Starting phenix.real_space_refine
on Tue Mar  3 22:45:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e5g_27912/03_2026/8e5g_27912.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e5g_27912/03_2026/8e5g_27912.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e5g_27912/03_2026/8e5g_27912.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e5g_27912/03_2026/8e5g_27912.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e5g_27912/03_2026/8e5g_27912.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e5g_27912/03_2026/8e5g_27912.map"
  }
  resolution = 3.9
  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
-------------------------------------------------------------------------------
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=   0.003 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe     20      7.16       5
     S      55      5.16       5
     C    5710      2.51       5
     N    1510      2.21       5
     O    1770      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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9065
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1641
          Classifications: {'peptide': 220}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 211}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 172
          Unusual residues: {'HEC': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 1.12, per 1000 atoms: 0.12
  Number of scatterers: 9065
  At special positions: 0
  Unit cell: (84.24, 71.28, 250.56, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe     20     26.01
     S      55     16.00
     O    1770      8.00
     N    1510      7.00
     C    5710      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=71, symmetry=0
  Number of additional bonds: simple=71, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.92
  Conformation dependent library (CDL) restraints added in 281.9 milliseconds
  

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1960

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 10 sheets defined
      20.5% alpha, 16.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 49
      removed outlier: 3.529A  pdb=" N   LYS A  48 " --> pdb=" O   PRO A  45 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   CYS A  49 " --> pdb=" O   CYS A  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 45 through 49'
    Processing helix  chain 'A' and resid 50 through 59
      removed outlier: 3.795A  pdb=" N   ASN A  59 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 86
      removed outlier: 3.524A  pdb=" N   ILE A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 175
    Processing helix  chain 'A' and resid 181 through 186
      removed outlier: 3.998A  pdb=" N   CYS A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 49
      removed outlier: 3.529A  pdb=" N   LYS B  48 " --> pdb=" O   PRO B  45 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   CYS B  49 " --> pdb=" O   CYS B  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 45 through 49'
    Processing helix  chain 'B' and resid 50 through 59
      removed outlier: 3.795A  pdb=" N   ASN B  59 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 86
      removed outlier: 3.524A  pdb=" N   ILE B  77 " --> pdb=" O   THR B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 175
    Processing helix  chain 'B' and resid 181 through 186
      removed outlier: 3.998A  pdb=" N   CYS B 185 " --> pdb=" O   SER B 181 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 49
      removed outlier: 3.529A  pdb=" N   LYS C  48 " --> pdb=" O   PRO C  45 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   CYS C  49 " --> pdb=" O   CYS C  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 49'
    Processing helix  chain 'C' and resid 50 through 59
      removed outlier: 3.796A  pdb=" N   ASN C  59 " --> pdb=" O   ALA C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 86
      removed outlier: 3.523A  pdb=" N   ILE C  77 " --> pdb=" O   THR C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 175
    Processing helix  chain 'C' and resid 181 through 186
      removed outlier: 3.998A  pdb=" N   CYS C 185 " --> pdb=" O   SER C 181 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 49
      removed outlier: 3.529A  pdb=" N   LYS D  48 " --> pdb=" O   PRO D  45 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   CYS D  49 " --> pdb=" O   CYS D  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 45 through 49'
    Processing helix  chain 'D' and resid 50 through 59
      removed outlier: 3.795A  pdb=" N   ASN D  59 " --> pdb=" O   ALA D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 86
      removed outlier: 3.523A  pdb=" N   ILE D  77 " --> pdb=" O   THR D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 175
    Processing helix  chain 'D' and resid 181 through 186
      removed outlier: 3.998A  pdb=" N   CYS D 185 " --> pdb=" O   SER D 181 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 49
      removed outlier: 3.529A  pdb=" N   LYS E  48 " --> pdb=" O   PRO E  45 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   CYS E  49 " --> pdb=" O   CYS E  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 45 through 49'
    Processing helix  chain 'E' and resid 50 through 59
      removed outlier: 3.795A  pdb=" N   ASN E  59 " --> pdb=" O   ALA E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 73 through 86
      removed outlier: 3.523A  pdb=" N   ILE E  77 " --> pdb=" O   THR E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 166 through 175
    Processing helix  chain 'E' and resid 181 through 186
      removed outlier: 3.998A  pdb=" N   CYS E 185 " --> pdb=" O   SER E 181 " (cutoff:3.500A)
    Processing sheet with id=1, first strand: chain 'A' and resid 95 through 96
    Processing sheet with id=2, first strand: chain 'A' and resid 194 through 210
      removed outlier: 4.438A  pdb=" N   LYS A 195 " --> pdb=" O   VAL A 238 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   VAL A 238 " --> pdb=" O   LYS A 195 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   ASN A 197 " --> pdb=" O   THR A 236 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   THR A 236 " --> pdb=" O   ASN A 197 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   THR A 199 " --> pdb=" O   ARG A 234 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   ARG A 234 " --> pdb=" O   THR A 199 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   LYS A 201 " --> pdb=" O   GLY A 232 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   GLY A 232 " --> pdb=" O   LYS A 201 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   SER A 203 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   VAL A 230 " --> pdb=" O   SER A 203 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   GLU A 205 " --> pdb=" O   TRP A 228 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   TRP A 228 " --> pdb=" O   GLU A 205 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASN A 207 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR A 226 " --> pdb=" O   ASN A 207 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER A 247 " --> pdb=" O   PHE A 239 " (cutoff:3.500A)
    Processing sheet with id=3, first strand: chain 'B' and resid 95 through 96
    Processing sheet with id=4, first strand: chain 'B' and resid 194 through 210
      removed outlier: 4.438A  pdb=" N   LYS B 195 " --> pdb=" O   VAL B 238 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   VAL B 238 " --> pdb=" O   LYS B 195 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   ASN B 197 " --> pdb=" O   THR B 236 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   THR B 236 " --> pdb=" O   ASN B 197 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   THR B 199 " --> pdb=" O   ARG B 234 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   ARG B 234 " --> pdb=" O   THR B 199 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   LYS B 201 " --> pdb=" O   GLY B 232 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   GLY B 232 " --> pdb=" O   LYS B 201 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   SER B 203 " --> pdb=" O   VAL B 230 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   VAL B 230 " --> pdb=" O   SER B 203 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   GLU B 205 " --> pdb=" O   TRP B 228 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   TRP B 228 " --> pdb=" O   GLU B 205 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASN B 207 " --> pdb=" O   THR B 226 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   THR B 226 " --> pdb=" O   ASN B 207 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   SER B 247 " --> pdb=" O   PHE B 239 " (cutoff:3.500A)
    Processing sheet with id=5, first strand: chain 'C' and resid 95 through 96
    Processing sheet with id=6, first strand: chain 'C' and resid 194 through 210
      removed outlier: 4.438A  pdb=" N   LYS C 195 " --> pdb=" O   VAL C 238 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   VAL C 238 " --> pdb=" O   LYS C 195 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   ASN C 197 " --> pdb=" O   THR C 236 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   THR C 236 " --> pdb=" O   ASN C 197 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   THR C 199 " --> pdb=" O   ARG C 234 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   ARG C 234 " --> pdb=" O   THR C 199 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   LYS C 201 " --> pdb=" O   GLY C 232 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   GLY C 232 " --> pdb=" O   LYS C 201 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   SER C 203 " --> pdb=" O   VAL C 230 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   VAL C 230 " --> pdb=" O   SER C 203 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   GLU C 205 " --> pdb=" O   TRP C 228 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   TRP C 228 " --> pdb=" O   GLU C 205 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASN C 207 " --> pdb=" O   THR C 226 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR C 226 " --> pdb=" O   ASN C 207 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER C 247 " --> pdb=" O   PHE C 239 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'D' and resid 95 through 96
    Processing sheet with id=8, first strand: chain 'D' and resid 194 through 210
      removed outlier: 4.438A  pdb=" N   LYS D 195 " --> pdb=" O   VAL D 238 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   VAL D 238 " --> pdb=" O   LYS D 195 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   ASN D 197 " --> pdb=" O   THR D 236 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   THR D 236 " --> pdb=" O   ASN D 197 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   THR D 199 " --> pdb=" O   ARG D 234 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   ARG D 234 " --> pdb=" O   THR D 199 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   LYS D 201 " --> pdb=" O   GLY D 232 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   GLY D 232 " --> pdb=" O   LYS D 201 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   SER D 203 " --> pdb=" O   VAL D 230 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   VAL D 230 " --> pdb=" O   SER D 203 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   GLU D 205 " --> pdb=" O   TRP D 228 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   TRP D 228 " --> pdb=" O   GLU D 205 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ASN D 207 " --> pdb=" O   THR D 226 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR D 226 " --> pdb=" O   ASN D 207 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER D 247 " --> pdb=" O   PHE D 239 " (cutoff:3.500A)
    Processing sheet with id=9, first strand: chain 'E' and resid 95 through 96
    Processing sheet with id=10, first strand: chain 'E' and resid 194 through 210
      removed outlier: 4.437A  pdb=" N   LYS E 195 " --> pdb=" O   VAL E 238 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   VAL E 238 " --> pdb=" O   LYS E 195 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   ASN E 197 " --> pdb=" O   THR E 236 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   THR E 236 " --> pdb=" O   ASN E 197 " (cutoff:3.500A)
      removed outlier: 5.366A  pdb=" N   THR E 199 " --> pdb=" O   ARG E 234 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   ARG E 234 " --> pdb=" O   THR E 199 " (cutoff:3.500A)
      removed outlier: 5.234A  pdb=" N   LYS E 201 " --> pdb=" O   GLY E 232 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   GLY E 232 " --> pdb=" O   LYS E 201 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   SER E 203 " --> pdb=" O   VAL E 230 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   VAL E 230 " --> pdb=" O   SER E 203 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   GLU E 205 " --> pdb=" O   TRP E 228 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   TRP E 228 " --> pdb=" O   GLU E 205 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASN E 207 " --> pdb=" O   THR E 226 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR E 226 " --> pdb=" O   ASN E 207 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER E 247 " --> pdb=" O   PHE E 239 " (cutoff:3.500A)

    130 hydrogen bonds defined for protein.
    375 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: 1.15

  Time building geometry restraints manager: 1.13 seconds

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

  Histogram of bond lengths:
        1.21 -     1.38: 3964
        1.38 -     1.56: 5296
        1.56 -     1.74: 10
        1.74 -     1.91: 65
        1.91 -     2.09: 80
  Bond restraints: 9415
  Sorted by residual:
  bond pdb=" N   GLU B 205 "
       pdb=" CA  GLU B 205 "
    ideal  model  delta    sigma   weight residual
    1.457  1.557 -0.099 1.29e-02 6.01e+03 5.93e+01
  bond pdb=" N   GLU E 205 "
       pdb=" CA  GLU E 205 "
    ideal  model  delta    sigma   weight residual
    1.457  1.557 -0.099 1.29e-02 6.01e+03 5.92e+01
  bond pdb=" N   GLU D 205 "
       pdb=" CA  GLU D 205 "
    ideal  model  delta    sigma   weight residual
    1.457  1.557 -0.099 1.29e-02 6.01e+03 5.92e+01
  bond pdb=" N   GLU A 205 "
       pdb=" CA  GLU A 205 "
    ideal  model  delta    sigma   weight residual
    1.457  1.557 -0.099 1.29e-02 6.01e+03 5.91e+01
  bond pdb=" N   GLU C 205 "
       pdb=" CA  GLU C 205 "
    ideal  model  delta    sigma   weight residual
    1.457  1.556 -0.099 1.29e-02 6.01e+03 5.90e+01
  ... (remaining 9410 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 12756
        2.68 -     5.35: 304
        5.35 -     8.03: 55
        8.03 -    10.71: 25
       10.71 -    13.38: 5
  Bond angle restraints: 13145
  Sorted by residual:
  angle pdb=" N   ASN E 207 "
        pdb=" CA  ASN E 207 "
        pdb=" C   ASN E 207 "
      ideal   model   delta    sigma   weight residual
     109.29  122.67  -13.38 1.41e+00 5.03e-01 9.01e+01
  angle pdb=" N   ASN D 207 "
        pdb=" CA  ASN D 207 "
        pdb=" C   ASN D 207 "
      ideal   model   delta    sigma   weight residual
     109.29  122.67  -13.38 1.41e+00 5.03e-01 9.00e+01
  angle pdb=" N   ASN A 207 "
        pdb=" CA  ASN A 207 "
        pdb=" C   ASN A 207 "
      ideal   model   delta    sigma   weight residual
     109.29  122.64  -13.35 1.41e+00 5.03e-01 8.97e+01
  angle pdb=" N   ASN B 207 "
        pdb=" CA  ASN B 207 "
        pdb=" C   ASN B 207 "
      ideal   model   delta    sigma   weight residual
     109.29  122.63  -13.34 1.41e+00 5.03e-01 8.95e+01
  angle pdb=" N   ASN C 207 "
        pdb=" CA  ASN C 207 "
        pdb=" C   ASN C 207 "
      ideal   model   delta    sigma   weight residual
     109.29  122.62  -13.33 1.41e+00 5.03e-01 8.94e+01
  ... (remaining 13140 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.78: 4280
       16.78 -    33.56: 475
       33.56 -    50.33: 85
       50.33 -    67.11: 45
       67.11 -    83.89: 40
  Dihedral angle restraints: 4925
    sinusoidal: 1820
      harmonic: 3105
  Sorted by residual:
  dihedral pdb=" N   ASN D 207 "
           pdb=" C   ASN D 207 "
           pdb=" CA  ASN D 207 "
           pdb=" CB  ASN D 207 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  151.68  -28.88     0      2.50e+00 1.60e-01 1.33e+02
  dihedral pdb=" N   ASN E 207 "
           pdb=" C   ASN E 207 "
           pdb=" CA  ASN E 207 "
           pdb=" CB  ASN E 207 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  151.65  -28.85     0      2.50e+00 1.60e-01 1.33e+02
  dihedral pdb=" N   ASN A 207 "
           pdb=" C   ASN A 207 "
           pdb=" CA  ASN A 207 "
           pdb=" CB  ASN A 207 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  151.62  -28.82     0      2.50e+00 1.60e-01 1.33e+02
  ... (remaining 4922 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.242: 1255
       0.242 -    0.484: 0
       0.484 -    0.726: 5
       0.726 -    0.968: 0
       0.968 -    1.210: 5
  Chirality restraints: 1265
  Sorted by residual:
  chirality pdb=" CA  ASN D 207 "
            pdb=" N   ASN D 207 "
            pdb=" C   ASN D 207 "
            pdb=" CB  ASN D 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.30    1.21 2.00e-01 2.50e+01 3.66e+01
  chirality pdb=" CA  ASN E 207 "
            pdb=" N   ASN E 207 "
            pdb=" C   ASN E 207 "
            pdb=" CB  ASN E 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.30    1.21 2.00e-01 2.50e+01 3.65e+01
  chirality pdb=" CA  ASN A 207 "
            pdb=" N   ASN A 207 "
            pdb=" C   ASN A 207 "
            pdb=" CB  ASN A 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.30    1.21 2.00e-01 2.50e+01 3.64e+01
  ... (remaining 1262 not shown)

  Planarity restraints: 1655
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C HEC D 301 "   -0.011 2.00e-02 2.50e+03   3.10e-02 2.16e+01
        pdb=" C2C HEC D 301 "    0.084 2.00e-02 2.50e+03
        pdb=" C3C HEC D 301 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4C HEC D 301 "   -0.004 2.00e-02 2.50e+03
        pdb=" CAC HEC D 301 "   -0.019 2.00e-02 2.50e+03
        pdb=" CHC HEC D 301 "   -0.014 2.00e-02 2.50e+03
        pdb=" CHD HEC D 301 "   -0.001 2.00e-02 2.50e+03
        pdb=" CMC HEC D 301 "   -0.029 2.00e-02 2.50e+03
        pdb=" NC  HEC D 301 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C HEC C 301 "   -0.011 2.00e-02 2.50e+03   3.10e-02 2.16e+01
        pdb=" C2C HEC C 301 "    0.084 2.00e-02 2.50e+03
        pdb=" C3C HEC C 301 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4C HEC C 301 "   -0.004 2.00e-02 2.50e+03
        pdb=" CAC HEC C 301 "   -0.019 2.00e-02 2.50e+03
        pdb=" CHC HEC C 301 "   -0.014 2.00e-02 2.50e+03
        pdb=" CHD HEC C 301 "   -0.001 2.00e-02 2.50e+03
        pdb=" CMC HEC C 301 "   -0.029 2.00e-02 2.50e+03
        pdb=" NC  HEC C 301 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C HEC E 301 "   -0.011 2.00e-02 2.50e+03   3.10e-02 2.16e+01
        pdb=" C2C HEC E 301 "    0.084 2.00e-02 2.50e+03
        pdb=" C3C HEC E 301 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4C HEC E 301 "   -0.004 2.00e-02 2.50e+03
        pdb=" CAC HEC E 301 "   -0.019 2.00e-02 2.50e+03
        pdb=" CHC HEC E 301 "   -0.014 2.00e-02 2.50e+03
        pdb=" CHD HEC E 301 "   -0.001 2.00e-02 2.50e+03
        pdb=" CMC HEC E 301 "   -0.029 2.00e-02 2.50e+03
        pdb=" NC  HEC E 301 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1652 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.51: 161
        2.51 -     3.11: 7232
        3.11 -     3.71: 14229
        3.71 -     4.30: 19688
        4.30 -     4.90: 30611
  Nonbonded interactions: 71921
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 197 "
            pdb=" ND2 ASN D 207 "
     model   vdw
     1.918 3.200
  nonbonded pdb=" ND2 ASN B 197 "
            pdb=" ND2 ASN C 207 "
     model   vdw
     1.918 3.200
  nonbonded pdb=" ND2 ASN D 197 "
            pdb=" ND2 ASN E 207 "
     model   vdw
     1.918 3.200
  nonbonded pdb=" ND2 ASN A 207 "
            pdb=" ND2 ASN C 197 "
     model   vdw
     1.918 3.200
  nonbonded pdb=" CD1 ILE D  37 "
            pdb=" O1A HEC E 303 "
     model   vdw
     2.016 3.460
  ... (remaining 71916 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             3.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.210
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
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      :  0.024   0.757   9486  Z= 2.212
  Angle     :  1.052  13.382  13145  Z= 0.580
  Chirality :  0.097   1.210   1265
  Planarity :  0.005   0.035   1655
  Dihedral  : 17.243  83.885   2965
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 46.48
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  9.63 %
    Favored  : 89.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  1.02 %
  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 are not related in a simple way.
  whole: -2.33 (0.25), residues: 1090
  helix:  1.43 (0.42), residues: 145
  sheet: -0.68 (0.50), residues: 100
  loop : -2.43 (0.21), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  86 
 TYR   0.015   0.002   TYR B 223 
 PHE   0.006   0.002   PHE D 239 
 TRP   0.008   0.001   TRP C  34 
 HIS   0.006   0.001   HIS E 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00646 ( 9415)
  covalent geometry    : angle       1.05219 (13145)
  hydrogen bonds       : bond        0.23856 (  130)
  hydrogen bonds       : angle       7.05222 (  375)
  Misc. bond           : bond        0.26289 (   71)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: B  163 GLU cc_start: 0.7276 (tp30) cc_final: 0.6110 (mm-30)
REVERT: C   59 ASN cc_start: 0.8837 (t0) cc_final: 0.8261 (t0)
REVERT: C   65 LYS cc_start: 0.8241 (ptpt) cc_final: 0.7998 (ptpt)
REVERT: D   65 LYS cc_start: 0.8297 (ptpt) cc_final: 0.8025 (ptpt)
REVERT: E   65 LYS cc_start: 0.8267 (ptpt) cc_final: 0.8059 (ptpt)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.1017
  time to fit residues: 20.1166
Evaluate side-chains
  107 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    0.6980
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
** A  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  43 ASN
B  60 ASN
C  43 ASN
** C  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.094016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.074585 restraints weight = 29455.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.077302 restraints weight = 17097.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.079087 restraints weight = 12227.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.080315 restraints weight = 9803.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.081084 restraints weight = 8420.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.2961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.015   0.533   9486  Z= 0.297
  Angle     :  1.097  17.430  13145  Z= 0.414
  Chirality :  0.046   0.179   1265
  Planarity :  0.003   0.026   1655
  Dihedral  : 15.743  88.888   1325
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 16.63
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 10.46 %
    Favored  : 89.08 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 10.46 %
    Favored  : 87.36 %
  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 are not related in a simple way.
  whole: -2.66 (0.25), residues: 1090
  helix:  0.10 (0.37), residues: 160
  sheet: -2.29 (0.37), residues: 145
  loop : -2.23 (0.23), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  78 
 TYR   0.019   0.002   TYR A 223 
 PHE   0.019   0.003   PHE D 239 
 TRP   0.007   0.001   TRP C 198 
 HIS   0.011   0.002   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00753 ( 9415)
  covalent geometry    : angle       1.09673 (13145)
  hydrogen bonds       : bond        0.03770 (  130)
  hydrogen bonds       : angle       5.84793 (  375)
  Misc. bond           : bond        0.15168 (   71)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 LYS cc_start: 0.8060 (pttt) cc_final: 0.7839 (ptpt)
REVERT: B   65 LYS cc_start: 0.8512 (ptpt) cc_final: 0.8263 (ptpt)
REVERT: B   72 ASP cc_start: 0.9164 (p0) cc_final: 0.8721 (p0)
REVERT: B  121 PHE cc_start: 0.6727 (m-10) cc_final: 0.6287 (m-10)
REVERT: C   33 MET cc_start: 0.6827 (mpp) cc_final: 0.6583 (mpp)
REVERT: C   65 LYS cc_start: 0.8193 (ptpt) cc_final: 0.7859 (ptpt)
  outliers start: 19
  outliers final: 12
  residues processed: 128
  average time/residue: 0.0849
  time to fit residues: 15.5186
Evaluate side-chains
  117 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain D residue  200 HIS
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain E residue  179 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 74 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 50 optimal weight:    6.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  64 HIS
C  64 HIS
D  43 ASN
D  64 HIS
E  64 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.097006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.077532 restraints weight = 29264.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.080329 restraints weight = 16811.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.082194 restraints weight = 11983.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.083464 restraints weight = 9569.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.084360 restraints weight = 8176.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.3312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.445   9486  Z= 0.170
  Angle     :  0.868  14.682  13145  Z= 0.326
  Chirality :  0.041   0.121   1265
  Planarity :  0.003   0.026   1655
  Dihedral  : 15.471  89.785   1325
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  7.52 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 14.25 %
    Favored  : 83.22 %
  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 are not related in a simple way.
  whole: -2.56 (0.26), residues: 1090
  helix:  0.13 (0.38), residues: 160
  sheet: -2.32 (0.37), residues: 145
  loop : -2.12 (0.24), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  78 
 TYR   0.013   0.001   TYR A 223 
 PHE   0.013   0.002   PHE A 138 
 TRP   0.006   0.001   TRP C 228 
 HIS   0.005   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 9415)
  covalent geometry    : angle       0.86757 (13145)
  hydrogen bonds       : bond        0.03672 (  130)
  hydrogen bonds       : angle       5.42459 (  375)
  Misc. bond           : bond        0.11986 (   71)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.8429 (ptpt) cc_final: 0.8153 (ptpt)
REVERT: D   33 MET cc_start: 0.7036 (ptp) cc_final: 0.6769 (ptp)
  outliers start: 22
  outliers final: 14
  residues processed: 128
  average time/residue: 0.0892
  time to fit residues: 16.2474
Evaluate side-chains
  113 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  179 ILE
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain C residue  201 LYS
Chi-restraints excluded: chain D residue  200 HIS
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue  179 ILE
Chi-restraints excluded: chain E residue  200 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0970
   chunk 108 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 95 optimal weight:    8.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.096238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.076825 restraints weight = 29727.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.079595 restraints weight = 17081.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.081430 restraints weight = 12159.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.082685 restraints weight = 9730.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.083531 restraints weight = 8344.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.452   9486  Z= 0.174
  Angle     :  0.865  15.011  13145  Z= 0.323
  Chirality :  0.041   0.125   1265
  Planarity :  0.003   0.027   1655
  Dihedral  : 15.381  89.902   1325
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  8.44 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 17.36 %
    Favored  : 79.43 %
  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 are not related in a simple way.
  whole: -2.61 (0.26), residues: 1090
  helix:  0.15 (0.39), residues: 160
  sheet: -2.43 (0.36), residues: 145
  loop : -2.15 (0.24), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 234 
 TYR   0.012   0.001   TYR D 152 
 PHE   0.017   0.002   PHE E  54 
 TRP   0.006   0.001   TRP D 228 
 HIS   0.003   0.001   HIS B 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 9415)
  covalent geometry    : angle       0.86542 (13145)
  hydrogen bonds       : bond        0.03409 (  130)
  hydrogen bonds       : angle       5.16832 (  375)
  Misc. bond           : bond        0.11884 (   71)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 LYS cc_start: 0.8395 (ptpt) cc_final: 0.8108 (ptpt)
REVERT: D  221 THR cc_start: 0.8377 (p) cc_final: 0.8139 (t)
  outliers start: 28
  outliers final: 18
  residues processed: 127
  average time/residue: 0.0858
  time to fit residues: 15.7233
Evaluate side-chains
  113 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   84 CYS
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain D residue   84 CYS
Chi-restraints excluded: chain D residue  121 PHE
Chi-restraints excluded: chain D residue  200 HIS
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   84 CYS
Chi-restraints excluded: chain E residue  200 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    0.4980
   chunk 89 optimal weight:    0.0870
   chunk 70 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9990
   chunk 43 optimal weight:    8.9990
   chunk 12 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0010
   chunk 2 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 95 optimal weight:    7.9990
   chunk 94 optimal weight:    4.9990
   overall best weight:    0.4964

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

Flipped N/Q/H residues before XYZ refinement:
A  60 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.099117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.079363 restraints weight = 29040.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.082220 restraints weight = 16845.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.084118 restraints weight = 11988.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.085429 restraints weight = 9584.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.086341 restraints weight = 8179.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.4075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.347   9486  Z= 0.134
  Angle     :  0.805  11.739  13145  Z= 0.309
  Chirality :  0.040   0.139   1265
  Planarity :  0.003   0.027   1655
  Dihedral  : 15.128  89.575   1325
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  7.06 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 18.28 %
    Favored  : 78.05 %
  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 are not related in a simple way.
  whole: -2.40 (0.26), residues: 1090
  helix:  0.64 (0.41), residues: 160
  sheet: -1.92 (0.38), residues: 130
  loop : -2.18 (0.24), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 234 
 TYR   0.010   0.001   TYR B 152 
 PHE   0.015   0.002   PHE E  54 
 TRP   0.010   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9415)
  covalent geometry    : angle       0.80543 (13145)
  hydrogen bonds       : bond        0.02870 (  130)
  hydrogen bonds       : angle       4.93470 (  375)
  Misc. bond           : bond        0.08742 (   71)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 MET cc_start: 0.7315 (ptp) cc_final: 0.6620 (ptp)
REVERT: A  221 THR cc_start: 0.8309 (p) cc_final: 0.8102 (t)
REVERT: B   47 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8167 (mp0)
REVERT: B   65 LYS cc_start: 0.8355 (ptpt) cc_final: 0.8023 (ptpt)
REVERT: B   72 ASP cc_start: 0.9103 (p0) cc_final: 0.8725 (p0)
REVERT: D   60 ASN cc_start: 0.8157 (t0) cc_final: 0.7402 (t0)
REVERT: E   48 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8307 (ttpt)
  outliers start: 32
  outliers final: 25
  residues processed: 139
  average time/residue: 0.0818
  time to fit residues: 16.5191
Evaluate side-chains
  127 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue  121 PHE
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   84 CYS
Chi-restraints excluded: chain C residue  121 PHE
Chi-restraints excluded: chain C residue  189 HIS
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain C residue  201 LYS
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain D residue   84 CYS
Chi-restraints excluded: chain D residue  121 PHE
Chi-restraints excluded: chain D residue  200 HIS
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain E residue   84 CYS
Chi-restraints excluded: chain E residue  121 PHE
Chi-restraints excluded: chain E residue  200 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0010
   chunk 80 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0670
   chunk 79 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 94 optimal weight:    0.6980
   overall best weight:    0.5124

-------------------------------------------------------------------------------
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 = 0.3708 r_free = 0.3708 target = 0.099627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.080097 restraints weight = 29166.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.082902 restraints weight = 16759.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.084783 restraints weight = 11934.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.086072 restraints weight = 9534.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.086987 restraints weight = 8140.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.4370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.289   9486  Z= 0.134
  Angle     :  0.802  11.200  13145  Z= 0.309
  Chirality :  0.040   0.186   1265
  Planarity :  0.003   0.028   1655
  Dihedral  : 14.967  89.857   1325
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  7.16 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 17.59 %
    Favored  : 77.59 %
  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 are not related in a simple way.
  whole: -2.43 (0.26), residues: 1090
  helix:  0.65 (0.41), residues: 160
  sheet: -1.91 (0.38), residues: 130
  loop : -2.22 (0.23), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  78 
 TYR   0.013   0.001   TYR B 152 
 PHE   0.029   0.002   PHE B  54 
 TRP   0.006   0.001   TRP A 228 
 HIS   0.002   0.001   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9415)
  covalent geometry    : angle       0.80152 (13145)
  hydrogen bonds       : bond        0.02970 (  130)
  hydrogen bonds       : angle       4.83573 (  375)
  Misc. bond           : bond        0.07772 (   71)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 111
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 MET cc_start: 0.7430 (ptp) cc_final: 0.6623 (ptp)
REVERT: B   72 ASP cc_start: 0.9141 (p0) cc_final: 0.8882 (p0)
REVERT: D   54 PHE cc_start: 0.8289 (t80) cc_final: 0.7942 (t80)
REVERT: D   60 ASN cc_start: 0.8345 (t0) cc_final: 0.7684 (t0)
REVERT: D  113 ILE cc_start: 0.9171 (tp) cc_final: 0.8851 (tt)
REVERT: E   48 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7930 (ttmm)
REVERT: E  221 THR cc_start: 0.8062 (p) cc_final: 0.7848 (t)
  outliers start: 42
  outliers final: 26
  residues processed: 141
  average time/residue: 0.0835
  time to fit residues: 17.1555
Evaluate side-chains
  130 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue  121 PHE
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   84 CYS
Chi-restraints excluded: chain C residue  121 PHE
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain C residue  201 LYS
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain D residue   84 CYS
Chi-restraints excluded: chain D residue  121 PHE
Chi-restraints excluded: chain D residue  200 HIS
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain E residue   84 CYS
Chi-restraints excluded: chain E residue  121 PHE
Chi-restraints excluded: chain E residue  200 HIS
Chi-restraints excluded: chain E residue  248 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0870
   chunk 100 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 98 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 89 optimal weight:    0.2980
   chunk 96 optimal weight:    0.0570
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.4076

-------------------------------------------------------------------------------
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 = 0.3725 r_free = 0.3725 target = 0.100671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.081840 restraints weight = 27857.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.084684 restraints weight = 15619.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.086595 restraints weight = 10934.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.087932 restraints weight = 8593.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.088763 restraints weight = 7223.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.4607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.253   9486  Z= 0.125
  Angle     :  0.808  12.706  13145  Z= 0.308
  Chirality :  0.040   0.123   1265
  Planarity :  0.003   0.028   1655
  Dihedral  : 14.793  89.512   1325
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  7.25 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 18.97 %
    Favored  : 77.01 %
  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 are not related in a simple way.
  whole: -2.48 (0.25), residues: 1090
  helix:  0.56 (0.40), residues: 165
  sheet: -1.90 (0.39), residues: 130
  loop : -2.27 (0.23), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  78 
 TYR   0.009   0.001   TYR E 152 
 PHE   0.011   0.001   PHE B  54 
 TRP   0.006   0.001   TRP A 228 
 HIS   0.004   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9415)
  covalent geometry    : angle       0.80764 (13145)
  hydrogen bonds       : bond        0.02902 (  130)
  hydrogen bonds       : angle       4.81106 (  375)
  Misc. bond           : bond        0.06951 (   71)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 115
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 MET cc_start: 0.7496 (ptp) cc_final: 0.6810 (ptp)
REVERT: B   72 ASP cc_start: 0.9104 (p0) cc_final: 0.8870 (p0)
REVERT: D   60 ASN cc_start: 0.8413 (t0) cc_final: 0.7904 (t0)
REVERT: D  113 ILE cc_start: 0.9127 (tp) cc_final: 0.8831 (tt)
REVERT: E   48 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7525 (ttmm)
REVERT: E   76 HIS cc_start: 0.8034 (m170) cc_final: 0.7595 (m-70)
  outliers start: 35
  outliers final: 28
  residues processed: 139
  average time/residue: 0.0862
  time to fit residues: 17.2254
Evaluate side-chains
  132 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue  121 PHE
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   84 CYS
Chi-restraints excluded: chain C residue  121 PHE
Chi-restraints excluded: chain C residue  189 HIS
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain C residue  201 LYS
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue   84 CYS
Chi-restraints excluded: chain D residue  121 PHE
Chi-restraints excluded: chain D residue  200 HIS
Chi-restraints excluded: chain D residue  221 THR
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain E residue   84 CYS
Chi-restraints excluded: chain E residue  121 PHE
Chi-restraints excluded: chain E residue  189 HIS
Chi-restraints excluded: chain E residue  200 HIS
Chi-restraints excluded: chain E residue  248 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 60 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0870
   chunk 65 optimal weight:    6.9990
   chunk 89 optimal weight:    0.0870
   chunk 27 optimal weight:    0.0980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.3536

-------------------------------------------------------------------------------
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 = 0.3744 r_free = 0.3744 target = 0.101540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.082660 restraints weight = 27830.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.085511 restraints weight = 15579.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.087460 restraints weight = 10867.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.088794 restraints weight = 8502.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.089740 restraints weight = 7151.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.4819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.327   9486  Z= 0.127
  Angle     :  0.819  15.773  13145  Z= 0.311
  Chirality :  0.040   0.160   1265
  Planarity :  0.003   0.027   1655
  Dihedral  : 14.661  89.276   1325
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  6.79 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 19.43 %
    Favored  : 76.21 %
  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 are not related in a simple way.
  whole: -2.38 (0.26), residues: 1090
  helix:  0.86 (0.41), residues: 165
  sheet: -1.93 (0.40), residues: 130
  loop : -2.23 (0.23), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  78 
 TYR   0.012   0.001   TYR B 152 
 PHE   0.020   0.001   PHE D  54 
 TRP   0.009   0.001   TRP D 228 
 HIS   0.012   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9415)
  covalent geometry    : angle       0.81891 (13145)
  hydrogen bonds       : bond        0.02541 (  130)
  hydrogen bonds       : angle       4.60826 (  375)
  Misc. bond           : bond        0.07557 (   71)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 112
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   72 ASP cc_start: 0.9067 (p0) cc_final: 0.8806 (p0)
  outliers start: 38
  outliers final: 28
  residues processed: 138
  average time/residue: 0.0858
  time to fit residues: 17.0212
Evaluate side-chains
  134 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue  121 PHE
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   84 CYS
Chi-restraints excluded: chain C residue  121 PHE
Chi-restraints excluded: chain C residue  179 ILE
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain C residue  201 LYS
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain D residue   84 CYS
Chi-restraints excluded: chain D residue  121 PHE
Chi-restraints excluded: chain D residue  200 HIS
Chi-restraints excluded: chain D residue  221 THR
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   84 CYS
Chi-restraints excluded: chain E residue  121 PHE
Chi-restraints excluded: chain E residue  189 HIS
Chi-restraints excluded: chain E residue  200 HIS
Chi-restraints excluded: chain E residue  248 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 95 optimal weight:    6.9990
   chunk 86 optimal weight:    3.9990
   chunk 96 optimal weight:    0.0970
   chunk 6 optimal weight:    9.9990
   chunk 81 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 12 optimal weight:    0.0040
   chunk 105 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    1.6194

-------------------------------------------------------------------------------
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 = 0.3641 r_free = 0.3641 target = 0.095694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.076310 restraints weight = 29383.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.078976 restraints weight = 17145.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.080709 restraints weight = 12363.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.081947 restraints weight = 10003.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.082783 restraints weight = 8609.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.4779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.016   0.596   9486  Z= 0.237
  Angle     :  1.003  24.398  13145  Z= 0.362
  Chirality :  0.042   0.175   1265
  Planarity :  0.003   0.027   1655
  Dihedral  : 15.140  89.277   1325
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.27 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 21.26 %
    Favored  : 75.29 %
  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 are not related in a simple way.
  whole: -2.55 (0.25), residues: 1090
  helix:  0.55 (0.41), residues: 165
  sheet: -2.07 (0.37), residues: 130
  loop : -2.31 (0.23), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D  78 
 TYR   0.013   0.001   TYR C 152 
 PHE   0.023   0.002   PHE E  54 
 TRP   0.009   0.001   TRP E  34 
 HIS   0.011   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00595 ( 9415)
  covalent geometry    : angle       1.00268 (13145)
  hydrogen bonds       : bond        0.03610 (  130)
  hydrogen bonds       : angle       4.74374 (  375)
  Misc. bond           : bond        0.16570 (   71)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 106
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   58 LYS cc_start: 0.9411 (ttpp) cc_final: 0.9150 (ttmm)
REVERT: E   65 LYS cc_start: 0.7699 (mttt) cc_final: 0.7478 (mttt)
REVERT: E   76 HIS cc_start: 0.8595 (m170) cc_final: 0.8003 (m170)
  outliers start: 30
  outliers final: 22
  residues processed: 129
  average time/residue: 0.0783
  time to fit residues: 14.8458
Evaluate side-chains
  114 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   84 CYS
Chi-restraints excluded: chain C residue  121 PHE
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain C residue  201 LYS
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue   84 CYS
Chi-restraints excluded: chain D residue  121 PHE
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   84 CYS
Chi-restraints excluded: chain E residue  121 PHE
Chi-restraints excluded: chain E residue  189 HIS
Chi-restraints excluded: chain E residue  248 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 90 optimal weight:   10.0000
   chunk 76 optimal weight:    0.8980
   chunk 65 optimal weight:    8.9990
   chunk 106 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   chunk 55 optimal weight:    8.9990
   chunk 98 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.2582

-------------------------------------------------------------------------------
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 = 0.3664 r_free = 0.3664 target = 0.096878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.077716 restraints weight = 29353.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.080437 restraints weight = 17047.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.082220 restraints weight = 12238.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.083425 restraints weight = 9848.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.084253 restraints weight = 8471.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.4953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.530   9486  Z= 0.205
  Angle     :  0.973  20.819  13145  Z= 0.358
  Chirality :  0.042   0.238   1265
  Planarity :  0.003   0.030   1655
  Dihedral  : 15.101  89.746   1325
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  8.17 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 21.84 %
    Favored  : 74.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.66 (0.25), residues: 1090
  helix:  0.34 (0.39), residues: 165
  sheet: -2.17 (0.37), residues: 130
  loop : -2.35 (0.23), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  78 
 TYR   0.015   0.002   TYR B 152 
 PHE   0.045   0.002   PHE D  54 
 TRP   0.006   0.001   TRP E  34 
 HIS   0.010   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 9415)
  covalent geometry    : angle       0.97289 (13145)
  hydrogen bonds       : bond        0.03532 (  130)
  hydrogen bonds       : angle       4.80141 (  375)
  Misc. bond           : bond        0.15645 (   71)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 96
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   58 LYS cc_start: 0.9471 (ttpp) cc_final: 0.9211 (ttmm)
REVERT: D   60 ASN cc_start: 0.8288 (t0) cc_final: 0.7913 (t0)
REVERT: E   65 LYS cc_start: 0.7713 (mttt) cc_final: 0.7491 (mttt)
REVERT: E   76 HIS cc_start: 0.8523 (m170) cc_final: 0.7924 (m170)
  outliers start: 29
  outliers final: 25
  residues processed: 117
  average time/residue: 0.0803
  time to fit residues: 13.6753
Evaluate side-chains
  115 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue  200 HIS
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   84 CYS
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   84 CYS
Chi-restraints excluded: chain C residue  121 PHE
Chi-restraints excluded: chain C residue  179 ILE
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain C residue  201 LYS
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain D residue   84 CYS
Chi-restraints excluded: chain D residue  121 PHE
Chi-restraints excluded: chain D residue  221 THR
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   84 CYS
Chi-restraints excluded: chain E residue  121 PHE
Chi-restraints excluded: chain E residue  189 HIS
Chi-restraints excluded: chain E residue  221 THR
Chi-restraints excluded: chain E residue  248 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 86 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 95 optimal weight:    2.9990
   chunk 84 optimal weight:    6.9990
   chunk 57 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.098027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.078883 restraints weight = 29020.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.081635 restraints weight = 16581.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.083469 restraints weight = 11790.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.084704 restraints weight = 9407.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.085576 restraints weight = 8053.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.5118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.616   9486  Z= 0.175
  Angle     :  0.940  20.850  13145  Z= 0.339
  Chirality :  0.042   0.206   1265
  Planarity :  0.003   0.032   1655
  Dihedral  : 14.975  89.107   1325
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.92 %
    Allowed  :  8.07 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 22.30 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.63 (0.25), residues: 1090
  helix:  0.44 (0.40), residues: 165
  sheet: -2.20 (0.37), residues: 130
  loop : -2.34 (0.23), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  78 
 TYR   0.013   0.001   TYR E 152 
 PHE   0.028   0.002   PHE D  54 
 TRP   0.008   0.001   TRP A  34 
 HIS   0.011   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 9415)
  covalent geometry    : angle       0.94041 (13145)
  hydrogen bonds       : bond        0.03196 (  130)
  hydrogen bonds       : angle       4.78716 (  375)
  Misc. bond           : bond        0.14490 (   71)

===============================================================================
Job complete
usr+sys time: 1499.27 seconds
wall clock time: 26 minutes 40.01 seconds (1600.01 seconds total)