Starting phenix.real_space_refine
on Tue Mar  3 19:15:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o6p_12739/03_2026/7o6p_12739.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o6p_12739/03_2026/7o6p_12739.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o6p_12739/03_2026/7o6p_12739.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o6p_12739/03_2026/7o6p_12739.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7o6p_12739/03_2026/7o6p_12739.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o6p_12739/03_2026/7o6p_12739.map"
  }
  resolution = 2.04
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.042
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    5014      2.51       5
     N    1451      2.21       5
     O    1759      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8276
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2010
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 256, 1913
          Classifications: {'peptide': 256}
          Link IDs: {'PTRANS': 8, 'TRANS': 247}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 256, 1913
          Classifications: {'peptide': 256}
          Link IDs: {'PTRANS': 8, 'TRANS': 247}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1837
    Chain: "B"
      Number of atoms: 1980
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 255, 1905
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 8, 'TRANS': 246}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 255, 1905
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 8, 'TRANS': 246}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1855
    Chain: "C"
      Number of atoms: 1991
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 254, 1901
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 8, 'TRANS': 245}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 254, 1901
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 8, 'TRANS': 245}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1833
    Chain: "D"
      Number of atoms: 2027
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 257, 1919
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 8, 'TRANS': 248}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 257, 1919
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 8, 'TRANS': 248}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1831
    Chain: "A"
      Number of atoms: 68
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 68, 68
          Classifications: {'water': 68}
          Link IDs: {None: 67}
    Chain: "B"
      Number of atoms: 71
      Number of conformers: 2
      Conformer: "B"
        Number of residues, atoms: 70, 70
          Classifications: {'water': 70}
          Link IDs: {None: 69}
      Conformer: "A"
        Number of residues, atoms: 70, 70
          Classifications: {'water': 70}
          Link IDs: {None: 69}
    Chain: "C"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 60, 60
          Classifications: {'water': 60}
          Link IDs: {None: 59}
    Chain: "D"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 69
          Classifications: {'water': 69}
          Link IDs: {None: 68}
  Residues with excluded nonbonded symmetry interactions: 43
    residue:
      pdb=" N  AARG A  20 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A  20 " occ=0.50
    residue:
      pdb=" N  ASER A  34 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER A  34 " occ=0.50
    residue:
      pdb=" N  AARG A  40 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A  40 " occ=0.50
    residue:
      pdb=" N  ALYS A  45 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS A  45 " occ=0.50
    residue:
      pdb=" N  AARG A  84 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A  84 " occ=0.50
    residue:
      pdb=" N  ALYS A 147 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS A 147 " occ=0.50
    residue:
      pdb=" N  ALYS A 181 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS A 181 " occ=0.50
    residue:
      pdb=" N  AARG A 225 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 225 " occ=0.50
    residue:
      pdb=" N  AGLU A 238 " occ=0.50
      ... (16 atoms not shown)
      pdb=" OE2BGLU A 238 " occ=0.50
    residue:
      pdb=" N  AARG A 257 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 257 " occ=0.50
    residue:
      pdb=" N  ALEU B  37 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CD2BLEU B  37 " occ=0.50
    residue:
      pdb=" N  ALYS B  83 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS B  83 " occ=0.50
    ... (remaining 31 not shown)
  Time building chain proxies: 3.35, per 1000 atoms: 0.40
  Number of scatterers: 8276
  At special positions: 0
  Unit cell: (81.536, 93.184, 79.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1759      8.00
     N    1451      7.00
     C    5014      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 529.8 milliseconds
  

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1914

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 4 sheets defined
      53.9% alpha, 12.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 42
      removed outlier: 3.507A  pdb=" N  ASER A  34 " --> pdb=" O   GLY A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 3.558A  pdb=" N   CYS A  60 " --> pdb=" O   GLY A  56 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY A  64 " --> pdb=" O   CYS A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 94
    Processing helix  chain 'A' and resid 112 through 116
    Processing helix  chain 'A' and resid 117 through 129
    Processing helix  chain 'A' and resid 129 through 147
      removed outlier: 3.726A  pdb=" N   ILE A 142 " --> pdb=" O   HIS A 138 " (cutoff:3.500A)
      Proline residue:  A 145  - end of helix
    Processing helix  chain 'A' and resid 156 through 160
    Processing helix  chain 'A' and resid 166 through 188
    Processing helix  chain 'A' and resid 220 through 231
    Processing helix  chain 'A' and resid 240 through 253
      removed outlier: 3.610A  pdb=" N   VAL A 244 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 257
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 52 through 64
      removed outlier: 3.842A  pdb=" N   GLN B  57 " --> pdb=" O   ASP B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 94
    Processing helix  chain 'B' and resid 112 through 116
    Processing helix  chain 'B' and resid 117 through 129
    Processing helix  chain 'B' and resid 129 through 147
      removed outlier: 3.727A  pdb=" N   ILE B 142 " --> pdb=" O   HIS B 138 " (cutoff:3.500A)
      Proline residue:  B 145  - end of helix
    Processing helix  chain 'B' and resid 156 through 160
    Processing helix  chain 'B' and resid 166 through 188
    Processing helix  chain 'B' and resid 221 through 231
    Processing helix  chain 'B' and resid 240 through 253
      removed outlier: 3.606A  pdb=" N   VAL B 244 " --> pdb=" O   THR B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 257
    Processing helix  chain 'C' and resid 30 through 42
    Processing helix  chain 'C' and resid 52 through 64
      removed outlier: 3.871A  pdb=" N   ARG C  58 " --> pdb=" O   ASN C  54 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   CYS C  60 " --> pdb=" O   GLY C  56 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 94
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'C' and resid 117 through 129
    Processing helix  chain 'C' and resid 129 through 147
      removed outlier: 3.730A  pdb=" N   ILE C 142 " --> pdb=" O   HIS C 138 " (cutoff:3.500A)
      Proline residue:  C 145  - end of helix
    Processing helix  chain 'C' and resid 156 through 160
    Processing helix  chain 'C' and resid 166 through 188
    Processing helix  chain 'C' and resid 220 through 231
    Processing helix  chain 'C' and resid 240 through 253
      removed outlier: 3.597A  pdb=" N   VAL C 244 " --> pdb=" O   THR C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 254 through 257
    Processing helix  chain 'D' and resid 30 through 42
    Processing helix  chain 'D' and resid 52 through 64
      removed outlier: 3.720A  pdb=" N   GLY D  64 " --> pdb=" O   CYS D  60 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 94
    Processing helix  chain 'D' and resid 112 through 116
    Processing helix  chain 'D' and resid 117 through 129
    Processing helix  chain 'D' and resid 129 through 147
      removed outlier: 3.732A  pdb=" N   ILE D 142 " --> pdb=" O   HIS D 138 " (cutoff:3.500A)
      Proline residue:  D 145  - end of helix
    Processing helix  chain 'D' and resid 156 through 160
    Processing helix  chain 'D' and resid 166 through 188
    Processing helix  chain 'D' and resid 220 through 231
    Processing helix  chain 'D' and resid 240 through 253
      removed outlier: 3.619A  pdb=" N   VAL D 244 " --> pdb=" O   THR D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 254 through 257
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 73
      removed outlier: 6.552A  pdb=" N   VAL A  21 " --> pdb=" O   ILE A  98 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   VAL A 100 " --> pdb=" O   VAL A  21 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   LEU A  23 " --> pdb=" O   VAL A 100 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   MET A  99 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   ILE A 154 " --> pdb=" O   MET A  99 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   ASN A 101 " --> pdb=" O   ILE A 154 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   MET A 262 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 69 through 73
      removed outlier: 6.537A  pdb=" N   VAL B  21 " --> pdb=" O   ILE B  98 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   VAL B 100 " --> pdb=" O   VAL B  21 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LEU B  23 " --> pdb=" O   VAL B 100 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   MET B  99 " --> pdb=" O   ILE B 152 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   ILE B 154 " --> pdb=" O   MET B  99 " (cutoff:3.500A)
      removed outlier: 7.411A  pdb=" N   ASN B 101 " --> pdb=" O   ILE B 154 " (cutoff:3.500A)
      removed outlier: 9.756A  pdb=" N   MET B 262 " --> pdb=" O   ILE B 192 " (cutoff:3.500A)
      removed outlier: 7.687A  pdb=" N   VAL B 194 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 8.615A  pdb=" N   LEU B 264 " --> pdb=" O   VAL B 194 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   CYS B 196 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   VAL B 266 " --> pdb=" O   CYS B 196 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   SER B 198 " --> pdb=" O   VAL B 266 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 69 through 73
      removed outlier: 6.563A  pdb=" N   VAL C  21 " --> pdb=" O   ILE C  98 " (cutoff:3.500A)
      removed outlier: 8.006A  pdb=" N   VAL C 100 " --> pdb=" O   VAL C  21 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   LEU C  23 " --> pdb=" O   VAL C 100 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   MET C  99 " --> pdb=" O   ILE C 152 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   ILE C 154 " --> pdb=" O   MET C  99 " (cutoff:3.500A)
      removed outlier: 7.412A  pdb=" N   ASN C 101 " --> pdb=" O   ILE C 154 " (cutoff:3.500A)
      removed outlier: 8.629A  pdb=" N   LEU C 264 " --> pdb=" O   VAL C 194 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   CYS C 196 " --> pdb=" O   LEU C 264 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   VAL C 266 " --> pdb=" O   CYS C 196 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   SER C 198 " --> pdb=" O   VAL C 266 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 69 through 73
      removed outlier: 6.558A  pdb=" N   VAL D  21 " --> pdb=" O   ILE D  98 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   VAL D 100 " --> pdb=" O   VAL D  21 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   LEU D  23 " --> pdb=" O   VAL D 100 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   MET D  99 " --> pdb=" O   ILE D 152 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   ILE D 154 " --> pdb=" O   MET D  99 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   ASN D 101 " --> pdb=" O   ILE D 154 " (cutoff:3.500A)
      removed outlier: 8.615A  pdb=" N   LEU D 264 " --> pdb=" O   VAL D 194 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   CYS D 196 " --> pdb=" O   LEU D 264 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   VAL D 266 " --> pdb=" O   CYS D 196 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   SER D 198 " --> pdb=" O   VAL D 266 " (cutoff:3.500A)

    460 hydrogen bonds defined for protein.
    1333 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.38

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2778
        1.34 -     1.46: 1652
        1.46 -     1.58: 3658
        1.58 -     1.70: 0
        1.70 -     1.81: 80
  Bond restraints: 8168
  Sorted by residual:
  bond pdb=" CB ALYS D 189 "
       pdb=" CG ALYS D 189 "
    ideal  model  delta    sigma   weight residual
    1.520  1.470  0.050 3.00e-02 1.11e+03 2.78e+00
  bond pdb=" CA  GLN D  52 "
       pdb=" C   GLN D  52 "
    ideal  model  delta    sigma   weight residual
    1.532  1.520  0.013 9.60e-03 1.09e+04 1.80e+00
  bond pdb=" CG1 ILE D  98 "
       pdb=" CD1 ILE D  98 "
    ideal  model  delta    sigma   weight residual
    1.513  1.463  0.050 3.90e-02 6.57e+02 1.62e+00
  bond pdb=" CG1 ILE B  98 "
       pdb=" CD1 ILE B  98 "
    ideal  model  delta    sigma   weight residual
    1.513  1.464  0.049 3.90e-02 6.57e+02 1.57e+00
  bond pdb=" CG1 ILE A  98 "
       pdb=" CD1 ILE A  98 "
    ideal  model  delta    sigma   weight residual
    1.513  1.464  0.049 3.90e-02 6.57e+02 1.56e+00
  ... (remaining 8163 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 10294
        1.06 -     2.11: 636
        2.11 -     3.17: 121
        3.17 -     4.23: 23
        4.23 -     5.28: 6
  Bond angle restraints: 11080
  Sorted by residual:
  angle pdb=" CA  SER B 155 "
        pdb=" C   SER B 155 "
        pdb=" N   SER B 156 "
      ideal   model   delta    sigma   weight residual
     117.21  120.45   -3.24 1.42e+00 4.96e-01 5.22e+00
  angle pdb=" CA  SER A 155 "
        pdb=" C   SER A 155 "
        pdb=" N   SER A 156 "
      ideal   model   delta    sigma   weight residual
     117.21  120.45   -3.24 1.42e+00 4.96e-01 5.20e+00
  angle pdb=" CA  SER C 155 "
        pdb=" C   SER C 155 "
        pdb=" N   SER C 156 "
      ideal   model   delta    sigma   weight residual
     117.21  120.43   -3.22 1.42e+00 4.96e-01 5.13e+00
  angle pdb=" CA  SER B 155 "
        pdb=" C   SER B 155 "
        pdb=" O   SER B 155 "
      ideal   model   delta    sigma   weight residual
     120.84  117.86    2.98 1.33e+00 5.65e-01 5.01e+00
  angle pdb=" C   ALA B 256 "
        pdb=" N  BARG B 257 "
        pdb=" CA BARG B 257 "
      ideal   model   delta    sigma   weight residual
     120.38  123.64   -3.26 1.46e+00 4.69e-01 4.99e+00
  ... (remaining 11075 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.21: 4535
       16.21 -    32.42: 316
       32.42 -    48.63: 48
       48.63 -    64.84: 12
       64.84 -    81.05: 5
  Dihedral angle restraints: 4916
    sinusoidal: 1901
      harmonic: 3015
  Sorted by residual:
  dihedral pdb=" CA  PRO A 199 "
           pdb=" C   PRO A 199 "
           pdb=" N   TYR A 200 "
           pdb=" CA  TYR A 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.59   16.41     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  PRO C 199 "
           pdb=" C   PRO C 199 "
           pdb=" N   TYR C 200 "
           pdb=" CA  TYR C 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.86   16.14     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CA  CYS A  60 "
           pdb=" C   CYS A  60 "
           pdb=" N   GLU A  61 "
           pdb=" CA  GLU A  61 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.94   16.06     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 4913 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 458
       0.027 -    0.054: 446
       0.054 -    0.081: 244
       0.081 -    0.108: 83
       0.108 -    0.135: 33
  Chirality restraints: 1264
  Sorted by residual:
  chirality pdb=" CB  ILE A 192 "
            pdb=" CA  ILE A 192 "
            pdb=" CG1 ILE A 192 "
            pdb=" CG2 ILE A 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.59e-01
  chirality pdb=" CB  ILE C 192 "
            pdb=" CA  ILE C 192 "
            pdb=" CG1 ILE C 192 "
            pdb=" CG2 ILE C 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.43e-01
  chirality pdb=" CB  ILE D 192 "
            pdb=" CA  ILE D 192 "
            pdb=" CG1 ILE D 192 "
            pdb=" CG2 ILE D 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.29e-01
  ... (remaining 1261 not shown)

  Planarity restraints: 1468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 198 "    0.035 5.00e-02 4.00e+02   5.22e-02 4.37e+00
        pdb=" N   PRO B 199 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO B 199 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 199 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D 198 "   -0.034 5.00e-02 4.00e+02   5.07e-02 4.12e+00
        pdb=" N   PRO D 199 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO D 199 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO D 199 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 198 "    0.033 5.00e-02 4.00e+02   4.96e-02 3.94e+00
        pdb=" N   PRO A 199 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 199 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 199 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1465 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 247
        2.69 -     3.24: 8750
        3.24 -     3.80: 14430
        3.80 -     4.35: 20153
        4.35 -     4.90: 31567
  Nonbonded interactions: 75147
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 112 "
            pdb=" O   HOH A 301 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" OD2 ASP D 112 "
            pdb=" O   HOH D 301 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" OD2 ASP C 112 "
            pdb=" O   HOH C 301 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" O   VAL C 237 "
            pdb=" O   HOH C 302 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" O   VAL A 237 "
            pdb=" O   HOH A 302 "
     model   vdw
     2.180 3.040
  ... (remaining 75142 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 13 through 19 or resid 21 through 33 or resid 35 through 3 \ 
6 or resid 38 through 39 or resid 41 through 44 or resid 46 through 82 or resid  \ 
85 through 89 or resid 91 through 116 or resid 118 through 146 or resid 149 thro \ 
ugh 180 or resid 182 through 188 or resid 190 through 202 or resid 220 through 2 \ 
24 or resid 226 through 237 or resid 239 through 256 or resid 258 through 282))
  selection = (chain 'B' and (resid 13 through 19 or resid 21 through 33 or resid 35 through 3 \ 
6 or resid 38 through 39 or resid 41 through 44 or resid 46 through 82 or resid  \ 
85 through 89 or resid 91 through 116 or resid 118 through 146 or resid 149 thro \ 
ugh 180 or resid 182 through 188 or resid 190 through 202 or resid 220 through 2 \ 
24 or resid 226 through 237 or resid 239 through 256 or resid 258 through 282))
  selection = (chain 'C' and (resid 13 through 19 or resid 21 through 33 or resid 35 through 3 \ 
6 or resid 38 through 39 or resid 41 through 44 or resid 46 through 82 or resid  \ 
85 through 89 or resid 91 through 116 or resid 118 through 146 or resid 149 thro \ 
ugh 180 or resid 182 through 188 or resid 190 through 202 or resid 220 through 2 \ 
24 or resid 226 through 237 or resid 239 through 256 or resid 258 through 282))
  selection = (chain 'D' and (resid 13 through 19 or resid 21 through 33 or resid 35 through 3 \ 
6 or resid 38 through 39 or resid 41 through 44 or resid 46 through 82 or resid  \ 
85 through 89 or resid 91 through 116 or resid 118 through 146 or resid 149 thro \ 
ugh 180 or resid 182 through 188 or resid 190 through 202 or resid 220 through 2 \ 
24 or resid 226 through 237 or resid 239 through 256 or resid 258 through 282))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.96
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.660
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     11.150
  Find NCS groups from input model:        0.170
  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:6.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
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      :  0.008   0.050   8168  Z= 0.329
  Angle     :  0.594   5.284  11080  Z= 0.334
  Chirality :  0.049   0.135   1264
  Planarity :  0.005   0.052   1468
  Dihedral  : 11.733  81.046   3002
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  5.10 %
    Favored  : 93.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.23), residues: 1117
  helix: -0.01 (0.22), residues: 511
  sheet:  0.38 (0.39), residues: 176
  loop : -0.96 (0.26), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  16 
 TYR   0.014   0.003   TYR C 200 
 PHE   0.016   0.003   PHE C 133 
 TRP   0.004   0.001   TRP C 221 
 HIS   0.012   0.002   HIS A 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00801 ( 8168)
  covalent geometry    : angle       0.59423 (11080)
  hydrogen bonds       : bond        0.21916 (  460)
  hydrogen bonds       : angle       8.17133 ( 1333)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 2
  residues processed: 113
  average time/residue: 0.9067
  time to fit residues: 106.4815
Evaluate side-chains
  79 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LYS
Chi-restraints excluded: chain D residue   92 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 235 GLN
B 235 GLN
C 235 GLN
D 233 ASN
D 235 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.101346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.073646 restraints weight = 128786.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 4.82
r_work: 0.2923 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2918
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2918 r_free = 0.2918    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2917
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8949
moved from start:          0.1484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8168  Z= 0.147
  Angle     :  0.518   8.580  11080  Z= 0.286
  Chirality :  0.044   0.146   1264
  Planarity :  0.004   0.048   1468
  Dihedral  :  5.087  55.717   1180
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  9.74 %
    Favored  : 89.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.25), residues: 1117
  helix:  1.35 (0.22), residues: 535
  sheet:  0.50 (0.37), residues: 180
  loop : -0.32 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  20 
 TYR   0.017   0.002   TYR C 169 
 PHE   0.011   0.002   PHE A 250 
 TRP   0.012   0.001   TRP C 221 
 HIS   0.003   0.001   HIS C 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8168)
  covalent geometry    : angle       0.51831 (11080)
  hydrogen bonds       : bond        0.04794 (  460)
  hydrogen bonds       : angle       4.99776 ( 1333)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8524 (tttt)
REVERT: B   20 ARG cc_start: 0.8810 (mmt90) cc_final: 0.8538 (mmm-85)
REVERT: D   92 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8530 (tttt)
  outliers start: 3
  outliers final: 0
  residues processed: 82
  average time/residue: 0.7638
  time to fit residues: 65.7495
Evaluate side-chains
  74 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LYS
Chi-restraints excluded: chain D residue   92 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 52 optimal weight:    0.7980
   chunk 94 optimal weight:    0.4980
   chunk 42 optimal weight:    1.9990
   chunk 96 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D 233 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.100184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.072855 restraints weight = 120601.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 4.68
r_work: 0.2913 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2916
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2916
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8960
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8168  Z= 0.165
  Angle     :  0.490   6.577  11080  Z= 0.268
  Chirality :  0.043   0.152   1264
  Planarity :  0.003   0.047   1468
  Dihedral  :  4.931  56.926   1180
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  9.63 %
    Favored  : 89.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.25), residues: 1117
  helix:  1.65 (0.22), residues: 535
  sheet:  0.40 (0.36), residues: 184
  loop :  0.03 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  20 
 TYR   0.019   0.002   TYR C 169 
 PHE   0.012   0.001   PHE C 133 
 TRP   0.006   0.001   TRP C 221 
 HIS   0.005   0.001   HIS C 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 8168)
  covalent geometry    : angle       0.48971 (11080)
  hydrogen bonds       : bond        0.04765 (  460)
  hydrogen bonds       : angle       4.66651 ( 1333)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   20 ARG cc_start: 0.8823 (mmt90) cc_final: 0.8572 (mmm-85)
REVERT: C   92 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8564 (tmtt)
REVERT: D   92 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8683 (tmtt)
  outliers start: 10
  outliers final: 1
  residues processed: 84
  average time/residue: 0.7206
  time to fit residues: 63.6235
Evaluate side-chains
  83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 LYS
Chi-restraints excluded: chain D residue   92 LYS
Chi-restraints excluded: chain D residue  161 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0670
   chunk 55 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.6918

-------------------------------------------------------------------------------
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 = 0.3610 r_free = 0.3610 target = 0.100367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.073087 restraints weight = 123930.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 4.70
r_work: 0.2920 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2920
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2920 r_free = 0.2920    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2920 r_free = 0.2920    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2920
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8958
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8168  Z= 0.157
  Angle     :  0.477   8.240  11080  Z= 0.258
  Chirality :  0.043   0.145   1264
  Planarity :  0.003   0.047   1468
  Dihedral  :  4.399  57.204   1176
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  9.86 %
    Favored  : 88.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.25), residues: 1117
  helix:  1.80 (0.22), residues: 535
  sheet:  0.47 (0.36), residues: 183
  loop :  0.17 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  20 
 TYR   0.019   0.002   TYR C 169 
 PHE   0.012   0.001   PHE B 133 
 TRP   0.007   0.001   TRP C 221 
 HIS   0.004   0.001   HIS A 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 8168)
  covalent geometry    : angle       0.47667 (11080)
  hydrogen bonds       : bond        0.04330 (  460)
  hydrogen bonds       : angle       4.44979 ( 1333)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8651 (tt0)
REVERT: B  186 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8658 (tt0)
REVERT: B  238 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8456 (pm20)
REVERT: C  186 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8637 (tt0)
REVERT: D  186 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8553 (tt0)
  outliers start: 10
  outliers final: 1
  residues processed: 80
  average time/residue: 0.7462
  time to fit residues: 62.6789
Evaluate side-chains
  85 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain D residue  161 MET
Chi-restraints excluded: chain D residue  186 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 23 optimal weight:    0.4980
   chunk 66 optimal weight:    0.9990
   chunk 90 optimal weight:    0.0980
   chunk 42 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3616 r_free = 0.3616 target = 0.100594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.073281 restraints weight = 134489.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 4.80
r_work: 0.2923 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2926
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2926 r_free = 0.2926    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2926 r_free = 0.2926    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2926
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8958
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8168  Z= 0.140
  Angle     :  0.457   8.761  11080  Z= 0.247
  Chirality :  0.042   0.137   1264
  Planarity :  0.003   0.046   1468
  Dihedral  :  3.815  18.253   1172
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 11.14 %
    Favored  : 88.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.26), residues: 1117
  helix:  1.92 (0.22), residues: 535
  sheet:  0.41 (0.37), residues: 185
  loop :  0.29 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  20 
 TYR   0.020   0.002   TYR C 169 
 PHE   0.012   0.001   PHE A 133 
 TRP   0.006   0.001   TRP C 221 
 HIS   0.004   0.001   HIS C 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8168)
  covalent geometry    : angle       0.45690 (11080)
  hydrogen bonds       : bond        0.04075 (  460)
  hydrogen bonds       : angle       4.30647 ( 1333)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8646 (tt0)
REVERT: B  186 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8675 (tt0)
REVERT: B  238 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8445 (pm20)
REVERT: C  186 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8647 (tt0)
REVERT: D  186 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8591 (tt0)
REVERT: D  226 ARG cc_start: 0.7957 (mtm110) cc_final: 0.7755 (mtm110)
  outliers start: 6
  outliers final: 1
  residues processed: 78
  average time/residue: 0.7104
  time to fit residues: 58.3339
Evaluate side-chains
  82 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain D residue  161 MET
Chi-restraints excluded: chain D residue  186 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 67 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 86 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 66 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3603 r_free = 0.3603 target = 0.099726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.072461 restraints weight = 132053.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 4.77
r_work: 0.2909 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2909
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8967
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8168  Z= 0.168
  Angle     :  0.478   9.800  11080  Z= 0.259
  Chirality :  0.043   0.168   1264
  Planarity :  0.003   0.044   1468
  Dihedral  :  3.880  19.975   1172
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 11.14 %
    Favored  : 88.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.26), residues: 1117
  helix:  1.92 (0.22), residues: 535
  sheet:  0.42 (0.37), residues: 185
  loop :  0.34 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  20 
 TYR   0.022   0.003   TYR C 169 
 PHE   0.010   0.001   PHE D 133 
 TRP   0.005   0.001   TRP C 221 
 HIS   0.005   0.001   HIS D 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 8168)
  covalent geometry    : angle       0.47776 (11080)
  hydrogen bonds       : bond        0.04332 (  460)
  hydrogen bonds       : angle       4.35178 ( 1333)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8663 (tt0)
REVERT: B   45 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8744 (mttt)
REVERT: B  186 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8683 (tt0)
REVERT: B  238 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8464 (pm20)
REVERT: C  186 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8669 (tt0)
REVERT: D  186 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8590 (tt0)
  outliers start: 7
  outliers final: 1
  residues processed: 78
  average time/residue: 0.7357
  time to fit residues: 60.3622
Evaluate side-chains
  82 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain D residue  161 MET
Chi-restraints excluded: chain D residue  186 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3601 r_free = 0.3601 target = 0.099630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.072419 restraints weight = 129359.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 4.74
r_work: 0.2909 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2909
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8966
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8168  Z= 0.170
  Angle     :  0.477   9.642  11080  Z= 0.258
  Chirality :  0.043   0.153   1264
  Planarity :  0.003   0.044   1468
  Dihedral  :  3.896  21.390   1172
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 11.02 %
    Favored  : 88.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.26), residues: 1117
  helix:  1.92 (0.22), residues: 535
  sheet:  0.49 (0.38), residues: 183
  loop :  0.31 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  20 
 TYR   0.022   0.003   TYR D 169 
 PHE   0.010   0.001   PHE C 133 
 TRP   0.005   0.001   TRP C 221 
 HIS   0.005   0.001   HIS C 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 8168)
  covalent geometry    : angle       0.47735 (11080)
  hydrogen bonds       : bond        0.04308 (  460)
  hydrogen bonds       : angle       4.33609 ( 1333)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8663 (tt0)
REVERT: B   45 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8781 (mttt)
REVERT: B  186 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8679 (tt0)
REVERT: B  238 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8471 (pm20)
REVERT: C  186 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8671 (tt0)
REVERT: D  186 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8582 (tt0)
REVERT: D  226 ARG cc_start: 0.7982 (mtm110) cc_final: 0.7730 (mtm110)
  outliers start: 7
  outliers final: 1
  residues processed: 77
  average time/residue: 0.7628
  time to fit residues: 61.6879
Evaluate side-chains
  81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain D residue  161 MET
Chi-restraints excluded: chain D residue  186 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 80 optimal weight:    0.0270
   chunk 9 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0470
   chunk 55 optimal weight:    2.9990
   chunk 96 optimal weight:    0.2980
   chunk 52 optimal weight:    0.8980
   chunk 4 optimal weight:    8.9990
   chunk 63 optimal weight:    0.5980
   chunk 53 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.3136

-------------------------------------------------------------------------------
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 = 0.3640 r_free = 0.3640 target = 0.102120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.074963 restraints weight = 118630.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 4.67
r_work: 0.2966 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2966
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2966 r_free = 0.2966    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2966 r_free = 0.2966    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.2966
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8926
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8168  Z= 0.101
  Angle     :  0.427   5.708  11080  Z= 0.232
  Chirality :  0.042   0.150   1264
  Planarity :  0.003   0.047   1468
  Dihedral  :  3.702  22.806   1172
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 11.14 %
    Favored  : 88.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.26), residues: 1117
  helix:  2.12 (0.22), residues: 535
  sheet:  0.48 (0.37), residues: 183
  loop :  0.48 (0.34), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  20 
 TYR   0.021   0.002   TYR C 169 
 PHE   0.009   0.001   PHE D 133 
 TRP   0.007   0.001   TRP A 221 
 HIS   0.003   0.001   HIS A 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 8168)
  covalent geometry    : angle       0.42736 (11080)
  hydrogen bonds       : bond        0.03479 (  460)
  hydrogen bonds       : angle       4.07301 ( 1333)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8649 (tt0)
REVERT: B   45 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8770 (mttt)
REVERT: B  186 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8651 (tt0)
REVERT: B  238 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8438 (pm20)
REVERT: C  186 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8604 (tt0)
REVERT: D  186 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8560 (tt0)
  outliers start: 6
  outliers final: 1
  residues processed: 80
  average time/residue: 0.6864
  time to fit residues: 57.8871
Evaluate side-chains
  84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain D residue  161 MET
Chi-restraints excluded: chain D residue  186 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 79 optimal weight:    0.2980
   chunk 46 optimal weight:    0.2980
   chunk 9 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0980
   chunk 6 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0970
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.2978

-------------------------------------------------------------------------------
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 = 0.3643 r_free = 0.3643 target = 0.102160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.075132 restraints weight = 133053.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 4.81
r_work: 0.2966 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2964
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2964 r_free = 0.2964    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2964 r_free = 0.2964    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.2964
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8930
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8168  Z= 0.101
  Angle     :  0.418   5.469  11080  Z= 0.227
  Chirality :  0.041   0.154   1264
  Planarity :  0.003   0.049   1468
  Dihedral  :  3.597  22.768   1172
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 11.25 %
    Favored  : 87.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.96 (0.26), residues: 1117
  helix:  2.22 (0.22), residues: 535
  sheet:  0.48 (0.37), residues: 183
  loop :  0.56 (0.34), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 226 
 TYR   0.019   0.002   TYR B 169 
 PHE   0.009   0.001   PHE D 133 
 TRP   0.006   0.001   TRP A 221 
 HIS   0.003   0.001   HIS B 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 8168)
  covalent geometry    : angle       0.41845 (11080)
  hydrogen bonds       : bond        0.03397 (  460)
  hydrogen bonds       : angle       3.92429 ( 1333)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8655 (tt0)
REVERT: B  186 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8667 (tt0)
REVERT: B  238 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8417 (pm20)
REVERT: C  186 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8632 (tt0)
REVERT: D  186 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8572 (tt0)
  outliers start: 7
  outliers final: 1
  residues processed: 81
  average time/residue: 0.7330
  time to fit residues: 62.4795
Evaluate side-chains
  83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain D residue  161 MET
Chi-restraints excluded: chain D residue  186 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 35 optimal weight:    0.0770
   chunk 10 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0670
   chunk 7 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.5076

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

Flipped N/Q/H residues before XYZ refinement:
A 235 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.101449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.073884 restraints weight = 131957.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 4.86
r_work: 0.2944 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8943
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8168  Z= 0.127
  Angle     :  0.439   6.961  11080  Z= 0.239
  Chirality :  0.042   0.174   1264
  Planarity :  0.003   0.046   1468
  Dihedral  :  3.671  23.239   1172
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 11.60 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.26), residues: 1117
  helix:  2.17 (0.22), residues: 535
  sheet:  0.49 (0.37), residues: 183
  loop :  0.61 (0.34), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 226 
 TYR   0.023   0.003   TYR C 169 
 PHE   0.011   0.001   PHE D 133 
 TRP   0.006   0.001   TRP A 221 
 HIS   0.003   0.001   HIS D 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8168)
  covalent geometry    : angle       0.43948 (11080)
  hydrogen bonds       : bond        0.03721 (  460)
  hydrogen bonds       : angle       4.00737 ( 1333)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8667 (tt0)
REVERT: B  186 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8651 (tt0)
REVERT: B  238 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8412 (pm20)
REVERT: C  186 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8630 (tt0)
REVERT: D  186 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8585 (tt0)
  outliers start: 5
  outliers final: 1
  residues processed: 77
  average time/residue: 0.7122
  time to fit residues: 57.7069
Evaluate side-chains
  82 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain D residue  161 MET
Chi-restraints excluded: chain D residue  186 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0670
   chunk 25 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 37 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.9922

-------------------------------------------------------------------------------
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 = 0.3593 r_free = 0.3593 target = 0.099106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.071822 restraints weight = 126112.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 4.70
r_work: 0.2897 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2898
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2898 r_free = 0.2898    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2898 r_free = 0.2898    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.2898
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8973
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8168  Z= 0.207
  Angle     :  0.489   8.767  11080  Z= 0.268
  Chirality :  0.044   0.164   1264
  Planarity :  0.003   0.044   1468
  Dihedral  :  3.910  23.936   1172
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 11.60 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.77 (0.26), residues: 1117
  helix:  2.00 (0.22), residues: 535
  sheet:  0.41 (0.37), residues: 185
  loop :  0.56 (0.34), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 226 
 TYR   0.026   0.003   TYR C 169 
 PHE   0.011   0.002   PHE B 133 
 TRP   0.003   0.001   TRP D 221 
 HIS   0.005   0.001   HIS C 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 8168)
  covalent geometry    : angle       0.48946 (11080)
  hydrogen bonds       : bond        0.04527 (  460)
  hydrogen bonds       : angle       4.27376 ( 1333)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4020.08 seconds
wall clock time: 68 minutes 53.51 seconds (4133.51 seconds total)