Starting phenix.real_space_refine
on Sat Oct 11 12:28:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wt7_37828/10_2025/8wt7_37828.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wt7_37828/10_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_37828/10_2025/8wt7_37828.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wt7_37828/10_2025/8wt7_37828.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wt7_37828/10_2025/8wt7_37828.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wt7_37828/10_2025/8wt7_37828.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 5.00, per 1000 atoms: 0.34
  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: 1.25
  Conformation dependent library (CDL) restraints added in 755.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 2.15
  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: 2.79

  Time building geometry restraints manager: 1.58 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:             1.280
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.390
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  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:9.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.610
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.68 (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
 ARG   0.025   0.002   ARG D 238 
 TYR   0.017   0.002   TYR D 307 
 PHE   0.017   0.002   PHE C 228 
 TRP   0.021   0.005   TRP A 169 
 HIS   0.010   0.002   HIS D 256 

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

*********************** 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  : 0.447 
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: 0.9258
  time to fit residues: 92.6209
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  : 0.408 
-------------------------------------------------------------------------------
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 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3263 r_free = 0.3263 target = 0.078821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.052422 restraints weight = 64879.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.2735 rms_B_bonded: 2.82
r_work: 0.2546 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2546
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2546
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2546 r_free = 0.2546    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 = 0.2546 r_free = 0.2546    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2546
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15620  Z= 0.156
  Angle     :  0.582   6.332  22160  Z= 0.326
  Chirality :  0.039   0.195   2570
  Planarity :  0.004   0.033   1986
  Dihedral  : 21.935 160.976   4602
  Min Nonbonded Distance : 1.805

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  4.84 %
    Favored  : 94.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.23), residues: 1243
  helix:  1.91 (0.17), residues: 809
  sheet: -0.70 (0.37), residues: 148
  loop : -0.85 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 237 
 TYR   0.019   0.002   TYR A 215 
 PHE   0.013   0.002   PHE A 280 
 TRP   0.017   0.002   TRP B 276 
 HIS   0.005   0.001   HIS B 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (15620)
  covalent geometry    : angle       0.58204 (22160)
  hydrogen bonds       : bond        0.05931 (  905)
  hydrogen bonds       : angle       4.10999 ( 2454)

*********************** 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  : 0.447 
Fit side-chains
   revert: symmetry clash
REVERT: B  107 ARG cc_start: 0.8659 (ttt90) cc_final: 0.8295 (ttm-80)
REVERT: B  298 MET cc_start: 0.9324 (tpt) cc_final: 0.8985 (tpt)
REVERT: C  258 SER cc_start: 0.9351 (m) cc_final: 0.8921 (p)
REVERT: D  108 MET cc_start: 0.8844 (tpp) cc_final: 0.8630 (mmt)
  outliers start: 5
  outliers final: 0
  residues processed: 67
  average time/residue: 0.7713
  time to fit residues: 55.9344
Evaluate side-chains
  61 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9990
   chunk 121 optimal weight:    6.9990
   chunk 82 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 39 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   chunk 99 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 135 optimal weight:    6.9990
   chunk 125 optimal weight:    7.9990
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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  54 HIS
C 287 ASN
D   6 HIS
D  99 ASN
D 287 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.075765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.049199 restraints weight = 75942.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.2624 rms_B_bonded: 3.02
r_work: 0.2426 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2426
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2459
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2459 r_free = 0.2459    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2459 r_free = 0.2459    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2459
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  15620  Z= 0.290
  Angle     :  0.589   6.415  22160  Z= 0.325
  Chirality :  0.042   0.203   2570
  Planarity :  0.005   0.057   1986
  Dihedral  : 22.131 160.481   4598
  Min Nonbonded Distance : 1.819

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.24), residues: 1243
  helix:  2.42 (0.18), residues: 808
  sheet: -0.80 (0.35), residues: 176
  loop : -0.61 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 261 
 TYR   0.018   0.002   TYR A 215 
 PHE   0.016   0.002   PHE C 316 
 TRP   0.019   0.002   TRP D  46 
 HIS   0.005   0.001   HIS B 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00647 (15620)
  covalent geometry    : angle       0.58911 (22160)
  hydrogen bonds       : bond        0.06165 (  905)
  hydrogen bonds       : angle       3.91672 ( 2454)

*********************** 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
  70 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: B   99 ASN cc_start: 0.8202 (m-40) cc_final: 0.7848 (m-40)
REVERT: B  298 MET cc_start: 0.9222 (tpt) cc_final: 0.8951 (tpt)
REVERT: D   99 ASN cc_start: 0.7836 (m-40) cc_final: 0.7574 (m-40)
REVERT: D  261 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8484 (ttm-80)
  outliers start: 8
  outliers final: 0
  residues processed: 66
  average time/residue: 0.7111
  time to fit residues: 51.0190
Evaluate side-chains
  58 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  261 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 129 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 90 optimal weight:    3.9990
   chunk 136 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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 = 0.3260 r_free = 0.3260 target = 0.077887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.051336 restraints weight = 72125.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.2684 rms_B_bonded: 3.00
r_work: 0.2487 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2487
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2520
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2520 r_free = 0.2520    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 = 0.2520 r_free = 0.2520    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2520
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  15620  Z= 0.160
  Angle     :  0.503   6.046  22160  Z= 0.280
  Chirality :  0.036   0.182   2570
  Planarity :  0.004   0.036   1986
  Dihedral  : 22.114 161.342   4598
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  6.32 %
    Favored  : 93.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.24), residues: 1243
  helix:  2.73 (0.18), residues: 807
  sheet: -0.28 (0.38), residues: 150
  loop : -0.66 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 261 
 TYR   0.014   0.001   TYR A 215 
 PHE   0.010   0.001   PHE A 280 
 TRP   0.013   0.002   TRP D  46 
 HIS   0.004   0.001   HIS B 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (15620)
  covalent geometry    : angle       0.50328 (22160)
  hydrogen bonds       : bond        0.04754 (  905)
  hydrogen bonds       : angle       3.66050 ( 2454)

*********************** 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
  69 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 MET cc_start: 0.9223 (tpt) cc_final: 0.8943 (tpt)
REVERT: B   99 ASN cc_start: 0.8031 (m-40) cc_final: 0.7618 (m-40)
REVERT: B  107 ARG cc_start: 0.8838 (ttt90) cc_final: 0.8545 (ttm-80)
REVERT: D  153 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8680 (tm-30)
REVERT: D  304 GLN cc_start: 0.9121 (tt0) cc_final: 0.8912 (mt0)
  outliers start: 5
  outliers final: 1
  residues processed: 67
  average time/residue: 0.7419
  time to fit residues: 54.0597
Evaluate side-chains
  63 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  258 SER
Chi-restraints excluded: chain D residue  153 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 116 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 128 optimal weight:    6.9990
   chunk 85 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   chunk 105 optimal weight:    0.4980
   chunk 29 optimal weight:    6.9990
   chunk 60 optimal weight:    5.9990
   chunk 139 optimal weight:    6.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 = 0.3253 r_free = 0.3253 target = 0.077424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.050804 restraints weight = 69893.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.2676 rms_B_bonded: 2.94
r_work: 0.2482 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2482
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2498
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2498 r_free = 0.2498    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2498 r_free = 0.2498    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2498
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  15620  Z= 0.170
  Angle     :  0.501   5.821  22160  Z= 0.277
  Chirality :  0.036   0.181   2570
  Planarity :  0.004   0.037   1986
  Dihedral  : 22.141 162.361   4598
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  6.52 %
    Favored  : 92.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.64 (0.24), residues: 1243
  helix:  2.85 (0.18), residues: 807
  sheet:  0.04 (0.39), residues: 148
  loop : -0.58 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 261 
 TYR   0.012   0.001   TYR A 215 
 PHE   0.011   0.002   PHE B 112 
 TRP   0.012   0.002   TRP D  46 
 HIS   0.003   0.001   HIS B 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (15620)
  covalent geometry    : angle       0.50083 (22160)
  hydrogen bonds       : bond        0.04732 (  905)
  hydrogen bonds       : angle       3.58723 ( 2454)

*********************** 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
  69 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 MET cc_start: 0.9224 (tpt) cc_final: 0.8964 (tpt)
REVERT: B  107 ARG cc_start: 0.8840 (ttt90) cc_final: 0.8463 (ttm-80)
REVERT: D  304 GLN cc_start: 0.9152 (tt0) cc_final: 0.8932 (mt0)
  outliers start: 7
  outliers final: 2
  residues processed: 66
  average time/residue: 0.7627
  time to fit residues: 54.4997
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  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  191 MET
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 31 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 137 optimal weight:    8.9990
   chunk 17 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 97 optimal weight:    0.0980
   chunk 115 optimal weight:    6.9990
   chunk 57 optimal weight:    4.9990
   chunk 131 optimal weight:    6.9990
   chunk 114 optimal weight:    5.9990
   chunk 122 optimal weight:   10.0000
   overall best weight:    3.6188

-------------------------------------------------------------------------------
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 = 0.3210 r_free = 0.3210 target = 0.075184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.048460 restraints weight = 72604.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.2610 rms_B_bonded: 2.99
r_work: 0.2411 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2411
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2449
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2449 r_free = 0.2449    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2449 r_free = 0.2449    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2449
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.080  15620  Z= 0.300
  Angle     :  0.571   8.551  22160  Z= 0.311
  Chirality :  0.041   0.203   2570
  Planarity :  0.004   0.035   1986
  Dihedral  : 22.284 160.766   4598
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  6.91 %
    Favored  : 92.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.54 (0.24), residues: 1243
  helix:  2.77 (0.18), residues: 808
  sheet: -0.06 (0.39), residues: 148
  loop : -0.61 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 237 
 TYR   0.017   0.002   TYR B 215 
 PHE   0.015   0.002   PHE C 316 
 TRP   0.015   0.002   TRP C  46 
 HIS   0.005   0.001   HIS D 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00673 (15620)
  covalent geometry    : angle       0.57098 (22160)
  hydrogen bonds       : bond        0.05736 (  905)
  hydrogen bonds       : angle       3.74172 ( 2454)

*********************** 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
  65 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: B   99 ASN cc_start: 0.8084 (m-40) cc_final: 0.7685 (m-40)
REVERT: B  107 ARG cc_start: 0.8799 (ttt90) cc_final: 0.8381 (ttm-80)
  outliers start: 7
  outliers final: 3
  residues processed: 62
  average time/residue: 0.7348
  time to fit residues: 49.6264
Evaluate side-chains
  61 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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 22 optimal weight:    0.9980
   chunk 29 optimal weight:    9.9990
   chunk 60 optimal weight:    5.9990
   chunk 107 optimal weight:    0.8980
   chunk 93 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 75 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 135 optimal weight:    6.9990
   chunk 122 optimal weight:   10.0000
   chunk 130 optimal weight:   10.0000
   overall best weight:    2.1384

-------------------------------------------------------------------------------
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
D  99 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.076618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.049917 restraints weight = 72334.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.2646 rms_B_bonded: 2.98
r_work: 0.2450 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2450
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2489
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2489 r_free = 0.2489    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2489 r_free = 0.2489    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2489
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.2492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  15620  Z= 0.197
  Angle     :  0.517   8.344  22160  Z= 0.284
  Chirality :  0.037   0.187   2570
  Planarity :  0.004   0.036   1986
  Dihedral  : 22.280 160.944   4598
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 3.56
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.66 (0.24), residues: 1243
  helix:  2.86 (0.18), residues: 806
  sheet:  0.05 (0.39), residues: 148
  loop : -0.57 (0.35), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 260 
 TYR   0.013   0.001   TYR B 215 
 PHE   0.011   0.002   PHE D 112 
 TRP   0.013   0.002   TRP D  46 
 HIS   0.004   0.001   HIS D 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (15620)
  covalent geometry    : angle       0.51742 (22160)
  hydrogen bonds       : bond        0.04907 (  905)
  hydrogen bonds       : angle       3.63483 ( 2454)

*********************** 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
  65 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 MET cc_start: 0.9257 (tpt) cc_final: 0.8860 (tpt)
REVERT: B  107 ARG cc_start: 0.8855 (ttt90) cc_final: 0.8469 (ttm-80)
REVERT: D   99 ASN cc_start: 0.7131 (m110) cc_final: 0.6898 (m-40)
  outliers start: 4
  outliers final: 3
  residues processed: 62
  average time/residue: 0.7177
  time to fit residues: 48.7605
Evaluate side-chains
  61 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
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 49 optimal weight:    2.9990
   chunk 136 optimal weight:    5.9990
   chunk 66 optimal weight:    8.9990
   chunk 104 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 128 optimal weight:    7.9990
   chunk 67 optimal weight:    0.6980
   chunk 132 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 41 optimal weight:    0.1980
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 = 0.3254 r_free = 0.3254 target = 0.077302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.050346 restraints weight = 96700.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.2662 rms_B_bonded: 3.36
r_work: 0.2456 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2456
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2490
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2490 r_free = 0.2490    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2490 r_free = 0.2490    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2490
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  15620  Z= 0.173
  Angle     :  0.498   7.366  22160  Z= 0.274
  Chirality :  0.035   0.180   2570
  Planarity :  0.004   0.036   1986
  Dihedral  : 22.241 162.295   4598
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  7.70 %
    Favored  : 91.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.77 (0.24), residues: 1243
  helix:  2.94 (0.18), residues: 807
  sheet:  0.06 (0.39), residues: 150
  loop : -0.50 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 261 
 TYR   0.015   0.001   TYR B 215 
 PHE   0.010   0.001   PHE D 112 
 TRP   0.012   0.001   TRP D  46 
 HIS   0.003   0.001   HIS B 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (15620)
  covalent geometry    : angle       0.49800 (22160)
  hydrogen bonds       : bond        0.04616 (  905)
  hydrogen bonds       : angle       3.56706 ( 2454)

*********************** 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
  69 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 MET cc_start: 0.9264 (tpt) cc_final: 0.8913 (tpt)
REVERT: B  107 ARG cc_start: 0.8850 (ttt90) cc_final: 0.8489 (ttm-80)
REVERT: D   99 ASN cc_start: 0.6909 (m110) cc_final: 0.6699 (m-40)
REVERT: D  304 GLN cc_start: 0.9171 (tt0) cc_final: 0.8827 (mt0)
  outliers start: 5
  outliers final: 3
  residues processed: 66
  average time/residue: 0.7574
  time to fit residues: 54.3162
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  : 0.434 
-------------------------------------------------------------------------------
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 52 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 14 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9980
   chunk 127 optimal weight:   10.0000
   chunk 83 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 117 optimal weight:    1.9990
   chunk 111 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.4586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.077560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.050860 restraints weight = 79027.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.2669 rms_B_bonded: 3.10
r_work: 0.2470 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.2470
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2507
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2507 r_free = 0.2507    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2507 r_free = 0.2507    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2507
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  15620  Z= 0.151
  Angle     :  0.495   9.013  22160  Z= 0.272
  Chirality :  0.035   0.178   2570
  Planarity :  0.004   0.036   1986
  Dihedral  : 22.241 162.348   4598
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.78 (0.24), residues: 1243
  helix:  2.96 (0.18), residues: 807
  sheet: -0.00 (0.39), residues: 148
  loop : -0.50 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 261 
 TYR   0.014   0.001   TYR B 215 
 PHE   0.011   0.001   PHE B 112 
 TRP   0.012   0.001   TRP C  46 
 HIS   0.003   0.001   HIS B 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (15620)
  covalent geometry    : angle       0.49515 (22160)
  hydrogen bonds       : bond        0.04544 (  905)
  hydrogen bonds       : angle       3.55359 ( 2454)

*********************** 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
  66 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 MET cc_start: 0.9257 (tpt) cc_final: 0.8933 (tpt)
REVERT: B  107 ARG cc_start: 0.8845 (ttt90) cc_final: 0.8482 (ttm-80)
REVERT: D   99 ASN cc_start: 0.6939 (m110) cc_final: 0.6722 (m-40)
REVERT: D  304 GLN cc_start: 0.9165 (tt0) cc_final: 0.8822 (mt0)
  outliers start: 4
  outliers final: 3
  residues processed: 64
  average time/residue: 0.6872
  time to fit residues: 48.1052
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  : 0.424 
-------------------------------------------------------------------------------
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 121 optimal weight:    6.9990
   chunk 109 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 66 optimal weight:    9.9990
   chunk 90 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   chunk 123 optimal weight:    7.9990
   overall best weight:    1.5384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.077678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.051492 restraints weight = 62078.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.2681 rms_B_bonded: 2.78
r_work: 0.2489 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2489
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2525
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2525 r_free = 0.2525    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 = 0.2525 r_free = 0.2525    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2525
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  15620  Z= 0.157
  Angle     :  0.493   6.333  22160  Z= 0.271
  Chirality :  0.035   0.179   2570
  Planarity :  0.004   0.036   1986
  Dihedral  : 22.227 162.232   4598
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  8.09 %
    Favored  : 91.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.80 (0.24), residues: 1243
  helix:  2.97 (0.18), residues: 807
  sheet:  0.05 (0.39), residues: 148
  loop : -0.51 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 261 
 TYR   0.014   0.001   TYR B 215 
 PHE   0.010   0.001   PHE B 112 
 TRP   0.012   0.001   TRP C  46 
 HIS   0.003   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (15620)
  covalent geometry    : angle       0.49282 (22160)
  hydrogen bonds       : bond        0.04529 (  905)
  hydrogen bonds       : angle       3.53953 ( 2454)

********************** 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
  65 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 MET cc_start: 0.9245 (tpt) cc_final: 0.8920 (tpt)
REVERT: B  107 ARG cc_start: 0.8833 (ttt90) cc_final: 0.8469 (ttm-80)
REVERT: D   99 ASN cc_start: 0.6979 (m110) cc_final: 0.6735 (m-40)
REVERT: D  304 GLN cc_start: 0.9155 (tt0) cc_final: 0.8812 (mt0)
  outliers start: 4
  outliers final: 3
  residues processed: 63
  average time/residue: 0.7097
  time to fit residues: 48.5844
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  : 0.449 
-------------------------------------------------------------------------------
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 66 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 86 optimal weight:    1.9990
   chunk 125 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0270
   chunk 0 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    1.2044

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.078634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.052377 restraints weight = 70010.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.2752 rms_B_bonded: 2.92
r_work: 0.2560 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2560
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2553
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2553 r_free = 0.2553    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2553 r_free = 0.2553    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2553
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.2797

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= 0.136
  Angle     :  0.478   8.232  22160  Z= 0.263
  Chirality :  0.034   0.177   2570
  Planarity :  0.003   0.036   1986
  Dihedral  : 22.171 162.954   4598
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  8.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.90 (0.24), residues: 1243
  helix:  3.02 (0.18), residues: 809
  sheet:  0.19 (0.39), residues: 146
  loop : -0.46 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 261 
 TYR   0.011   0.001   TYR B 215 
 PHE   0.010   0.001   PHE B 112 
 TRP   0.011   0.001   TRP C  46 
 HIS   0.003   0.000   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (15620)
  covalent geometry    : angle       0.47752 (22160)
  hydrogen bonds       : bond        0.04175 (  905)
  hydrogen bonds       : angle       3.47993 ( 2454)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4130.26 seconds
wall clock time: 71 minutes 19.19 seconds (4279.19 seconds total)