Starting phenix.real_space_refine
on Sun Jul 27 04:49:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e5g_27912/07_2025/8e5g_27912.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e5g_27912/07_2025/8e5g_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e5g_27912/07_2025/8e5g_27912.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e5g_27912/07_2025/8e5g_27912.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e5g_27912/07_2025/8e5g_27912.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e5g_27912/07_2025/8e5g_27912.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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:
    C, B, E, D
  Time building chain proxies: 4.82, per 1000 atoms: 0.53
  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: 2.96
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.87
  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: 2.07

  Time building geometry restraints manager: 3.39 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

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:             20.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.710
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.700
-------------------------------------------------------------------------------
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 : 47.42
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.008   0.001   TRP C  34 
 HIS   0.006   0.001   HIS E 189 
 PHE   0.006   0.002   PHE D 239 
 TYR   0.015   0.002   TYR B 223 
 ARG   0.001   0.000   ARG B  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23856 (  130)
  hydrogen bonds       : angle       7.05222 (  375)
  covalent geometry    : bond        0.00646 ( 9415)
  covalent geometry    : angle       1.05219 (13145)
  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  : 0.847 
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: 0.2265
  time to fit residues: 44.3076
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  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 83 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 56 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 86 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0970
   chunk 64 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
A  64 HIS
B  43 ASN
B  60 ASN
C  64 HIS
D  64 HIS
E  64 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.094436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.075081 restraints weight = 29172.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.077815 restraints weight = 16934.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.079616 restraints weight = 12064.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.015   0.528   9486  Z= 0.284
  Angle     :  1.046  16.819  13145  Z= 0.401
  Chirality :  0.045   0.171   1265
  Planarity :  0.003   0.025   1655
  Dihedral  : 15.678  88.621   1325
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 16.86
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  9.91 %
    Favored  : 89.63 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.34 %
    Favored  : 87.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.25), residues: 1090
  helix:  0.24 (0.37), residues: 160
  sheet: -2.21 (0.37), residues: 145
  loop : -2.21 (0.23), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 198 
 HIS   0.011   0.002   HIS A  64 
 PHE   0.018   0.002   PHE D 239 
 TYR   0.018   0.002   TYR A 223 
 ARG   0.003   0.001   ARG D  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04049 (  130)
  hydrogen bonds       : angle       5.82070 (  375)
  covalent geometry    : bond        0.00714 ( 9415)
  covalent geometry    : angle       1.04561 (13145)
  Misc. bond           : bond        0.15206 (   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
  134 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.909 
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: 0.8062 (pttt) cc_final: 0.7841 (ptpt)
REVERT: B   65 LYS cc_start: 0.8485 (ptpt) cc_final: 0.8267 (ptpt)
REVERT: B   72 ASP cc_start: 0.9223 (p0) cc_final: 0.8786 (p0)
REVERT: C   33 MET cc_start: 0.6744 (mpp) cc_final: 0.6462 (mpp)
REVERT: C   65 LYS cc_start: 0.8191 (ptpt) cc_final: 0.7854 (ptpt)
  outliers start: 17
  outliers final: 13
  residues processed: 128
  average time/residue: 0.2077
  time to fit residues: 37.6949
Evaluate side-chains
  119 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain E residue  200 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 65 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0570
   chunk 31 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    1.3102

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.095659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.076310 restraints weight = 29766.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.079083 restraints weight = 17045.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.080916 restraints weight = 12118.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.3287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.516   9486  Z= 0.204
  Angle     :  0.906  16.327  13145  Z= 0.340
  Chirality :  0.042   0.120   1265
  Planarity :  0.003   0.027   1655
  Dihedral  : 15.563  89.920   1325
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  7.43 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.02 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.25), residues: 1090
  helix: -0.02 (0.37), residues: 160
  sheet: -2.34 (0.36), residues: 145
  loop : -2.15 (0.23), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 228 
 HIS   0.003   0.001   HIS B 108 
 PHE   0.014   0.002   PHE E 138 
 TYR   0.014   0.002   TYR A 223 
 ARG   0.001   0.000   ARG D  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03851 (  130)
  hydrogen bonds       : angle       5.42292 (  375)
  covalent geometry    : bond        0.00505 ( 9415)
  covalent geometry    : angle       0.90598 (13145)
  Misc. bond           : bond        0.14107 (   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
  139 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.905 
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: 0.8422 (ptpt) cc_final: 0.8153 (ptpt)
REVERT: D   33 MET cc_start: 0.7043 (ptp) cc_final: 0.6787 (ptp)
  outliers start: 24
  outliers final: 13
  residues processed: 127
  average time/residue: 0.2043
  time to fit residues: 36.8087
Evaluate side-chains
  112 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 87 optimal weight:    9.9990
   chunk 45 optimal weight:    0.0570
   chunk 35 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 99 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 96 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.7300

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

Flipped N/Q/H residues before XYZ refinement:
A  60 ASN
D  43 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.097346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.078014 restraints weight = 28969.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.080793 restraints weight = 16645.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.082648 restraints weight = 11872.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.3754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.413   9486  Z= 0.152
  Angle     :  0.843  14.099  13145  Z= 0.317
  Chirality :  0.040   0.124   1265
  Planarity :  0.003   0.026   1655
  Dihedral  : 15.363  89.507   1325
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  7.89 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 17.36 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.26), residues: 1090
  helix:  0.26 (0.39), residues: 160
  sheet: -2.37 (0.36), residues: 145
  loop : -2.12 (0.24), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 228 
 HIS   0.003   0.001   HIS B 108 
 PHE   0.016   0.002   PHE E  54 
 TYR   0.014   0.001   TYR D 152 
 ARG   0.001   0.000   ARG B 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03232 (  130)
  hydrogen bonds       : angle       5.20312 (  375)
  covalent geometry    : bond        0.00369 ( 9415)
  covalent geometry    : angle       0.84266 (13145)
  Misc. bond           : bond        0.10884 (   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
  139 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 0.924 
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: B   65 LYS cc_start: 0.8431 (ptpt) cc_final: 0.8165 (ptpt)
REVERT: D  221 THR cc_start: 0.8372 (p) cc_final: 0.8128 (t)
REVERT: E   48 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8253 (ttpt)
  outliers start: 29
  outliers final: 19
  residues processed: 130
  average time/residue: 0.1954
  time to fit residues: 36.1373
Evaluate side-chains
  117 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
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  121 PHE
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   48 LYS
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 1 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 63 optimal weight:    0.2980
   chunk 40 optimal weight:    5.9990
   chunk 70 optimal weight:    7.9990
   chunk 60 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 102 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3678 r_free = 0.3678 target = 0.097972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.078653 restraints weight = 29102.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.081462 restraints weight = 16682.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.083341 restraints weight = 11843.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.4005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.373   9486  Z= 0.145
  Angle     :  0.828  13.353  13145  Z= 0.313
  Chirality :  0.040   0.135   1265
  Planarity :  0.003   0.026   1655
  Dihedral  : 15.206  89.620   1325
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  7.43 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 18.28 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.50 (0.26), residues: 1090
  helix:  0.50 (0.40), residues: 160
  sheet: -2.39 (0.36), residues: 145
  loop : -2.13 (0.24), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 228 
 HIS   0.002   0.001   HIS B 108 
 PHE   0.017   0.002   PHE B  54 
 TYR   0.011   0.001   TYR D 152 
 ARG   0.001   0.000   ARG B 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03040 (  130)
  hydrogen bonds       : angle       4.94713 (  375)
  covalent geometry    : bond        0.00356 ( 9415)
  covalent geometry    : angle       0.82783 (13145)
  Misc. bond           : bond        0.09661 (   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
  142 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 112
  time to evaluate  : 0.846 
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  221 THR cc_start: 0.8324 (p) cc_final: 0.8085 (t)
REVERT: B   47 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8236 (mp0)
REVERT: B   65 LYS cc_start: 0.8371 (ptpt) cc_final: 0.8050 (ptpt)
REVERT: E   48 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8207 (ttpt)
  outliers start: 30
  outliers final: 27
  residues processed: 133
  average time/residue: 0.1942
  time to fit residues: 36.8716
Evaluate side-chains
  128 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
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  121 PHE
Chi-restraints excluded: chain B residue  200 HIS
Chi-restraints excluded: chain B residue  201 LYS
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  189 HIS
Chi-restraints excluded: chain C residue  200 HIS
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 36 optimal weight:    8.9990
   chunk 96 optimal weight:    0.4980
   chunk 8 optimal weight:    0.0970
   chunk 2 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 97 optimal weight:    0.0670
   chunk 108 optimal weight:    0.9990
   overall best weight:    0.5316

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

Flipped N/Q/H residues before XYZ refinement:
B 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.098927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.080144 restraints weight = 27781.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.082953 restraints weight = 15594.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.084838 restraints weight = 10951.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.4288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.301   9486  Z= 0.135
  Angle     :  0.808  11.680  13145  Z= 0.312
  Chirality :  0.040   0.176   1265
  Planarity :  0.003   0.026   1655
  Dihedral  : 15.061  89.698   1325
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  7.25 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 17.70 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.43 (0.26), residues: 1090
  helix:  0.60 (0.40), residues: 160
  sheet: -1.86 (0.39), residues: 130
  loop : -2.22 (0.23), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 228 
 HIS   0.002   0.001   HIS D  50 
 PHE   0.029   0.002   PHE B  54 
 TYR   0.013   0.001   TYR B 152 
 ARG   0.002   0.000   ARG D  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03027 (  130)
  hydrogen bonds       : angle       4.89247 (  375)
  covalent geometry    : bond        0.00334 ( 9415)
  covalent geometry    : angle       0.80753 (13145)
  Misc. bond           : bond        0.08013 (   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
  154 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 115
  time to evaluate  : 1.161 
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: B   72 ASP cc_start: 0.9165 (p0) cc_final: 0.8910 (p0)
REVERT: D   54 PHE cc_start: 0.8323 (t80) cc_final: 0.7998 (t80)
REVERT: E   48 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7952 (mtpp)
REVERT: E  221 THR cc_start: 0.8112 (p) cc_final: 0.7910 (t)
  outliers start: 39
  outliers final: 24
  residues processed: 142
  average time/residue: 0.2609
  time to fit residues: 53.1211
Evaluate side-chains
  129 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
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  121 PHE
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  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 97 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 74 optimal weight:    0.3980
   chunk 54 optimal weight:    5.9990
   chunk 23 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 77 optimal weight:   20.0000
   chunk 18 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.6584

-------------------------------------------------------------------------------
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 = 0.3628 r_free = 0.3628 target = 0.094924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.075742 restraints weight = 29771.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.078443 restraints weight = 17276.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.080260 restraints weight = 12375.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.4526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.499   9486  Z= 0.235
  Angle     :  0.970  18.431  13145  Z= 0.366
  Chirality :  0.043   0.157   1265
  Planarity :  0.003   0.028   1655
  Dihedral  : 15.372  89.360   1325
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  9.17 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 19.31 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.68 (0.25), residues: 1090
  helix:  0.28 (0.39), residues: 160
  sheet: -2.11 (0.37), residues: 130
  loop : -2.34 (0.23), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E  34 
 HIS   0.006   0.001   HIS A 189 
 PHE   0.033   0.002   PHE E  54 
 TYR   0.015   0.001   TYR B 152 
 ARG   0.004   0.001   ARG D  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04094 (  130)
  hydrogen bonds       : angle       5.00599 (  375)
  covalent geometry    : bond        0.00591 ( 9415)
  covalent geometry    : angle       0.96967 (13145)
  Misc. bond           : bond        0.14396 (   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
  141 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 104
  time to evaluate  : 0.959 
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: B   54 PHE cc_start: 0.7978 (m-80) cc_final: 0.7712 (m-10)
REVERT: B   72 ASP cc_start: 0.9185 (p0) cc_final: 0.8877 (p0)
REVERT: B   76 HIS cc_start: 0.8500 (m170) cc_final: 0.8012 (m-70)
REVERT: D   60 ASN cc_start: 0.8716 (t0) cc_final: 0.8472 (t0)
REVERT: E   48 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7357 (ttmm)
REVERT: E   65 LYS cc_start: 0.7748 (mttt) cc_final: 0.7516 (mttt)
REVERT: E   76 HIS cc_start: 0.8373 (m170) cc_final: 0.7762 (m170)
  outliers start: 37
  outliers final: 25
  residues processed: 133
  average time/residue: 0.1965
  time to fit residues: 37.4562
Evaluate side-chains
  120 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
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  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  121 PHE
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  189 HIS
Chi-restraints excluded: chain C residue  200 HIS
Chi-restraints excluded: chain C residue  216 THR
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   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 51 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 0 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0770
   chunk 46 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0980
   chunk 81 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 95 optimal weight:    4.9990
   overall best weight:    0.5140

-------------------------------------------------------------------------------
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 = 0.3705 r_free = 0.3705 target = 0.099304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.079901 restraints weight = 29505.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.082730 restraints weight = 16938.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.084654 restraints weight = 11996.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.4793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.438   9486  Z= 0.145
  Angle     :  0.857  16.601  13145  Z= 0.326
  Chirality :  0.040   0.138   1265
  Planarity :  0.003   0.031   1655
  Dihedral  : 15.156  89.178   1325
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  1.01 %
    Allowed  :  6.70 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 19.54 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.60 (0.25), residues: 1090
  helix:  0.35 (0.40), residues: 165
  sheet: -2.14 (0.38), residues: 130
  loop : -2.28 (0.23), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 228 
 HIS   0.010   0.001   HIS A 189 
 PHE   0.050   0.002   PHE E  54 
 TYR   0.013   0.001   TYR B 152 
 ARG   0.002   0.000   ARG D  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03289 (  130)
  hydrogen bonds       : angle       4.95515 (  375)
  covalent geometry    : bond        0.00336 ( 9415)
  covalent geometry    : angle       0.85730 (13145)
  Misc. bond           : bond        0.11018 (   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
  136 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 104
  time to evaluate  : 1.581 
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: A  121 PHE cc_start: 0.6822 (m-80) cc_final: 0.6615 (m-10)
REVERT: B   54 PHE cc_start: 0.8312 (m-80) cc_final: 0.7883 (m-10)
REVERT: B   65 LYS cc_start: 0.8800 (ptpt) cc_final: 0.8278 (ptpt)
REVERT: B   72 ASP cc_start: 0.9164 (p0) cc_final: 0.8894 (p0)
REVERT: E   76 HIS cc_start: 0.8350 (m170) cc_final: 0.7831 (m-70)
  outliers start: 32
  outliers final: 27
  residues processed: 127
  average time/residue: 0.2034
  time to fit residues: 37.3622
Evaluate side-chains
  122 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
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  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  129 TYR
Chi-restraints excluded: chain C residue  189 HIS
Chi-restraints excluded: chain C residue  200 HIS
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  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 5 optimal weight:   30.0000
   chunk 61 optimal weight:    5.9990
   chunk 57 optimal weight:    8.9990
   chunk 56 optimal weight:    5.9990
   chunk 13 optimal weight:    0.6980
   chunk 105 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0040
   chunk 53 optimal weight:    0.6980
   chunk 77 optimal weight:    7.9990
   overall best weight:    0.8796

-------------------------------------------------------------------------------
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 = 0.3678 r_free = 0.3678 target = 0.097576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.079000 restraints weight = 28238.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.081767 restraints weight = 15851.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.083610 restraints weight = 11125.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.4866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.492   9486  Z= 0.168
  Angle     :  0.914  20.132  13145  Z= 0.333
  Chirality :  0.041   0.155   1265
  Planarity :  0.003   0.032   1655
  Dihedral  : 15.072  89.755   1325
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  1.01 %
    Allowed  :  8.35 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 21.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.25), residues: 1090
  helix:  0.34 (0.40), residues: 165
  sheet: -2.20 (0.37), residues: 130
  loop : -2.32 (0.23), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  34 
 HIS   0.008   0.001   HIS A 189 
 PHE   0.043   0.002   PHE E  54 
 TYR   0.015   0.001   TYR E 152 
 ARG   0.002   0.000   ARG B  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03432 (  130)
  hydrogen bonds       : angle       4.79662 (  375)
  covalent geometry    : bond        0.00409 ( 9415)
  covalent geometry    : angle       0.91439 (13145)
  Misc. bond           : bond        0.12546 (   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
  134 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 100
  time to evaluate  : 0.864 
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: B   54 PHE cc_start: 0.8400 (m-80) cc_final: 0.7983 (m-10)
REVERT: B   65 LYS cc_start: 0.8670 (ptpt) cc_final: 0.8268 (ptpt)
REVERT: B   72 ASP cc_start: 0.9150 (p0) cc_final: 0.8862 (p0)
REVERT: D   60 ASN cc_start: 0.8244 (t0) cc_final: 0.7500 (t0)
REVERT: E   65 LYS cc_start: 0.7705 (mttt) cc_final: 0.7500 (mttt)
REVERT: E   76 HIS cc_start: 0.8447 (m170) cc_final: 0.7920 (m-70)
  outliers start: 34
  outliers final: 26
  residues processed: 127
  average time/residue: 0.2019
  time to fit residues: 36.9360
Evaluate side-chains
  117 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 91
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
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  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  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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 80 optimal weight:    0.8980
   chunk 14 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 8 optimal weight:    0.3980
   chunk 40 optimal weight:    0.0010
   chunk 107 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 81 optimal weight:    0.0870
   chunk 67 optimal weight:    0.0670
   chunk 54 optimal weight:    5.9990
   overall best weight:    0.2902

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

Flipped N/Q/H residues before XYZ refinement:
D  43 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.101058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.082466 restraints weight = 28070.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.085373 restraints weight = 15601.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.087316 restraints weight = 10786.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.5145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.345   9486  Z= 0.141
  Angle     :  0.884  14.982  13145  Z= 0.334
  Chirality :  0.041   0.245   1265
  Planarity :  0.003   0.031   1655
  Dihedral  : 14.871  86.949   1325
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  1.01 %
    Allowed  :  6.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 21.95 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.26), residues: 1090
  helix:  0.54 (0.41), residues: 165
  sheet: -2.04 (0.34), residues: 195
  loop : -2.34 (0.24), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 198 
 HIS   0.005   0.001   HIS A 189 
 PHE   0.035   0.001   PHE E  54 
 TYR   0.010   0.001   TYR B 152 
 ARG   0.003   0.000   ARG A 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02961 (  130)
  hydrogen bonds       : angle       4.68579 (  375)
  covalent geometry    : bond        0.00330 ( 9415)
  covalent geometry    : angle       0.88429 (13145)
  Misc. bond           : bond        0.09086 (   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
  130 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 100
  time to evaluate  : 0.878 
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: B   54 PHE cc_start: 0.8658 (m-80) cc_final: 0.8192 (m-10)
REVERT: B   65 LYS cc_start: 0.8594 (ptpt) cc_final: 0.8176 (ptpt)
REVERT: B   72 ASP cc_start: 0.9104 (p0) cc_final: 0.8818 (p0)
REVERT: D   33 MET cc_start: 0.7273 (pmm) cc_final: 0.6593 (pmm)
REVERT: D   60 ASN cc_start: 0.8086 (t0) cc_final: 0.7394 (t0)
REVERT: E   76 HIS cc_start: 0.8390 (m170) cc_final: 0.7857 (m-70)
  outliers start: 30
  outliers final: 24
  residues processed: 124
  average time/residue: 0.1826
  time to fit residues: 33.1522
Evaluate side-chains
  119 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
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 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  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  200 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 40 optimal weight:    0.0060
   chunk 107 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 84 optimal weight:    0.2980
   chunk 41 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 89 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9990
   chunk 103 optimal weight:    0.0070
   chunk 19 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.3416

-------------------------------------------------------------------------------
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 = 0.101541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.082790 restraints weight = 28229.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.085717 restraints weight = 15874.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.087669 restraints weight = 11043.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.5291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.400   9486  Z= 0.134
  Angle     :  0.875  16.659  13145  Z= 0.328
  Chirality :  0.041   0.198   1265
  Planarity :  0.003   0.032   1655
  Dihedral  : 14.644  87.746   1325
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  1.01 %
    Allowed  :  6.97 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 22.07 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.55 (0.26), residues: 1090
  helix:  0.77 (0.41), residues: 165
  sheet: -2.04 (0.34), residues: 195
  loop : -2.33 (0.24), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  34 
 HIS   0.005   0.001   HIS A 189 
 PHE   0.034   0.001   PHE E  54 
 TYR   0.011   0.001   TYR A 191 
 ARG   0.002   0.000   ARG B  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02809 (  130)
  hydrogen bonds       : angle       4.56341 (  375)
  covalent geometry    : bond        0.00323 ( 9415)
  covalent geometry    : angle       0.87484 (13145)
  Misc. bond           : bond        0.08860 (   71)

===============================================================================
Job complete
usr+sys time: 3309.08 seconds
wall clock time: 59 minutes 57.89 seconds (3597.89 seconds total)