVERT: D   28 ILE cc_start: 0.5954 (pt) cc_final: 0.5538 (mm)
REVERT: D  122 MET cc_start: 0.6719 (mtt) cc_final: 0.6487 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0815
  time to fit residues: 13.0368
Evaluate side-chains
  86 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.4588

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
C  39 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.194691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.151604 restraints weight = 43124.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 9.06
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3768
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3768 r_free = 0.3768    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3767 r_free = 0.3767    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3767
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079   7886  Z= 0.247
  Angle     :  0.695   7.365  10725  Z= 0.366
  Chirality :  0.049   0.193   1152
  Planarity :  0.005   0.054   1388
  Dihedral  :  4.508  17.690   1078
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  6.13 %
    Favored  : 92.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.27), residues: 988
  helix:  0.88 (0.27), residues: 348
  sheet:  1.13 (0.37), residues: 164
  loop :  0.88 (0.31), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  67 
 TYR   0.019   0.002   TYR C  99 
 PHE   0.027   0.003   PHE D 111 
 TRP   0.031   0.002   TRP C  62 
 HIS   0.024   0.006   HIS C  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00598 ( 7883)
  covalent geometry    : angle       0.69010 (10719)
  SS BOND              : bond        0.00279 (    3)
  SS BOND              : angle       3.50485 (    6)
  hydrogen bonds       : bond        0.04658 (  355)
  hydrogen bonds       : angle       5.40574 ( 1023)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A  170 LYS cc_start: 0.8072 (tppt) cc_final: 0.7610 (tppt)
REVERT: C  102 LYS cc_start: 0.7706 (mttm) cc_final: 0.6993 (pttm)
REVERT: C  170 LYS cc_start: 0.8056 (tppt) cc_final: 0.7638 (tppt)
REVERT: C  218 ASN cc_start: 0.8150 (m-40) cc_final: 0.7805 (m110)
REVERT: C  239 LYS cc_start: 0.6691 (ptmm) cc_final: 0.6318 (ptpp)
  outliers start: 9
  outliers final: 4
  residues processed: 110
  average time/residue: 0.0907
  time to fit residues: 13.5959
Evaluate side-chains
  99 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   79 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 94 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 48 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  72 GLN
C 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.198319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.152371 restraints weight = 42716.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 7.86
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3784 r_free = 0.3784    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3783 r_free = 0.3783    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3783
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7886  Z= 0.142
  Angle     :  0.544   5.852  10725  Z= 0.295
  Chirality :  0.043   0.184   1152
  Planarity :  0.004   0.051   1388
  Dihedral  :  4.141  18.422   1078
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  9.39 %
    Favored  : 89.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.27), residues: 988
  helix:  0.91 (0.27), residues: 362
  sheet:  0.89 (0.37), residues: 164
  loop :  1.08 (0.32), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  67 
 TYR   0.012   0.001   TYR D 114 
 PHE   0.015   0.002   PHE B 111 
 TRP   0.015   0.001   TRP C  62 
 HIS   0.005   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 7883)
  covalent geometry    : angle       0.54044 (10719)
  SS BOND              : bond        0.00304 (    3)
  SS BOND              : angle       2.60042 (    6)
  hydrogen bonds       : bond        0.03794 (  355)
  hydrogen bonds       : angle       5.15554 ( 1023)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A  170 LYS cc_start: 0.8201 (tppt) cc_final: 0.7754 (tppt)
REVERT: C  102 LYS cc_start: 0.7771 (mttm) cc_final: 0.7075 (pttt)
REVERT: C  170 LYS cc_start: 0.8147 (tppt) cc_final: 0.7745 (tppt)
REVERT: C  222 THR cc_start: 0.7811 (p) cc_final: 0.7568 (p)
REVERT: C  239 LYS cc_start: 0.6664 (ptmm) cc_final: 0.6371 (ptpp)
  outliers start: 8
  outliers final: 8
  residues processed: 99
  average time/residue: 0.0875
  time to fit residues: 11.9073
Evaluate side-chains
  97 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 GLN
Chi-restraints excluded: chain B residue   44 GLU
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain C residue  185 ASN
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain D residue   44 GLU
Chi-restraints excluded: chain D residue   79 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 93 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 29 optimal weight:    0.3980
   chunk 12 optimal weight:    0.5980
   chunk 42 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9990
   chunk 18 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C 218 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.197761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.151711 restraints weight = 43609.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3787 rms_B_bonded: 7.45
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3785
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3785 r_free = 0.3785    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3785 r_free = 0.3785    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3785
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.2559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7886  Z= 0.132
  Angle     :  0.522   5.629  10725  Z= 0.280
  Chirality :  0.043   0.187   1152
  Planarity :  0.004   0.051   1388
  Dihedral  :  4.036  18.689   1078
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 11.01 %
    Favored  : 87.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.27), residues: 988
  helix:  0.92 (0.27), residues: 364
  sheet:  0.83 (0.37), residues: 164
  loop :  0.99 (0.32), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  67 
 TYR   0.008   0.001   TYR C  99 
 PHE   0.014   0.002   PHE D 111 
 TRP   0.014   0.001   TRP C  62 
 HIS   0.004   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 7883)
  covalent geometry    : angle       0.51922 (10719)
  SS BOND              : bond        0.00234 (    3)
  SS BOND              : angle       2.16733 (    6)
  hydrogen bonds       : bond        0.03547 (  355)
  hydrogen bonds       : angle       5.01247 ( 1023)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  170 LYS cc_start: 0.8176 (tppt) cc_final: 0.7749 (tppt)
REVERT: C  102 LYS cc_start: 0.7767 (mttm) cc_final: 0.7037 (pttm)
REVERT: C  170 LYS cc_start: 0.8158 (tppt) cc_final: 0.7768 (tppt)
REVERT: C  222 THR cc_start: 0.7933 (p) cc_final: 0.7713 (p)
REVERT: C  239 LYS cc_start: 0.6696 (ptmm) cc_final: 0.6370 (ptpp)
  outliers start: 8
  outliers final: 5
  residues processed: 92
  average time/residue: 0.0906
  time to fit residues: 11.3223
Evaluate side-chains
  90 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain D residue   79 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 36 optimal weight:    8.9990
   chunk 91 optimal weight:    0.0030
   chunk 38 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
A  72 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.197213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.167580 restraints weight = 40306.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3968 rms_B_bonded: 9.20
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3968
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3968 r_free = 0.3968    target_work(ls_wunit_k1) = 0.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3968 r_free = 0.3968    target_work(ls_wunit_k1) = 0.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
r_final: 0.3968
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7886  Z= 0.136
  Angle     :  0.523   6.337  10725  Z= 0.279
  Chirality :  0.043   0.203   1152
  Planarity :  0.004   0.051   1388
  Dihedral  :  4.026  19.531   1078
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.76 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.27), residues: 988
  helix:  0.96 (0.27), residues: 364
  sheet:  0.63 (0.36), residues: 166
  loop :  0.88 (0.32), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  67 
 TYR   0.009   0.001   TYR C  17 
 PHE   0.015   0.002   PHE D 111 
 TRP   0.014   0.001   TRP C  62 
 HIS   0.003   0.001   HIS C  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7883)
  covalent geometry    : angle       0.52089 (10719)
  SS BOND              : bond        0.00244 (    3)
  SS BOND              : angle       2.08345 (    6)
  hydrogen bonds       : bond        0.03489 (  355)
  hydrogen bonds       : angle       4.94021 ( 1023)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A   72 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.6817 (tm-30)
REVERT: A  170 LYS cc_start: 0.8204 (tppt) cc_final: 0.7925 (tppt)
REVERT: C  170 LYS cc_start: 0.7954 (tppt) cc_final: 0.7751 (tppt)
REVERT: C  239 LYS cc_start: 0.6661 (ptmm) cc_final: 0.6429 (ptpp)
  outliers start: 9
  outliers final: 8
  residues processed: 100
  average time/residue: 0.0889
  time to fit residues: 12.2069
Evaluate side-chains
  90 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 GLN
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain B residue   44 GLU
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain C residue  185 ASN
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 67 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4228 r_free = 0.4228 target = 0.195537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.143539 restraints weight = 47765.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 8.69
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3679
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3679 r_free = 0.3679    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3678 r_free = 0.3678    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3678
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7886  Z= 0.150
  Angle     :  0.532   5.385  10725  Z= 0.285
  Chirality :  0.044   0.194   1152
  Planarity :  0.004   0.050   1388
  Dihedral  :  4.125  19.799   1078
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 12.27 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.27), residues: 988
  helix:  0.94 (0.27), residues: 364
  sheet:  0.21 (0.34), residues: 186
  loop :  0.88 (0.33), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  67 
 TYR   0.006   0.001   TYR C  99 
 PHE   0.016   0.002   PHE D 111 
 TRP   0.012   0.001   TRP C  62 
 HIS   0.003   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 7883)
  covalent geometry    : angle       0.52947 (10719)
  SS BOND              : bond        0.00232 (    3)
  SS BOND              : angle       2.08328 (    6)
  hydrogen bonds       : bond        0.03547 (  355)
  hydrogen bonds       : angle       4.95209 ( 1023)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A   72 GLN cc_start: 0.8095 (tt0) cc_final: 0.6920 (tm-30)
REVERT: A  170 LYS cc_start: 0.8143 (tppt) cc_final: 0.7743 (tppt)
REVERT: A  235 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7836 (mp)
REVERT: C  102 LYS cc_start: 0.6649 (mmtt) cc_final: 0.5814 (pttt)
REVERT: C  170 LYS cc_start: 0.8109 (tppt) cc_final: 0.7768 (tppt)
REVERT: C  239 LYS cc_start: 0.6708 (ptmm) cc_final: 0.6442 (ptpp)
  outliers start: 11
  outliers final: 8
  residues processed: 91
  average time/residue: 0.0901
  time to fit residues: 11.4451
Evaluate side-chains
  94 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain C residue  185 ASN
Chi-restraints excluded: chain D residue   44 GLU
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 80 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 58 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 62 optimal weight:    0.2980
   chunk 46 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4237 r_free = 0.4237 target = 0.196964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.167919 restraints weight = 38803.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3967 rms_B_bonded: 8.91
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3968
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3968 r_free = 0.3968    target_work(ls_wunit_k1) = 0.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3968 r_free = 0.3968    target_work(ls_wunit_k1) = 0.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
r_final: 0.3968
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.3213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7886  Z= 0.124
  Angle     :  0.513   6.709  10725  Z= 0.273
  Chirality :  0.042   0.197   1152
  Planarity :  0.004   0.049   1388
  Dihedral  :  3.986  20.152   1078
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 12.14 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.27), residues: 988
  helix:  1.05 (0.27), residues: 364
  sheet:  0.40 (0.35), residues: 170
  loop :  0.75 (0.32), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  67 
 TYR   0.006   0.001   TYR C  99 
 PHE   0.013   0.001   PHE D 111 
 TRP   0.010   0.001   TRP C  62 
 HIS   0.002   0.001   HIS C  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7883)
  covalent geometry    : angle       0.51102 (10719)
  SS BOND              : bond        0.00180 (    3)
  SS BOND              : angle       1.89964 (    6)
  hydrogen bonds       : bond        0.03335 (  355)
  hydrogen bonds       : angle       4.87437 ( 1023)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 GLN cc_start: 0.7908 (tt0) cc_final: 0.6797 (tm-30)
REVERT: A  170 LYS cc_start: 0.8205 (tppt) cc_final: 0.7924 (tppt)
REVERT: A  235 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7608 (mp)
REVERT: C  102 LYS cc_start: 0.6836 (mmtt) cc_final: 0.6197 (pttt)
REVERT: C  170 LYS cc_start: 0.8100 (tppt) cc_final: 0.7843 (tppt)
REVERT: C  285 LEU cc_start: 0.5825 (mm) cc_final: 0.5618 (mm)
  outliers start: 12
  outliers final: 10
  residues processed: 105
  average time/residue: 0.0797
  time to fit residues: 11.8046
Evaluate side-chains
  102 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain B residue   67 ARG
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain C residue  185 ASN
Chi-restraints excluded: chain C residue  309 GLU
Chi-restraints excluded: chain D residue   44 GLU
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 95 optimal weight:    0.6980
   chunk 94 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 55 optimal weight:    8.9990
   chunk 1 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0770
   chunk 72 optimal weight:    0.0770
   chunk 68 optimal weight:    0.1980
   overall best weight:    0.3696

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

Flipped N/Q/H residues before XYZ refinement:
A  72 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.197490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.148421 restraints weight = 44153.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 7.77
r_work: 0.3479 rms_B_bonded: 7.53 restraints_weight: 2.0000
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3472
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.3472
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.3362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7886  Z= 0.109
  Angle     :  0.514  10.556  10725  Z= 0.269
  Chirality :  0.042   0.198   1152
  Planarity :  0.004   0.050   1388
  Dihedral  :  3.960  20.835   1078
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 12.52 %
    Favored  : 86.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.27), residues: 988
  helix:  1.18 (0.28), residues: 364
  sheet:  0.56 (0.35), residues: 168
  loop :  0.72 (0.32), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  67 
 TYR   0.029   0.001   TYR A 106 
 PHE   0.011   0.001   PHE D 111 
 TRP   0.010   0.001   TRP A  94 
 HIS   0.002   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7883)
  covalent geometry    : angle       0.51250 (10719)
  SS BOND              : bond        0.00136 (    3)
  SS BOND              : angle       1.55405 (    6)
  hydrogen bonds       : bond        0.03213 (  355)
  hydrogen bonds       : angle       4.82849 ( 1023)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.6555 (tm-30)
REVERT: A   99 TYR cc_start: 0.7556 (t80) cc_final: 0.7248 (t80)
REVERT: A  170 LYS cc_start: 0.8234 (tppt) cc_final: 0.7946 (tppt)
REVERT: A  235 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7907 (mp)
REVERT: C  102 LYS cc_start: 0.6862 (mmtt) cc_final: 0.5991 (pttt)
REVERT: C  170 LYS cc_start: 0.8252 (tppt) cc_final: 0.7973 (tppt)
REVERT: C  222 THR cc_start: 0.8449 (p) cc_final: 0.8236 (p)
REVERT: C  267 ASN cc_start: 0.7298 (t0) cc_final: 0.6796 (t0)
REVERT: C  285 LEU cc_start: 0.6022 (mm) cc_final: 0.5749 (mm)
  outliers start: 10
  outliers final: 6
  residues processed: 96
  average time/residue: 0.0746
  time to fit residues: 9.9882
Evaluate side-chains
  96 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 GLN
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain C residue  309 GLU
Chi-restraints excluded: chain D residue   44 GLU
Chi-restraints excluded: chain D residue   91 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A  72 GLN
C 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.193365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.147875 restraints weight = 36019.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 7.40
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3729
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3729 r_free = 0.3729    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3729 r_free = 0.3729    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3729
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.3627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7886  Z= 0.184
  Angle     :  0.600   9.859  10725  Z= 0.312
  Chirality :  0.045   0.218   1152
  Planarity :  0.004   0.048   1388
  Dihedral  :  4.223  23.396   1078
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 12.77 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.27), residues: 988
  helix:  0.88 (0.27), residues: 362
  sheet:  0.02 (0.33), residues: 190
  loop :  0.72 (0.33), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  67 
 TYR   0.021   0.002   TYR A  99 
 PHE   0.018   0.002   PHE D 111 
 TRP   0.013   0.001   TRP C  62 
 HIS   0.003   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 7883)
  covalent geometry    : angle       0.59754 (10719)
  SS BOND              : bond        0.00247 (    3)
  SS BOND              : angle       2.20305 (    6)
  hydrogen bonds       : bond        0.03807 (  355)
  hydrogen bonds       : angle       4.92230 ( 1023)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.6748 (tm-30)
REVERT: A   99 TYR cc_start: 0.7784 (t80) cc_final: 0.7367 (t80)
REVERT: A  170 LYS cc_start: 0.8253 (tppt) cc_final: 0.7852 (tppt)
REVERT: A  235 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7810 (mp)
REVERT: C  170 LYS cc_start: 0.8239 (tppt) cc_final: 0.7856 (tppt)
REVERT: C  267 ASN cc_start: 0.7539 (t0) cc_final: 0.6971 (t0)
REVERT: C  285 LEU cc_start: 0.6068 (mm) cc_final: 0.5811 (mm)
  outliers start: 11
  outliers final: 6
  residues processed: 101
  average time/residue: 0.0793
  time to fit residues: 11.2905
Evaluate side-chains
  97 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 GLN
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain C residue  309 GLU
Chi-restraints excluded: chain D residue   44 GLU
Chi-restraints excluded: chain D residue   91 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 40 optimal weight:    0.5980
   chunk 82 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 92 optimal weight:    0.3980
   chunk 11 optimal weight:    0.2980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  72 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.195173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.152113 restraints weight = 43004.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 8.92
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3779
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3779 r_free = 0.3779    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3779 r_free = 0.3779    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7886  Z= 0.129
  Angle     :  0.552  10.235  10725  Z= 0.289
  Chirality :  0.043   0.220   1152
  Planarity :  0.004   0.050   1388
  Dihedral  :  4.163  22.074   1078
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 13.27 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.27), residues: 988
  helix:  1.01 (0.27), residues: 362
  sheet:  0.46 (0.35), residues: 170
  loop :  0.61 (0.32), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  67 
 TYR   0.019   0.001   TYR A  99 
 PHE   0.013   0.002   PHE D 111 
 TRP   0.010   0.001   TRP C  62 
 HIS   0.002   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7883)
  covalent geometry    : angle       0.54556 (10719)
  SS BOND              : bond        0.00321 (    3)
  SS BOND              : angle       3.65678 (    6)
  hydrogen bonds       : bond        0.03470 (  355)
  hydrogen bonds       : angle       4.91645 ( 1023)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.6688 (tm-30)
REVERT: A  170 LYS cc_start: 0.8234 (tppt) cc_final: 0.7802 (tppt)
REVERT: A  235 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7708 (mp)
REVERT: A  285 LEU cc_start: 0.6153 (mm) cc_final: 0.5805 (mm)
REVERT: C  170 LYS cc_start: 0.8234 (tppt) cc_final: 0.7833 (tppt)
REVERT: C  267 ASN cc_start: 0.7542 (t0) cc_final: 0.6974 (t0)
REVERT: C  285 LEU cc_start: 0.6051 (mm) cc_final: 0.5833 (mm)
  outliers start: 9
  outliers final: 7
  residues processed: 93
  average time/residue: 0.0826
  time to fit residues: 10.6383
Evaluate side-chains
  96 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 GLN
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain C residue  185 ASN
Chi-restraints excluded: chain C residue  309 GLU
Chi-restraints excluded: chain D residue   44 GLU
Chi-restraints excluded: chain D residue   91 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 93 optimal weight:    0.9990
   chunk 79 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0030
   chunk 83 optimal weight:    0.5980
   chunk 92 optimal weight:    0.9990
   chunk 80 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.6592

-------------------------------------------------------------------------------
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 = 0.4221 r_free = 0.4221 target = 0.195392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.152198 restraints weight = 43333.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 8.91
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3778
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3778 r_free = 0.3778    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3778 r_free = 0.3778    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3778
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.3689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7886  Z= 0.138
  Angle     :  0.561   9.961  10725  Z= 0.293
  Chirality :  0.043   0.226   1152
  Planarity :  0.004   0.049   1388
  Dihedral  :  4.151  21.815   1078
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 12.89 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.27), residues: 988
  helix:  1.01 (0.27), residues: 362
  sheet:  0.45 (0.35), residues: 170
  loop :  0.62 (0.32), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  67 
 TYR   0.022   0.001   TYR A  99 
 PHE   0.014   0.002   PHE D 111 
 TRP   0.011   0.001   TRP C  62 
 HIS   0.002   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 7883)
  covalent geometry    : angle       0.55795 (10719)
  SS BOND              : bond        0.00160 (    3)
  SS BOND              : angle       2.64057 (    6)
  hydrogen bonds       : bond        0.03455 (  355)
  hydrogen bonds       : angle       4.89395 ( 1023)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1690.67 seconds
wall clock time: 29 minutes 45.86 seconds (1785.86 seconds total)