Starting phenix.real_space_refine
on Fri Jun 13 02:53:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wt7_37828/06_2025/8wt7_37828.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wt7_37828/06_2025/8wt7_37828.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wt7_37828/06_2025/8wt7_37828.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wt7_37828/06_2025/8wt7_37828.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wt7_37828/06_2025/8wt7_37828.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wt7_37828/06_2025/8wt7_37828.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.082
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: 6
    Type Number    sf(0)   Gaussians
     P     239      5.49       5
     Mg      2      5.21       5
     S      48      5.16       5
     C    8481      2.51       5
     N    2743      2.21       5
     O    3333      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14846
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 2429
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 306, 2420
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 12, 'TRANS': 293}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 306, 2420
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 12, 'TRANS': 293}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2457
    Chain: "B"
      Number of atoms: 2512
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 318, 2503
          Classifications: {'peptide': 318}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 305}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
      Conformer: "B"
        Number of residues, atoms: 318, 2503
          Classifications: {'peptide': 318}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 305}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
          bond proxies already assigned to first conformer: 2542
    Chain: "C"
      Number of atoms: 2420
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 305, 2411
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 12, 'TRANS': 292}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 305, 2411
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 12, 'TRANS': 292}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2448
    Chain: "D"
      Number of atoms: 2494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2494
          Classifications: {'peptide': 317}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 304}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "E"
      Number of atoms: 1250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 1250
          Classifications: {'RNA': 59}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 11, 'rna3p_pur': 22, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 15, 'rna3p': 43}
    Chain: "F"
      Number of atoms: 1441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 1441
          Classifications: {'RNA': 68}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 27, 'rna3p_pyr': 28}
          Link IDs: {'rna2p': 13, 'rna3p': 54}
    Chain: "G"
      Number of atoms: 548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 548
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 557
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "I"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 587
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 602
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N  AGLN A 139 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NE2BGLN A 139 " occ=0.50
    residue:
      pdb=" N  AGLN B 139 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NE2BGLN B 139 " occ=0.50
    residue:
      pdb=" N  AGLN C 139 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NE2BGLN C 139 " occ=0.50
  Time building chain proxies: 12.73, per 1000 atoms: 0.86
  Number of scatterers: 14846
  At special positions: 0
  Unit cell: (118.413, 125.053, 117.307, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      48     16.00
     P     239     15.00
     Mg      2     11.99
     O    3333      8.00
     N    2743      7.00
     C    8481      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.71
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2338

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 8 sheets defined
      68.7% alpha, 9.3% beta
      91 base pairs and 140 stacking pairs defined.
    Time for finding SS restraints: 6.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 49
    Processing helix  chain 'A' and resid 66 through 77
    Processing helix  chain 'A' and resid 84 through 95
      removed outlier: 3.574A  pdb=" N   GLY A  88 " --> pdb=" O   ASN A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 117
    Processing helix  chain 'A' and resid 125 through 155
      removed outlier: 3.550A  pdb=" N   THR A 152 " --> pdb=" O   GLU A 148 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   GLU A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   THR A 154 " --> pdb=" O   ASN A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 158
      No H-bonds generated for 'chain 'A' and resid 156 through 158'
    Processing helix  chain 'A' and resid 159 through 188
      removed outlier: 3.839A  pdb=" N   ASP A 188 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 200
    Processing helix  chain 'A' and resid 205 through 217
      removed outlier: 3.531A  pdb=" N   ALA A 210 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 233
      removed outlier: 3.768A  pdb=" N   PHE A 228 " --> pdb=" O   HIS A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 262
      removed outlier: 3.642A  pdb=" N   ALA A 262 " --> pdb=" O   SER A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 274
    Processing helix  chain 'A' and resid 274 through 288
    Processing helix  chain 'A' and resid 290 through 313
    Processing helix  chain 'A' and resid 317 through 321
      removed outlier: 3.665A  pdb=" N   ARG A 320 " --> pdb=" O   ASP A 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 50
    Processing helix  chain 'B' and resid 66 through 77
    Processing helix  chain 'B' and resid 84 through 96
      removed outlier: 3.613A  pdb=" N   GLY B  88 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLY B  96 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 117
    Processing helix  chain 'B' and resid 125 through 155
      removed outlier: 3.736A  pdb=" N   GLU B 153 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   THR B 154 " --> pdb=" O   ASN B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 188
      removed outlier: 3.613A  pdb=" N   ASP B 188 " --> pdb=" O   LEU B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 200
    Processing helix  chain 'B' and resid 205 through 217
    Processing helix  chain 'B' and resid 224 through 232
      removed outlier: 3.750A  pdb=" N   PHE B 228 " --> pdb=" O   HIS B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 263
    Processing helix  chain 'B' and resid 263 through 274
    Processing helix  chain 'B' and resid 274 through 287
      removed outlier: 3.565A  pdb=" N   ASN B 287 " --> pdb=" O   ARG B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 313
    Processing helix  chain 'B' and resid 317 through 321
    Processing helix  chain 'C' and resid 36 through 50
    Processing helix  chain 'C' and resid 66 through 77
    Processing helix  chain 'C' and resid 84 through 95
      removed outlier: 3.643A  pdb=" N   GLY C  88 " --> pdb=" O   ASN C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 117
    Processing helix  chain 'C' and resid 125 through 155
      removed outlier: 3.527A  pdb=" N   THR C 152 " --> pdb=" O   GLU C 148 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLU C 153 " --> pdb=" O   LEU C 149 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   THR C 154 " --> pdb=" O   ASN C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 188
      removed outlier: 3.633A  pdb=" N   ASP C 188 " --> pdb=" O   LEU C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 188 through 200
    Processing helix  chain 'C' and resid 205 through 217
    Processing helix  chain 'C' and resid 224 through 232
      removed outlier: 3.677A  pdb=" N   PHE C 228 " --> pdb=" O   HIS C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 256 through 262
      removed outlier: 3.566A  pdb=" N   ALA C 262 " --> pdb=" O   SER C 258 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 263 through 274
    Processing helix  chain 'C' and resid 274 through 288
    Processing helix  chain 'C' and resid 290 through 313
    Processing helix  chain 'C' and resid 317 through 321
      removed outlier: 3.613A  pdb=" N   ARG C 320 " --> pdb=" O   ASP C 317 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 50
    Processing helix  chain 'D' and resid 66 through 77
    Processing helix  chain 'D' and resid 84 through 95
      removed outlier: 3.794A  pdb=" N   GLY D  88 " --> pdb=" O   ASN D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 117
    Processing helix  chain 'D' and resid 125 through 155
      removed outlier: 4.086A  pdb=" N   GLU D 153 " --> pdb=" O   LEU D 149 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   THR D 154 " --> pdb=" O   ASN D 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 188
      removed outlier: 3.649A  pdb=" N   ASP D 188 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 199
    Processing helix  chain 'D' and resid 205 through 217
    Processing helix  chain 'D' and resid 224 through 232
      removed outlier: 3.610A  pdb=" N   PHE D 228 " --> pdb=" O   HIS D 224 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 256 through 263
      removed outlier: 3.558A  pdb=" N   LEU D 263 " --> pdb=" O   LEU D 259 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 263 through 274
    Processing helix  chain 'D' and resid 274 through 288
    Processing helix  chain 'D' and resid 290 through 313
    Processing helix  chain 'D' and resid 317 through 321
      removed outlier: 3.505A  pdb=" N   ARG D 320 " --> pdb=" O   ASP D 317 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 34
      removed outlier: 6.522A  pdb=" N   HIS A   6 " --> pdb=" O   HIS A  56 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   CYS A  58 " --> pdb=" O   HIS A   6 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ILE A   8 " --> pdb=" O   CYS A  58 " (cutoff:3.500A)
      removed outlier: 8.527A  pdb=" N   GLU A  60 " --> pdb=" O   ILE A   8 " (cutoff:3.500A)
      removed outlier: 8.336A  pdb=" N   ILE A  10 " --> pdb=" O   GLU A  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 28 through 34
      removed outlier: 6.831A  pdb=" N   HIS B   6 " --> pdb=" O   HIS B  56 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   CYS B  58 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   ILE B   8 " --> pdb=" O   CYS B  58 " (cutoff:3.500A)
      removed outlier: 8.587A  pdb=" N   GLU B  60 " --> pdb=" O   ILE B   8 " (cutoff:3.500A)
      removed outlier: 8.471A  pdb=" N   ILE B  10 " --> pdb=" O   GLU B  60 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ALA B  55 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   SER B  81 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   ILE B  57 " --> pdb=" O   SER B  81 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   ILE B  83 " --> pdb=" O   ILE B  57 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ILE B  59 " --> pdb=" O   ILE B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 236 through 237
      removed outlier: 3.751A  pdb=" N   ARG B 250 " --> pdb=" O   ARG B 237 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 240 through 241
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 34
      removed outlier: 6.526A  pdb=" N   HIS C   6 " --> pdb=" O   HIS C  56 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   CYS C  58 " --> pdb=" O   HIS C   6 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ILE C   8 " --> pdb=" O   CYS C  58 " (cutoff:3.500A)
      removed outlier: 8.635A  pdb=" N   GLU C  60 " --> pdb=" O   ILE C   8 " (cutoff:3.500A)
      removed outlier: 8.330A  pdb=" N   ILE C  10 " --> pdb=" O   GLU C  60 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 28 through 34
      removed outlier: 6.722A  pdb=" N   HIS D   6 " --> pdb=" O   HIS D  56 " (cutoff:3.500A)
      removed outlier: 8.018A  pdb=" N   CYS D  58 " --> pdb=" O   HIS D   6 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   ILE D   8 " --> pdb=" O   CYS D  58 " (cutoff:3.500A)
      removed outlier: 8.759A  pdb=" N   GLU D  60 " --> pdb=" O   ILE D   8 " (cutoff:3.500A)
      removed outlier: 8.390A  pdb=" N   ILE D  10 " --> pdb=" O   GLU D  60 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 236 through 237
      removed outlier: 3.755A  pdb=" N   ARG D 250 " --> pdb=" O   ARG D 237 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 240 through 241

    677 hydrogen bonds defined for protein.
    2004 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      228 hydrogen bonds
      450 hydrogen bond angles
      0 basepair planarities
      91 basepair parallelities
      140 stacking parallelities
  Total time for adding SS restraints: 5.19

  Time building geometry restraints manager: 4.39 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: 3274
        1.34 -     1.46: 5506
        1.46 -     1.58: 6286
        1.58 -     1.69: 470
        1.69 -     1.81: 84
  Bond restraints: 15620
  Sorted by residual:
  bond pdb=" C   ILE B 201 "
       pdb=" N   PRO B 202 "
    ideal  model  delta    sigma   weight residual
    1.333  1.358 -0.025 1.01e-02 9.80e+03 6.09e+00
  bond pdb=" C   ILE A 201 "
       pdb=" N   PRO A 202 "
    ideal  model  delta    sigma   weight residual
    1.333  1.358 -0.024 1.01e-02 9.80e+03 5.81e+00
  bond pdb=" C   ILE C 201 "
       pdb=" N   PRO C 202 "
    ideal  model  delta    sigma   weight residual
    1.333  1.358 -0.024 1.01e-02 9.80e+03 5.67e+00
  bond pdb=" O5'   G E  60 "
       pdb=" C5'   G E  60 "
    ideal  model  delta    sigma   weight residual
    1.420  1.455 -0.035 1.50e-02 4.44e+03 5.55e+00
  bond pdb=" O5'   G F 169 "
       pdb=" C5'   G F 169 "
    ideal  model  delta    sigma   weight residual
    1.420  1.455 -0.035 1.50e-02 4.44e+03 5.52e+00
  ... (remaining 15615 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 17312
        1.48 -     2.96: 3967
        2.96 -     4.43: 779
        4.43 -     5.91: 87
        5.91 -     7.39: 15
  Bond angle restraints: 22160
  Sorted by residual:
  angle pdb=" O3'  DA G  26 "
        pdb=" P    DC G  27 "
        pdb=" O5'  DC G  27 "
      ideal   model   delta    sigma   weight residual
     104.00   96.61    7.39 1.50e+00 4.44e-01 2.43e+01
  angle pdb=" O3'   U F 132 "
        pdb=" P     G F 133 "
        pdb=" O5'   G F 133 "
      ideal   model   delta    sigma   weight residual
     104.00  110.87   -6.87 1.50e+00 4.44e-01 2.10e+01
  angle pdb=" CA  ASP C  25 "
        pdb=" CB  ASP C  25 "
        pdb=" CG  ASP C  25 "
      ideal   model   delta    sigma   weight residual
     112.60  117.05   -4.45 1.00e+00 1.00e+00 1.98e+01
  angle pdb=" CA  ASP C  11 "
        pdb=" CB  ASP C  11 "
        pdb=" CG  ASP C  11 "
      ideal   model   delta    sigma   weight residual
     112.60  116.86   -4.26 1.00e+00 1.00e+00 1.82e+01
  angle pdb=" CA  ASP D 105 "
        pdb=" CB  ASP D 105 "
        pdb=" CG  ASP D 105 "
      ideal   model   delta    sigma   weight residual
     112.60  116.81   -4.21 1.00e+00 1.00e+00 1.77e+01
  ... (remaining 22155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.43: 8684
       34.43 -    68.86: 630
       68.86 -   103.29: 52
      103.29 -   137.72: 0
      137.72 -   172.15: 1
  Dihedral angle restraints: 9367
    sinusoidal: 5753
      harmonic: 3614
  Sorted by residual:
  dihedral pdb=" O4'   U F 159 "
           pdb=" C1'   U F 159 "
           pdb=" N1    U F 159 "
           pdb=" C2    U F 159 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   59.85  172.15     1      1.70e+01 3.46e-03 6.61e+01
  dihedral pdb=" C5'   U E  86 "
           pdb=" C4'   U E  86 "
           pdb=" C3'   U E  86 "
           pdb=" O3'   U E  86 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  102.18   44.82     1      8.00e+00 1.56e-02 4.36e+01
  dihedral pdb=" O4'   U E  86 "
           pdb=" C4'   U E  86 "
           pdb=" C3'   U E  86 "
           pdb=" C2'   U E  86 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -16.12   40.12     1      8.00e+00 1.56e-02 3.53e+01
  ... (remaining 9364 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.127: 2266
       0.127 -    0.255: 298
       0.255 -    0.382: 0
       0.382 -    0.509: 0
       0.509 -    0.636: 6
  Chirality restraints: 2570
  Sorted by residual:
  chirality pdb=" P    DG J  12 "
            pdb=" OP1  DG J  12 "
            pdb=" OP2  DG J  12 "
            pdb=" O5'  DG J  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.98   -0.64 2.00e-01 2.50e+01 1.01e+01
  chirality pdb=" P    DA H   3 "
            pdb=" OP1  DA H   3 "
            pdb=" OP2  DA H   3 "
            pdb=" O5'  DA H   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.98   -0.64 2.00e-01 2.50e+01 1.01e+01
  chirality pdb=" P    DG I   5 "
            pdb=" OP1  DG I   5 "
            pdb=" OP2  DG I   5 "
            pdb=" O5'  DG I   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.96   -0.62 2.00e-01 2.50e+01 9.50e+00
  ... (remaining 2567 not shown)

  Planarity restraints: 1986
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F 157 "   -0.035 2.00e-02 2.50e+03   1.42e-02 5.55e+00
        pdb=" N9    A F 157 "    0.021 2.00e-02 2.50e+03
        pdb=" C8    A F 157 "    0.008 2.00e-02 2.50e+03
        pdb=" N7    A F 157 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    A F 157 "    0.006 2.00e-02 2.50e+03
        pdb=" C6    A F 157 "   -0.006 2.00e-02 2.50e+03
        pdb=" N6    A F 157 "   -0.016 2.00e-02 2.50e+03
        pdb=" N1    A F 157 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    A F 157 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    A F 157 "    0.008 2.00e-02 2.50e+03
        pdb=" C4    A F 157 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U F 159 "    0.027 2.00e-02 2.50e+03   1.39e-02 4.32e+00
        pdb=" N1    U F 159 "   -0.026 2.00e-02 2.50e+03
        pdb=" C2    U F 159 "   -0.001 2.00e-02 2.50e+03
        pdb=" O2    U F 159 "   -0.010 2.00e-02 2.50e+03
        pdb=" N3    U F 159 "    0.010 2.00e-02 2.50e+03
        pdb=" C4    U F 159 "    0.005 2.00e-02 2.50e+03
        pdb=" O4    U F 159 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    U F 159 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    U F 159 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  27 "    0.027 2.00e-02 2.50e+03   1.22e-02 4.12e+00
        pdb=" N9   DA I  27 "   -0.028 2.00e-02 2.50e+03
        pdb=" C8   DA I  27 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7   DA I  27 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DA I  27 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I  27 "    0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I  27 "    0.008 2.00e-02 2.50e+03
        pdb=" N1   DA I  27 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I  27 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DA I  27 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I  27 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1983 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.27: 14
        2.27 -     2.92: 5194
        2.92 -     3.58: 21613
        3.58 -     4.24: 39550
        4.24 -     4.90: 60383
  Nonbonded interactions: 126754
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 241 "
            pdb=" P    DA G  26 "
     model   vdw
     1.608 3.400
  nonbonded pdb=" OG  SER B 241 "
            pdb=" P    DT I  21 "
     model   vdw
     1.608 3.400
  nonbonded pdb=" OE2 GLU A  60 "
            pdb="MG    MG A 401 "
     model   vdw
     1.884 2.170
  nonbonded pdb="MG    MG C 401 "
            pdb=" O   HOH C 501 "
     model   vdw
     1.922 2.170
  nonbonded pdb=" O3'  DT G  25 "
            pdb="MG    MG A 401 "
     model   vdw
     2.066 2.170
  ... (remaining 126749 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 5 through 99 or (resid 100 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 101 through 138 or resid 140 through 321))
  selection = (chain 'B' and (resid 5 through 138 or resid 140 through 238 or resid 251 throug \ 
h 321))
  selection = (chain 'C' and (resid 5 through 99 or (resid 100 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 101 through 138 or resid 140 through 321))
  selection = (chain 'D' and (resid 5 through 138 or resid 140 through 238 or resid 251 throug \ 
h 321))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  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:          0.630
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     44.110
  Find NCS groups from input model:        0.590
  Set up NCS constraints:                  0.070
  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:             0.010
  Load rotamer database and sin/cos tables:11.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   57.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
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   0.039  15620  Z= 0.475
  Angle     :  1.311   7.391  22160  Z= 0.851
  Chirality :  0.078   0.636   2570
  Planarity :  0.004   0.052   1986
  Dihedral  : 19.845 172.147   7029
  Min Nonbonded Distance : 1.608

Molprobity Statistics.
  All-atom Clashscore : 0.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  2.07 %
    Favored  : 97.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.68 (0.20), residues: 1243
  helix: -0.83 (0.15), residues: 805
  sheet: -1.25 (0.36), residues: 162
  loop : -1.19 (0.32), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.005   TRP A 169 
 HIS   0.010   0.002   HIS D 256 
 PHE   0.017   0.002   PHE C 228 
 TYR   0.017   0.002   TYR D 307 
 ARG   0.025   0.002   ARG D 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22277 (  905)
  hydrogen bonds       : angle       6.95784 ( 2454)
  covalent geometry    : bond        0.00790 (15620)
  covalent geometry    : angle       1.31119 (22160)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 1.281 
Fit side-chains
   revert: symmetry clash
REVERT: A  261 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8458 (tpt-90)
REVERT: A  268 MET cc_start: 0.8680 (ttp) cc_final: 0.8458 (ttp)
REVERT: A  299 MET cc_start: 0.9323 (mtp) cc_final: 0.9112 (mtp)
REVERT: B   99 ASN cc_start: 0.8400 (m-40) cc_final: 0.8060 (m-40)
REVERT: B  298 MET cc_start: 0.9398 (tpt) cc_final: 0.8624 (tpt)
REVERT: C  268 MET cc_start: 0.8765 (mtm) cc_final: 0.8562 (mtm)
REVERT: D  108 MET cc_start: 0.8901 (tpp) cc_final: 0.8671 (mmt)
REVERT: D  239 TYR cc_start: 0.9156 (t80) cc_final: 0.8926 (t80)
REVERT: D  268 MET cc_start: 0.8979 (ttp) cc_final: 0.8776 (ttm)
  outliers start: 5
  outliers final: 0
  residues processed: 94
  average time/residue: 1.9311
  time to fit residues: 194.2979
Evaluate side-chains
  62 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 1.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 119 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0270
   chunk 128 optimal weight:    5.9990
   overall best weight:    1.4044

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

Flipped N/Q/H residues before XYZ refinement:
A 287 ASN
C 287 ASN
D  93 GLN
D  99 ASN
D 287 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.078153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.051937 restraints weight = 62704.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.2713 rms_B_bonded: 2.77
r_work: 0.2522 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2522
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2529
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2529 r_free = 0.2529    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2529 r_free = 0.2529    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2529
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15620  Z= 0.173
  Angle     :  0.592   6.233  22160  Z= 0.331
  Chirality :  0.040   0.198   2570
  Planarity :  0.004   0.032   1986
  Dihedral  : 21.954 160.840   4602
  Min Nonbonded Distance : 1.792

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  4.94 %
    Favored  : 94.57 %
  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:  1.46 (0.23), residues: 1243
  helix:  1.94 (0.17), residues: 809
  sheet: -0.85 (0.36), residues: 160
  loop : -0.73 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 276 
 HIS   0.005   0.001   HIS B 256 
 PHE   0.013   0.002   PHE A 280 
 TYR   0.020   0.002   TYR A 215 
 ARG   0.005   0.001   ARG D 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05865 (  905)
  hydrogen bonds       : angle       4.10263 ( 2454)
  covalent geometry    : bond        0.00362 (15620)
  covalent geometry    : angle       0.59200 (22160)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 1.371 
Fit side-chains
   revert: symmetry clash
REVERT: B  107 ARG cc_start: 0.8676 (ttt90) cc_final: 0.8334 (ttm-80)
REVERT: B  298 MET cc_start: 0.9318 (tpt) cc_final: 0.8977 (tpt)
REVERT: C  258 SER cc_start: 0.9386 (m) cc_final: 0.8952 (p)
REVERT: D  108 MET cc_start: 0.8855 (tpp) cc_final: 0.8635 (mmt)
  outliers start: 5
  outliers final: 0
  residues processed: 67
  average time/residue: 1.7959
  time to fit residues: 130.5255
Evaluate side-chains
  60 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 1.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 136 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 72 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 67 optimal weight:    4.9990
   chunk 30 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   chunk 84 optimal weight:    4.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 287 ASN
B  93 GLN
C 287 ASN
D   6 HIS
D  99 ASN
D 287 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.077816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.050878 restraints weight = 79871.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.2657 rms_B_bonded: 3.15
r_work: 0.2457 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2457
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2496
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2496 r_free = 0.2496    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2496 r_free = 0.2496    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2496
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  15620  Z= 0.174
  Angle     :  0.523   6.128  22160  Z= 0.293
  Chirality :  0.037   0.182   2570
  Planarity :  0.004   0.073   1986
  Dihedral  : 22.075 162.085   4598
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  5.13 %
    Favored  : 94.08 %
  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:  2.23 (0.24), residues: 1243
  helix:  2.59 (0.18), residues: 808
  sheet: -0.45 (0.38), residues: 152
  loop : -0.74 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D  46 
 HIS   0.005   0.001   HIS B 256 
 PHE   0.012   0.002   PHE B 112 
 TYR   0.016   0.002   TYR A 215 
 ARG   0.009   0.000   ARG A 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05199 (  905)
  hydrogen bonds       : angle       3.74095 ( 2454)
  covalent geometry    : bond        0.00380 (15620)
  covalent geometry    : angle       0.52341 (22160)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 1.287 
Fit side-chains
   revert: symmetry clash
REVERT: B   99 ASN cc_start: 0.8037 (m-40) cc_final: 0.7655 (m-40)
REVERT: B  107 ARG cc_start: 0.8865 (ttt90) cc_final: 0.8506 (ttm-80)
REVERT: B  298 MET cc_start: 0.9214 (tpt) cc_final: 0.8996 (tpt)
REVERT: B  299 MET cc_start: 0.9326 (mtp) cc_final: 0.9016 (mtp)
REVERT: C   54 HIS cc_start: 0.8648 (m-70) cc_final: 0.8318 (m90)
REVERT: D   99 ASN cc_start: 0.7852 (m-40) cc_final: 0.7589 (m-40)
REVERT: D  304 GLN cc_start: 0.9145 (tt0) cc_final: 0.8874 (mt0)
  outliers start: 8
  outliers final: 1
  residues processed: 72
  average time/residue: 1.5740
  time to fit residues: 123.4974
Evaluate side-chains
  62 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 1.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  157 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 100 optimal weight:    9.9990
   chunk 104 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 54 optimal weight:   10.0000
   chunk 79 optimal weight:    0.5980
   chunk 117 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 107 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    3.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 287 ASN
B  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.075103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.048300 restraints weight = 80505.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.2640 rms_B_bonded: 3.12
r_work: 0.2442 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2442
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2432
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2432 r_free = 0.2432    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2432 r_free = 0.2432    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2432
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.093  15620  Z= 0.325
  Angle     :  0.597   6.290  22160  Z= 0.326
  Chirality :  0.042   0.206   2570
  Planarity :  0.005   0.036   1986
  Dihedral  : 22.239 160.265   4598
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  5.63 %
    Favored  : 93.58 %
  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:  2.29 (0.24), residues: 1243
  helix:  2.61 (0.18), residues: 808
  sheet: -0.58 (0.36), residues: 174
  loop : -0.50 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D  46 
 HIS   0.005   0.001   HIS D 256 
 PHE   0.016   0.002   PHE C 316 
 TYR   0.017   0.002   TYR D 215 
 ARG   0.003   0.000   ARG D 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06042 (  905)
  hydrogen bonds       : angle       3.85130 ( 2454)
  covalent geometry    : bond        0.00732 (15620)
  covalent geometry    : angle       0.59650 (22160)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 1.373 
Fit side-chains
   revert: symmetry clash
REVERT: B   99 ASN cc_start: 0.8144 (m-40) cc_final: 0.7739 (m-40)
REVERT: B  298 MET cc_start: 0.9133 (tpt) cc_final: 0.8919 (tpt)
REVERT: C   54 HIS cc_start: 0.8645 (m-70) cc_final: 0.8356 (m90)
REVERT: C  237 ARG cc_start: 0.6770 (tmm160) cc_final: 0.6345 (tmm160)
REVERT: D   99 ASN cc_start: 0.7858 (m-40) cc_final: 0.7606 (m-40)
REVERT: D  206 GLU cc_start: 0.7951 (mp0) cc_final: 0.7731 (mm-30)
  outliers start: 8
  outliers final: 4
  residues processed: 63
  average time/residue: 1.6126
  time to fit residues: 111.2870
Evaluate side-chains
  62 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 1.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  157 GLU
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain C residue  258 SER
Chi-restraints excluded: chain D residue  191 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 131 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 104 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 125 optimal weight:    5.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 287 ASN
B  93 GLN
C  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.078545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.052105 restraints weight = 71376.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.2703 rms_B_bonded: 2.96
r_work: 0.2509 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2509
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2544
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2544 r_free = 0.2544    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2544 r_free = 0.2544    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2544
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  15620  Z= 0.136
  Angle     :  0.492   6.593  22160  Z= 0.273
  Chirality :  0.035   0.183   2570
  Planarity :  0.004   0.036   1986
  Dihedral  : 22.145 161.443   4598
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  7.01 %
    Favored  : 92.50 %
  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 (0.24), residues: 1243
  helix:  2.85 (0.18), residues: 807
  sheet: -0.00 (0.39), residues: 148
  loop : -0.60 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  46 
 HIS   0.004   0.001   HIS B 256 
 PHE   0.010   0.001   PHE A 280 
 TYR   0.012   0.001   TYR D 307 
 ARG   0.005   0.000   ARG D 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04367 (  905)
  hydrogen bonds       : angle       3.56691 ( 2454)
  covalent geometry    : bond        0.00291 (15620)
  covalent geometry    : angle       0.49196 (22160)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 1.431 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 MET cc_start: 0.9212 (tpt) cc_final: 0.8966 (tpt)
REVERT: B  107 ARG cc_start: 0.8765 (ttt90) cc_final: 0.8476 (ttm-80)
REVERT: C   54 HIS cc_start: 0.8668 (m-70) cc_final: 0.8408 (m90)
REVERT: C  237 ARG cc_start: 0.6779 (tmm160) cc_final: 0.6384 (tmm160)
REVERT: D  304 GLN cc_start: 0.9134 (tt0) cc_final: 0.8858 (mt0)
  outliers start: 5
  outliers final: 1
  residues processed: 70
  average time/residue: 1.5620
  time to fit residues: 119.8831
Evaluate side-chains
  62 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 1.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  258 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 137 optimal weight:    8.9990
   chunk 118 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   chunk 15 optimal weight:    0.8980
   chunk 124 optimal weight:    7.9990
   chunk 113 optimal weight:    0.2980
   chunk 67 optimal weight:    2.9990
   chunk 130 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   overall best weight:    2.8386

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

Flipped N/Q/H residues before XYZ refinement:
A 287 ASN
B  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.076369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.049476 restraints weight = 84192.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.2632 rms_B_bonded: 3.17
r_work: 0.2429 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.2429
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2465
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2465 r_free = 0.2465    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2465 r_free = 0.2465    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2465
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  15620  Z= 0.240
  Angle     :  0.535   8.697  22160  Z= 0.292
  Chirality :  0.038   0.192   2570
  Planarity :  0.004   0.036   1986
  Dihedral  : 22.228 161.279   4598
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  7.11 %
    Favored  : 92.30 %
  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:  2.66 (0.24), residues: 1243
  helix:  2.87 (0.18), residues: 807
  sheet:  0.02 (0.39), residues: 148
  loop : -0.60 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  46 
 HIS   0.004   0.001   HIS B 256 
 PHE   0.013   0.002   PHE C 231 
 TYR   0.013   0.001   TYR D 215 
 ARG   0.003   0.000   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05143 (  905)
  hydrogen bonds       : angle       3.63899 ( 2454)
  covalent geometry    : bond        0.00537 (15620)
  covalent geometry    : angle       0.53546 (22160)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 1.460 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 MET cc_start: 0.9272 (tpt) cc_final: 0.8958 (tpt)
REVERT: B  107 ARG cc_start: 0.8871 (ttt90) cc_final: 0.8477 (ttm-80)
REVERT: C   54 HIS cc_start: 0.8698 (m-70) cc_final: 0.8423 (m90)
REVERT: D  304 GLN cc_start: 0.9181 (tt0) cc_final: 0.8831 (mt0)
  outliers start: 6
  outliers final: 3
  residues processed: 64
  average time/residue: 1.6584
  time to fit residues: 116.1058
Evaluate side-chains
  64 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 1.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain C residue  258 SER
Chi-restraints excluded: chain D residue  191 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9990
   chunk 96 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 104 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 106 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 287 ASN
B  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.077991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.051178 restraints weight = 80273.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.2676 rms_B_bonded: 3.13
r_work: 0.2476 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.2476
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2519
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2519 r_free = 0.2519    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2519 r_free = 0.2519    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2519
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  15620  Z= 0.144
  Angle     :  0.496   8.573  22160  Z= 0.272
  Chirality :  0.035   0.178   2570
  Planarity :  0.004   0.036   1986
  Dihedral  : 22.214 162.064   4598
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  7.50 %
    Favored  : 92.10 %
  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:  2.77 (0.24), residues: 1243
  helix:  2.94 (0.18), residues: 807
  sheet:  0.10 (0.40), residues: 148
  loop : -0.53 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  46 
 HIS   0.003   0.000   HIS B 256 
 PHE   0.010   0.001   PHE B 112 
 TYR   0.012   0.001   TYR D 307 
 ARG   0.003   0.000   ARG A 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04413 (  905)
  hydrogen bonds       : angle       3.52646 ( 2454)
  covalent geometry    : bond        0.00314 (15620)
  covalent geometry    : angle       0.49566 (22160)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 1.288 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 MET cc_start: 0.9235 (tpt) cc_final: 0.8986 (tpt)
REVERT: B  107 ARG cc_start: 0.8832 (ttt90) cc_final: 0.8481 (ttm-80)
REVERT: C   54 HIS cc_start: 0.8726 (m-70) cc_final: 0.8470 (m90)
REVERT: D  304 GLN cc_start: 0.9161 (tt0) cc_final: 0.8814 (mt0)
  outliers start: 4
  outliers final: 3
  residues processed: 64
  average time/residue: 1.5520
  time to fit residues: 108.9498
Evaluate side-chains
  65 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 1.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain C residue  258 SER
Chi-restraints excluded: chain D residue  191 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 140 optimal weight:    6.9990
   chunk 48 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 133 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 118 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
D  99 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.076745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.050047 restraints weight = 75859.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.2656 rms_B_bonded: 3.05
r_work: 0.2458 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2458
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2470
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2470 r_free = 0.2470    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2470 r_free = 0.2470    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2470
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  15620  Z= 0.204
  Angle     :  0.518   9.112  22160  Z= 0.283
  Chirality :  0.037   0.185   2570
  Planarity :  0.004   0.035   1986
  Dihedral  : 22.233 161.858   4598
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  8.09 %
    Favored  : 91.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.76 (0.24), residues: 1243
  helix:  2.94 (0.18), residues: 807
  sheet:  0.05 (0.39), residues: 150
  loop : -0.53 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  46 
 HIS   0.004   0.001   HIS A 145 
 PHE   0.012   0.002   PHE B 112 
 TYR   0.012   0.001   TYR D 307 
 ARG   0.002   0.000   ARG A 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04881 (  905)
  hydrogen bonds       : angle       3.57681 ( 2454)
  covalent geometry    : bond        0.00454 (15620)
  covalent geometry    : angle       0.51810 (22160)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 1.372 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 MET cc_start: 0.9258 (tpt) cc_final: 0.8975 (tpt)
REVERT: B  107 ARG cc_start: 0.8851 (ttt90) cc_final: 0.8454 (ttm-80)
REVERT: C   54 HIS cc_start: 0.8723 (m-70) cc_final: 0.8470 (m90)
REVERT: D  304 GLN cc_start: 0.9148 (tt0) cc_final: 0.8801 (mt0)
  outliers start: 3
  outliers final: 3
  residues processed: 62
  average time/residue: 1.6172
  time to fit residues: 110.0946
Evaluate side-chains
  63 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain C residue  258 SER
Chi-restraints excluded: chain D residue  191 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   chunk 134 optimal weight:    5.9990
   chunk 105 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 113 optimal weight:    0.0470
   chunk 17 optimal weight:    0.9980
   chunk 135 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   chunk 39 optimal weight:   10.0000
   overall best weight:    1.3882

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
D  99 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.077639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.051261 restraints weight = 64451.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.2719 rms_B_bonded: 2.82
r_work: 0.2535 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2542
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2542 r_free = 0.2542    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2542 r_free = 0.2542    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2542
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  15620  Z= 0.150
  Angle     :  0.501   9.615  22160  Z= 0.274
  Chirality :  0.035   0.177   2570
  Planarity :  0.004   0.035   1986
  Dihedral  : 22.229 161.892   4598
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  7.90 %
    Favored  : 91.71 %
  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:  2.79 (0.24), residues: 1243
  helix:  2.98 (0.18), residues: 807
  sheet: -0.03 (0.39), residues: 148
  loop : -0.52 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  46 
 HIS   0.003   0.001   HIS A 145 
 PHE   0.011   0.001   PHE B 112 
 TYR   0.012   0.001   TYR D 307 
 ARG   0.003   0.000   ARG B 260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04541 (  905)
  hydrogen bonds       : angle       3.52725 ( 2454)
  covalent geometry    : bond        0.00330 (15620)
  covalent geometry    : angle       0.50136 (22160)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 1.416 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 MET cc_start: 0.9218 (tpt) cc_final: 0.8971 (tpt)
REVERT: B  107 ARG cc_start: 0.8822 (ttt90) cc_final: 0.8458 (ttm-80)
REVERT: C   54 HIS cc_start: 0.8728 (m-70) cc_final: 0.8460 (m90)
REVERT: D  304 GLN cc_start: 0.9125 (tt0) cc_final: 0.8906 (mt0)
  outliers start: 4
  outliers final: 3
  residues processed: 64
  average time/residue: 1.6116
  time to fit residues: 112.9612
Evaluate side-chains
  65 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 1.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain C residue  258 SER
Chi-restraints excluded: chain D residue  191 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 97 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 137 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 114 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0030
   chunk 91 optimal weight:    0.1980
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
D  50 HIS
D  99 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.079888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.053235 restraints weight = 82192.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.2728 rms_B_bonded: 3.17
r_work: 0.2529 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.2529
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2571 r_free = 0.2571    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2571 r_free = 0.2571    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  15620  Z= 0.116
  Angle     :  0.474   8.382  22160  Z= 0.259
  Chirality :  0.033   0.167   2570
  Planarity :  0.003   0.035   1986
  Dihedral  : 22.120 164.588   4598
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  8.19 %
    Favored  : 91.41 %
  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:  2.96 (0.24), residues: 1243
  helix:  3.09 (0.18), residues: 809
  sheet:  0.20 (0.40), residues: 145
  loop : -0.49 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  46 
 HIS   0.002   0.000   HIS B 166 
 PHE   0.009   0.001   PHE B 112 
 TYR   0.012   0.001   TYR C  74 
 ARG   0.003   0.000   ARG A 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03829 (  905)
  hydrogen bonds       : angle       3.41550 ( 2454)
  covalent geometry    : bond        0.00243 (15620)
  covalent geometry    : angle       0.47436 (22160)

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

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

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2486 Ramachandran restraints generated.
    1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 1.261 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.9437 (m-80) cc_final: 0.9215 (m-80)
REVERT: A  298 MET cc_start: 0.9212 (tpt) cc_final: 0.8989 (tpt)
REVERT: B  107 ARG cc_start: 0.8775 (ttt90) cc_final: 0.8504 (ttm-80)
REVERT: C   54 HIS cc_start: 0.8735 (m-70) cc_final: 0.8494 (m90)
REVERT: C  258 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.8910 (t)
REVERT: D  304 GLN cc_start: 0.9144 (tt0) cc_final: 0.8923 (mt0)
  outliers start: 4
  outliers final: 1
  residues processed: 70
  average time/residue: 1.5552
  time to fit residues: 119.1128
Evaluate side-chains
  64 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 1.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  258 SER
Chi-restraints excluded: chain D residue  191 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0270
   chunk 84 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 140 optimal weight:    6.9990
   chunk 139 optimal weight:    5.9990
   chunk 99 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.9842

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
D  99 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.077613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.051287 restraints weight = 60614.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.2682 rms_B_bonded: 2.75
r_work: 0.2489 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2489
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2527
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2527 r_free = 0.2527    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2527 r_free = 0.2527    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2527
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.2775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  15620  Z= 0.182
  Angle     :  0.501   9.067  22160  Z= 0.273
  Chirality :  0.035   0.178   2570
  Planarity :  0.004   0.035   1986
  Dihedral  : 22.149 163.414   4598
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  8.69 %
    Favored  : 91.12 %
  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:  2.98 (0.24), residues: 1243
  helix:  3.09 (0.18), residues: 809
  sheet:  0.28 (0.40), residues: 147
  loop : -0.52 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  46 
 HIS   0.004   0.001   HIS A 166 
 PHE   0.012   0.002   PHE D 112 
 TYR   0.014   0.001   TYR A 215 
 ARG   0.007   0.000   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04551 (  905)
  hydrogen bonds       : angle       3.47913 ( 2454)
  covalent geometry    : bond        0.00407 (15620)
  covalent geometry    : angle       0.50077 (22160)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9174.91 seconds
wall clock time: 158 minutes 49.19 seconds (9529.19 seconds total)