Starting phenix.real_space_refine
on Fri Jul  3 13:51:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wt6_37827/07_2026/8wt6_37827.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wt6_37827/07_2026/8wt6_37827.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wt6_37827/07_2026/8wt6_37827.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wt6_37827/07_2026/8wt6_37827.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wt6_37827/07_2026/8wt6_37827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wt6_37827/07_2026/8wt6_37827.map"
  }
  resolution = 2.5
  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=   0.000 sd=   0.071
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     234      5.49       5
     Mg      2      5.21       5
     S      48      5.16       5
     C    8431      2.51       5
     N    2726      2.21       5
     O    3302      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14743
  Number of models: 1
  Model: ""
    Number of chains: 15
    Chain: "A"
      Number of atoms: 2420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2420
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 12, 'TRANS': 293}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2514
      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: 2540
    Chain: "C"
      Number of atoms: 2411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2411
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 12, 'TRANS': 292}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2498
          Classifications: {'peptide': 317}
          Link IDs: {'PTRANS': 12, 'TRANS': 304}
    Chain: "E"
      Number of atoms: 1275
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 59, 1252
          Classifications: {'RNA': 59}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 12, 'rna3p_pur': 23, 'rna3p_pyr': 20}
          Link IDs: {'rna2p': 16, 'rna3p': 42}
      Conformer: "B"
        Number of residues, atoms: 59, 1252
          Classifications: {'RNA': 59}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 12, 'rna3p_pur': 23, 'rna3p_pyr': 20}
          Link IDs: {'rna2p': 16, 'rna3p': 42}
          bond proxies already assigned to first conformer: 1369
    Chain: "F"
      Number of atoms: 1443
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 1443
          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: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 509
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 558
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "I"
      Number of atoms: 507
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 507
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
          Chain breaks: 2
    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: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 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}
    Chain: "G"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AARG B 221 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG B 221 " occ=0.50
    residue:
      pdb=" P  A  G E  75 " occ=0.50
      ... (44 atoms not shown)
      pdb=" C4 B  G E  75 " occ=0.50
  Time building chain proxies: 3.92, per 1000 atoms: 0.27
  Number of scatterers: 14743
  At special positions: 0
  Unit cell: (119.52, 123.314, 115.726, 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     234     15.00
     Mg      2     11.99
     O    3302      8.00
     N    2726      7.00
     C    8431      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: 1.16
  Conformation dependent library (CDL) restraints added in 585.2 milliseconds
  

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2334

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 8 sheets defined
      68.4% alpha, 9.3% beta
      87 base pairs and 138 stacking pairs defined.
    Time for finding SS restraints: 1.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 50
    Processing helix  chain 'A' and resid 66 through 77
    Processing helix  chain 'A' and resid 84 through 95
      removed outlier: 3.827A  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: 4.112A  pdb=" N   GLU A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   THR A 154 " --> pdb=" O   ASN A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 187
    Processing helix  chain 'A' and resid 188 through 200
    Processing helix  chain 'A' and resid 205 through 217
      removed outlier: 3.539A  pdb=" N   ALA A 210 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 232
      removed outlier: 3.566A  pdb=" N   PHE A 228 " --> pdb=" O   HIS A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 262
      removed outlier: 3.591A  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 287
      removed outlier: 3.715A  pdb=" N   ASN A 287 " --> pdb=" O   ARG A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 313
    Processing helix  chain 'A' and resid 317 through 321
    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 95
      removed outlier: 3.714A  pdb=" N   GLY B  88 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 117
    Processing helix  chain 'B' and resid 125 through 155
      removed outlier: 3.769A  pdb=" N   GLU B 153 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   THR B 154 " --> pdb=" O   ASN B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 158
      No H-bonds generated for 'chain 'B' and resid 156 through 158'
    Processing helix  chain 'B' and resid 159 through 188
      removed outlier: 3.623A  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
      removed outlier: 3.508A  pdb=" N   ALA B 210 " --> pdb=" O   GLU B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 233
      removed outlier: 3.704A  pdb=" N   PHE B 228 " --> pdb=" O   HIS B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 263
      removed outlier: 3.567A  pdb=" N   ARG B 260 " --> pdb=" O   HIS B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 274
    Processing helix  chain 'B' and resid 274 through 287
    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 76
    Processing helix  chain 'C' and resid 84 through 95
      removed outlier: 3.739A  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 153
      removed outlier: 3.790A  pdb=" N   GLU C 153 " --> pdb=" O   LEU C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 188
      removed outlier: 3.558A  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: 3.723A  pdb=" N   PHE C 228 " --> pdb=" O   HIS C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 256 through 262
      removed outlier: 3.576A  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 287
      removed outlier: 3.600A  pdb=" N   ASN C 287 " --> pdb=" O   ARG C 283 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 290 through 313
    Processing helix  chain 'C' and resid 317 through 321
    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: 3.670A  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: 3.956A  pdb=" N   GLU D 153 " --> pdb=" O   LEU D 149 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   THR D 154 " --> pdb=" O   ASN D 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 156 through 158
      No H-bonds generated for 'chain 'D' and resid 156 through 158'
    Processing helix  chain 'D' and resid 159 through 187
    Processing helix  chain 'D' and resid 188 through 199
    Processing helix  chain 'D' and resid 205 through 217
      removed outlier: 3.570A  pdb=" N   ALA D 210 " --> pdb=" O   GLU D 206 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 224 through 233
      removed outlier: 3.537A  pdb=" N   PHE D 228 " --> pdb=" O   HIS D 224 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 256 through 263
      removed outlier: 3.584A  pdb=" N   LEU D 263 " --> pdb=" O   LEU D 259 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 263 through 274
      removed outlier: 3.549A  pdb=" N   SER D 272 " --> pdb=" O   MET D 268 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   THR D 274 " --> pdb=" O   ALA D 270 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 274 through 287
    Processing helix  chain 'D' and resid 290 through 313
    Processing helix  chain 'D' and resid 317 through 321
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 34
      removed outlier: 6.480A  pdb=" N   HIS A   6 " --> pdb=" O   HIS A  56 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   CYS A  58 " --> pdb=" O   HIS A   6 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   ILE A   8 " --> pdb=" O   CYS A  58 " (cutoff:3.500A)
      removed outlier: 8.446A  pdb=" N   GLU A  60 " --> pdb=" O   ILE A   8 " (cutoff:3.500A)
      removed outlier: 8.275A  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: 6.775A  pdb=" N   HIS B   6 " --> pdb=" O   HIS B  56 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   CYS B  58 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   ILE B   8 " --> pdb=" O   CYS B  58 " (cutoff:3.500A)
      removed outlier: 8.621A  pdb=" N   GLU B  60 " --> pdb=" O   ILE B   8 " (cutoff:3.500A)
      removed outlier: 8.437A  pdb=" N   ILE B  10 " --> pdb=" O   GLU B  60 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 236 through 237
      removed outlier: 3.796A  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: 6.520A  pdb=" N   HIS C   6 " --> pdb=" O   HIS C  56 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   CYS C  58 " --> pdb=" O   HIS C   6 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ILE C   8 " --> pdb=" O   CYS C  58 " (cutoff:3.500A)
      removed outlier: 8.465A  pdb=" N   GLU C  60 " --> pdb=" O   ILE C   8 " (cutoff:3.500A)
      removed outlier: 8.383A  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: 6.673A  pdb=" N   HIS D   6 " --> pdb=" O   HIS D  56 " (cutoff:3.500A)
      removed outlier: 8.085A  pdb=" N   CYS D  58 " --> pdb=" O   HIS D   6 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ILE D   8 " --> pdb=" O   CYS D  58 " (cutoff:3.500A)
      removed outlier: 8.477A  pdb=" N   GLU D  60 " --> pdb=" O   ILE D   8 " (cutoff:3.500A)
      removed outlier: 8.288A  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: 3.776A  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

    672 hydrogen bonds defined for protein.
    1974 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      220 hydrogen bonds
      424 hydrogen bond angles
      0 basepair planarities
      87 basepair parallelities
      140 stacking parallelities
  Total time for adding SS restraints: 2.88

  Time building geometry restraints manager: 1.61 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: 3123
        1.34 -     1.46: 5359
        1.46 -     1.57: 6479
        1.57 -     1.69: 459
        1.69 -     1.81: 84
  Bond restraints: 15504
  Sorted by residual:
  bond pdb=" P    DA I  18 "
       pdb=" O5'  DA I  18 "
    ideal  model  delta    sigma   weight residual
    1.593  1.622 -0.029 1.00e-02 1.00e+04 8.66e+00
  bond pdb=" P    DA H   3 "
       pdb=" O5'  DA H   3 "
    ideal  model  delta    sigma   weight residual
    1.593  1.622 -0.029 1.00e-02 1.00e+04 8.42e+00
  bond pdb=" P    DG J  12 "
       pdb=" O5'  DG J  12 "
    ideal  model  delta    sigma   weight residual
    1.593  1.619 -0.026 1.00e-02 1.00e+04 6.90e+00
  bond pdb=" P    DT G  10 "
       pdb=" O5'  DT G  10 "
    ideal  model  delta    sigma   weight residual
    1.593  1.618 -0.025 1.00e-02 1.00e+04 6.45e+00
  bond pdb=" C   ILE C 201 "
       pdb=" N   PRO C 202 "
    ideal  model  delta    sigma   weight residual
    1.333  1.359 -0.026 1.01e-02 9.80e+03 6.41e+00
  ... (remaining 15499 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 19239
        2.01 -     4.02: 2464
        4.02 -     6.03: 251
        6.03 -     8.04: 22
        8.04 -    10.05: 4
  Bond angle restraints: 21980
  Sorted by residual:
  angle pdb=" O4'  DG H  15 "
        pdb=" C4'  DG H  15 "
        pdb=" C3'  DG H  15 "
      ideal   model   delta    sigma   weight residual
     106.00  101.94    4.06 6.00e-01 2.78e+00 4.58e+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  114.05  -10.05 1.50e+00 4.44e-01 4.49e+01
  angle pdb=" O3'  DG J  32 "
        pdb=" P    DT J  33 "
        pdb=" O5'  DT J  33 "
      ideal   model   delta    sigma   weight residual
     104.00   95.56    8.44 1.50e+00 4.44e-01 3.17e+01
  angle pdb=" O3'  DA H  21 "
        pdb=" P    DT H  22 "
        pdb=" O5'  DT H  22 "
      ideal   model   delta    sigma   weight residual
     104.00   95.72    8.28 1.50e+00 4.44e-01 3.04e+01
  angle pdb=" O3'  DA I  24 "
        pdb=" P    DT I  25 "
        pdb=" O5'  DT I  25 "
      ideal   model   delta    sigma   weight residual
     104.00   95.81    8.19 1.50e+00 4.44e-01 2.98e+01
  ... (remaining 21975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.82: 8658
       34.82 -    69.63: 606
       69.63 -   104.45: 53
      104.45 -   139.27: 0
      139.27 -   174.09: 1
  Dihedral angle restraints: 9318
    sinusoidal: 5712
      harmonic: 3606
  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
    -128.00   46.09 -174.09     1      1.70e+01 3.46e-03 6.63e+01
  dihedral pdb=" O4'   C E  42 "
           pdb=" C2'   C E  42 "
           pdb=" C1'   C E  42 "
           pdb=" C3'   C E  42 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00   -9.61   34.61     1      8.00e+00 1.56e-02 2.65e+01
  dihedral pdb=" C4'   C E  42 "
           pdb=" O4'   C E  42 "
           pdb=" C1'   C E  42 "
           pdb=" C2'   C E  42 "
      ideal   model   delta sinusoidal    sigma   weight residual
       3.00  -29.14   32.14     1      8.00e+00 1.56e-02 2.30e+01
  ... (remaining 9315 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.132: 2256
       0.132 -    0.265: 285
       0.265 -    0.397: 0
       0.397 -    0.529: 0
       0.529 -    0.662: 8
  Chirality restraints: 2549
  Sorted by residual:
  chirality pdb=" P    DA I  18 "
            pdb=" OP1  DA I  18 "
            pdb=" OP2  DA I  18 "
            pdb=" O5'  DA I  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -3.00   -0.66 2.00e-01 2.50e+01 1.10e+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       2.34   -2.99   -0.66 2.00e-01 2.50e+01 1.07e+01
  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       2.34   -2.99   -0.65 2.00e-01 2.50e+01 1.06e+01
  ... (remaining 2546 not shown)

  Planarity restraints: 1975
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F 157 "   -0.071 2.00e-02 2.50e+03   2.87e-02 2.27e+01
        pdb=" N9    A F 157 "    0.046 2.00e-02 2.50e+03
        pdb=" C8    A F 157 "    0.016 2.00e-02 2.50e+03
        pdb=" N7    A F 157 "    0.007 2.00e-02 2.50e+03
        pdb=" C5    A F 157 "    0.005 2.00e-02 2.50e+03
        pdb=" C6    A F 157 "   -0.016 2.00e-02 2.50e+03
        pdb=" N6    A F 157 "   -0.028 2.00e-02 2.50e+03
        pdb=" N1    A F 157 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    A F 157 "    0.006 2.00e-02 2.50e+03
        pdb=" N3    A F 157 "    0.015 2.00e-02 2.50e+03
        pdb=" C4    A F 157 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U F 132 "    0.040 2.00e-02 2.50e+03   2.08e-02 9.72e+00
        pdb=" N1    U F 132 "   -0.043 2.00e-02 2.50e+03
        pdb=" C2    U F 132 "   -0.012 2.00e-02 2.50e+03
        pdb=" O2    U F 132 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    U F 132 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    U F 132 "    0.010 2.00e-02 2.50e+03
        pdb=" O4    U F 132 "    0.008 2.00e-02 2.50e+03
        pdb=" C5    U F 132 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    U F 132 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  26 "    0.040 2.00e-02 2.50e+03   1.96e-02 9.64e+00
        pdb=" N1   DT I  26 "   -0.042 2.00e-02 2.50e+03
        pdb=" C2   DT I  26 "   -0.009 2.00e-02 2.50e+03
        pdb=" O2   DT I  26 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DT I  26 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DT I  26 "    0.008 2.00e-02 2.50e+03
        pdb=" O4   DT I  26 "    0.015 2.00e-02 2.50e+03
        pdb=" C5   DT I  26 "   -0.001 2.00e-02 2.50e+03
        pdb=" C7   DT I  26 "   -0.006 2.00e-02 2.50e+03
        pdb=" C6   DT I  26 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1972 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.27: 15
        2.27 -     2.92: 5204
        2.92 -     3.58: 21840
        3.58 -     4.24: 39791
        4.24 -     4.90: 60500
  Nonbonded interactions: 127350
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 241 "
            pdb=" P    DT I  21 "
     model   vdw
     1.607 3.400
  nonbonded pdb=" OG  SER D 241 "
            pdb=" P    DA G  26 "
     model   vdw
     1.609 3.400
  nonbonded pdb=" OE2 GLU C  60 "
            pdb="MG    MG C 401 "
     model   vdw
     1.856 2.170
  nonbonded pdb="MG    MG C 401 "
            pdb=" O   HOH C 502 "
     model   vdw
     1.908 2.170
  nonbonded pdb="MG    MG A 401 "
            pdb=" O   HOH G 101 "
     model   vdw
     1.965 2.170
  ... (remaining 127345 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 220 or resid 222 through 321))
  selection = (chain 'B' and (resid 5 through 220 or resid 222 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 220 or resid 222 through 321))
  selection = (chain 'D' 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 220 or resid 222 through 238 or r \ 
esid 251 through 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:             2.170
  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:          0.300
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     15.990
  Find NCS groups from input model:        0.260
  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:             0.000
  Load rotamer database and sin/cos tables:8.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8988
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   0.044  15504  Z= 0.548
  Angle     :  1.356  10.051  21980  Z= 0.923
  Chirality :  0.085   0.662   2549
  Planarity :  0.005   0.044   1975
  Dihedral  : 19.929 174.086   6984
  Min Nonbonded Distance : 1.607

Molprobity Statistics.
  All-atom Clashscore : 0.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  2.47 %
    Favored  : 97.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.54 (0.20), residues: 1237
  helix: -0.78 (0.15), residues: 786
  sheet: -0.88 (0.37), residues: 160
  loop : -1.21 (0.30), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.003   ARG A 300 
 TYR   0.024   0.003   TYR B 264 
 PHE   0.024   0.004   PHE A 231 
 TRP   0.037   0.009   TRP D 169 
 HIS   0.012   0.002   HIS D 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00818 /  0.55 (15504)
  covalent geometry    : angle       1.35614 /  0.92 (21980)
  hydrogen bonds       : bond        0.20172 / 13.52 (  892)
  hydrogen bonds       : angle       6.42089 /  4.60 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   51 LYS cc_start: 0.9418 (mttm) cc_final: 0.9211 (mtmm)
REVERT: B   71 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8372 (mt-10)
REVERT: C  265 MET cc_start: 0.9357 (mmm) cc_final: 0.9029 (mmt)
REVERT: D  105 ASP cc_start: 0.8265 (t70) cc_final: 0.8041 (p0)
REVERT: D  287 ASN cc_start: 0.9065 (t0) cc_final: 0.8504 (t0)
REVERT: D  307 TYR cc_start: 0.9076 (t80) cc_final: 0.8660 (t80)
  outliers start: 4
  outliers final: 2
  residues processed: 106
  average time/residue: 0.8672
  time to fit residues: 97.9677
Evaluate side-chains
  77 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain C residue   60 GLU
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:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    1.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 139 GLN
B  93 GLN
B  99 ASN
B 139 GLN
D  99 ASN
D 256 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.081902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.054574 restraints weight = 46898.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.2583 rms_B_bonded: 2.43
r_work: 0.2386 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2386
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2423
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2423 r_free = 0.2423    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2423 r_free = 0.2423    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2423
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15504  Z= 0.174
  Angle     :  0.605   7.153  21980  Z= 0.360
  Chirality :  0.044   0.318   2549
  Planarity :  0.005   0.040   1975
  Dihedral  : 22.111 175.072   4558
  Min Nonbonded Distance : 1.770

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  6.72 %
    Favored  : 92.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.74 (0.23), residues: 1237
  helix:  2.02 (0.18), residues: 794
  sheet: -0.17 (0.39), residues: 160
  loop : -0.48 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  27 
 TYR   0.020   0.002   TYR B 215 
 PHE   0.013   0.001   PHE C 280 
 TRP   0.026   0.003   TRP D  46 
 HIS   0.004   0.001   HIS D 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.17 (15504)
  covalent geometry    : angle       0.60457 /  0.36 (21980)
  hydrogen bonds       : bond        0.06244 /  4.16 (  892)
  hydrogen bonds       : angle       4.05476 /  2.94 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 HIS cc_start: 0.8695 (m-70) cc_final: 0.8469 (m-70)
REVERT: A  221 ARG cc_start: 0.8520 (ttp80) cc_final: 0.8232 (ttm-80)
REVERT: A  258 SER cc_start: 0.9320 (m) cc_final: 0.8958 (t)
REVERT: B   27 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.7740 (mtm110)
REVERT: B   51 LYS cc_start: 0.9400 (mttm) cc_final: 0.9192 (mtmm)
REVERT: D  105 ASP cc_start: 0.7749 (t70) cc_final: 0.7180 (p0)
REVERT: D  187 ASP cc_start: 0.8414 (m-30) cc_final: 0.8172 (t0)
REVERT: D  287 ASN cc_start: 0.8795 (t0) cc_final: 0.8521 (t160)
  outliers start: 8
  outliers final: 0
  residues processed: 85
  average time/residue: 0.7479
  time to fit residues: 68.6093
Evaluate side-chains
  75 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 128 optimal weight:   10.0000
   chunk 127 optimal weight:   20.0000
   chunk 28 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0870
   chunk 100 optimal weight:    4.9990
   chunk 63 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9990
   chunk 132 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   chunk 121 optimal weight:    5.9990
   overall best weight:    3.2166

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN
B 139 GLN
C 287 ASN
D  99 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.079359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.051732 restraints weight = 55895.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.2556 rms_B_bonded: 2.62
r_work: 0.2349 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2349
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2360
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2360 r_free = 0.2360    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2360 r_free = 0.2360    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2360
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  15504  Z= 0.263
  Angle     :  0.579   7.323  21980  Z= 0.342
  Chirality :  0.044   0.252   2549
  Planarity :  0.005   0.046   1975
  Dihedral  : 22.082 173.637   4554
  Min Nonbonded Distance : 1.737

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  7.81 %
    Favored  : 91.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.14 (0.24), residues: 1237
  helix:  2.36 (0.18), residues: 794
  sheet: -0.31 (0.37), residues: 176
  loop : -0.20 (0.37), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  98 
 TYR   0.014   0.002   TYR B 307 
 PHE   0.016   0.002   PHE B 231 
 TRP   0.020   0.002   TRP D  46 
 HIS   0.007   0.001   HIS D 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00565 /  0.26 (15504)
  covalent geometry    : angle       0.57871 /  0.34 (21980)
  hydrogen bonds       : bond        0.06529 /  4.34 (  892)
  hydrogen bonds       : angle       3.89644 /  2.82 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.467 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8585 (ttp80) cc_final: 0.8252 (ttm-80)
REVERT: A  258 SER cc_start: 0.9302 (m) cc_final: 0.8947 (t)
REVERT: B   27 ARG cc_start: 0.8257 (mtm-85) cc_final: 0.7872 (mtm110)
REVERT: B   51 LYS cc_start: 0.9396 (mttm) cc_final: 0.9173 (mtmm)
REVERT: D  105 ASP cc_start: 0.7910 (t70) cc_final: 0.7280 (p0)
REVERT: D  187 ASP cc_start: 0.8441 (m-30) cc_final: 0.8239 (t0)
REVERT: D  287 ASN cc_start: 0.8857 (t0) cc_final: 0.8523 (t160)
  outliers start: 7
  outliers final: 1
  residues processed: 77
  average time/residue: 0.7665
  time to fit residues: 63.6601
Evaluate side-chains
  72 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   60 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 20 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 64 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 95 optimal weight:    5.9990
   chunk 99 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    1.9388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN
B 139 GLN
C 287 ASN
D  99 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.080751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.053506 restraints weight = 42989.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.2573 rms_B_bonded: 2.31
r_work: 0.2380 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2245 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2245
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2282 r_free = 0.2282    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2282 r_free = 0.2282    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15504  Z= 0.180
  Angle     :  0.518   7.435  21980  Z= 0.309
  Chirality :  0.040   0.232   2549
  Planarity :  0.004   0.047   1975
  Dihedral  : 22.068 174.294   4554
  Min Nonbonded Distance : 1.801

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  9.09 %
    Favored  : 90.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.33 (0.24), residues: 1237
  helix:  2.54 (0.18), residues: 794
  sheet: -0.19 (0.38), residues: 162
  loop : -0.28 (0.35), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 221 
 TYR   0.013   0.002   TYR B 215 
 PHE   0.012   0.002   PHE B 112 
 TRP   0.017   0.002   TRP D  46 
 HIS   0.005   0.001   HIS D 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00378 /  0.18 (15504)
  covalent geometry    : angle       0.51773 /  0.31 (21980)
  hydrogen bonds       : bond        0.05403 /  3.60 (  892)
  hydrogen bonds       : angle       3.77357 /  2.73 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8740 (ttp80) cc_final: 0.8318 (ttm-80)
REVERT: A  258 SER cc_start: 0.9281 (m) cc_final: 0.8940 (t)
REVERT: B   27 ARG cc_start: 0.8321 (mtm-85) cc_final: 0.7884 (mtm110)
REVERT: B   51 LYS cc_start: 0.9403 (mttm) cc_final: 0.9183 (mtmm)
REVERT: D  287 ASN cc_start: 0.8804 (t0) cc_final: 0.8490 (t160)
  outliers start: 6
  outliers final: 2
  residues processed: 79
  average time/residue: 0.7443
  time to fit residues: 63.4003
Evaluate side-chains
  75 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   60 GLU
Chi-restraints excluded: chain C residue  150 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 119 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 82 optimal weight:    6.9990
   chunk 95 optimal weight:    0.2980
   chunk 2 optimal weight:    0.8980
   chunk 70 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 120 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 140 optimal weight:   10.0000
   overall best weight:    1.2384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN
B 139 GLN
C 287 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.081535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.054632 restraints weight = 38147.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.2598 rms_B_bonded: 2.18
r_work: 0.2409 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2272 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2272
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2309
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2309 r_free = 0.2309    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2309 r_free = 0.2309    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2309
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15504  Z= 0.145
  Angle     :  0.496   7.477  21980  Z= 0.298
  Chirality :  0.039   0.232   2549
  Planarity :  0.004   0.048   1975
  Dihedral  : 22.019 174.530   4554
  Min Nonbonded Distance : 1.837

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  8.99 %
    Favored  : 90.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.49 (0.24), residues: 1237
  helix:  2.64 (0.18), residues: 794
  sheet: -0.13 (0.38), residues: 162
  loop : -0.17 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  27 
 TYR   0.014   0.001   TYR B 307 
 PHE   0.011   0.001   PHE B 112 
 TRP   0.014   0.002   TRP D  46 
 HIS   0.005   0.001   HIS D 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.14 (15504)
  covalent geometry    : angle       0.49574 /  0.30 (21980)
  hydrogen bonds       : bond        0.05057 /  3.36 (  892)
  hydrogen bonds       : angle       3.70701 /  2.69 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: A  258 SER cc_start: 0.9278 (m) cc_final: 0.8942 (t)
REVERT: B   27 ARG cc_start: 0.8334 (mtm-85) cc_final: 0.7875 (mtm110)
REVERT: B   51 LYS cc_start: 0.9395 (mttm) cc_final: 0.9187 (mtmm)
REVERT: D  287 ASN cc_start: 0.8764 (t0) cc_final: 0.8442 (t160)
  outliers start: 6
  outliers final: 4
  residues processed: 80
  average time/residue: 0.7340
  time to fit residues: 63.3820
Evaluate side-chains
  77 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   60 GLU
Chi-restraints excluded: chain C residue  150 ASN
Chi-restraints excluded: chain D residue   84 ASN
Chi-restraints excluded: chain D residue  158 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 138 optimal weight:   10.0000
   chunk 64 optimal weight:    4.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN
B 139 GLN
C 287 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.082302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.055483 restraints weight = 36039.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.2619 rms_B_bonded: 2.13
r_work: 0.2434 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2303 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2303
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2339
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2339 r_free = 0.2339    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2339 r_free = 0.2339    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2339
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  15504  Z= 0.130
  Angle     :  0.479   7.099  21980  Z= 0.290
  Chirality :  0.038   0.228   2549
  Planarity :  0.004   0.048   1975
  Dihedral  : 21.983 174.736   4554
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  8.99 %
    Favored  : 90.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.61 (0.24), residues: 1237
  helix:  2.73 (0.18), residues: 794
  sheet: -0.06 (0.39), residues: 162
  loop : -0.10 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 129 
 TYR   0.015   0.001   TYR D 307 
 PHE   0.011   0.001   PHE B 112 
 TRP   0.013   0.001   TRP D  46 
 HIS   0.005   0.001   HIS D 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.13 (15504)
  covalent geometry    : angle       0.47936 /  0.29 (21980)
  hydrogen bonds       : bond        0.04749 /  3.16 (  892)
  hydrogen bonds       : angle       3.63328 /  2.64 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8740 (ttp80) cc_final: 0.8323 (ttm-80)
REVERT: A  258 SER cc_start: 0.9284 (m) cc_final: 0.8958 (t)
REVERT: B   27 ARG cc_start: 0.8289 (mtm-85) cc_final: 0.7823 (mtm110)
REVERT: B   51 LYS cc_start: 0.9386 (mttm) cc_final: 0.9170 (mtmm)
REVERT: B   66 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.7562 (ppp)
  outliers start: 8
  outliers final: 2
  residues processed: 78
  average time/residue: 0.7000
  time to fit residues: 59.0724
Evaluate side-chains
  76 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 MET
Chi-restraints excluded: chain C residue  150 ASN
Chi-restraints excluded: chain D residue  158 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 67 optimal weight:    0.6980
   chunk 131 optimal weight:   10.0000
   chunk 92 optimal weight:    3.9990
   chunk 101 optimal weight:    5.9990
   chunk 59 optimal weight:    7.9990
   chunk 109 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 132 optimal weight:    8.9990
   overall best weight:    2.2986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 304 GLN
B  93 GLN
B 139 GLN
C 287 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.080591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.053014 restraints weight = 52922.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.2563 rms_B_bonded: 2.55
r_work: 0.2360 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2360
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2399
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2399 r_free = 0.2399    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2399 r_free = 0.2399    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2399
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  15504  Z= 0.206
  Angle     :  0.515   6.673  21980  Z= 0.304
  Chirality :  0.040   0.247   2549
  Planarity :  0.004   0.048   1975
  Dihedral  : 21.980 174.448   4554
  Min Nonbonded Distance : 1.786

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  9.68 %
    Favored  : 89.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.61 (0.24), residues: 1237
  helix:  2.72 (0.18), residues: 794
  sheet: -0.01 (0.39), residues: 162
  loop : -0.08 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 129 
 TYR   0.014   0.001   TYR B 307 
 PHE   0.014   0.002   PHE B 112 
 TRP   0.013   0.002   TRP D  46 
 HIS   0.005   0.001   HIS D 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00439 /  0.21 (15504)
  covalent geometry    : angle       0.51467 /  0.30 (21980)
  hydrogen bonds       : bond        0.05364 /  3.56 (  892)
  hydrogen bonds       : angle       3.65888 /  2.65 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.467 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8664 (ttp80) cc_final: 0.8291 (ttm-80)
REVERT: A  258 SER cc_start: 0.9221 (m) cc_final: 0.8886 (t)
REVERT: B   27 ARG cc_start: 0.8207 (mtm-85) cc_final: 0.7686 (mtm110)
  outliers start: 7
  outliers final: 4
  residues processed: 79
  average time/residue: 0.7878
  time to fit residues: 67.2742
Evaluate side-chains
  76 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   60 GLU
Chi-restraints excluded: chain C residue  150 ASN
Chi-restraints excluded: chain C residue  191 MET
Chi-restraints excluded: chain D residue  158 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 90 optimal weight:    3.9990
   chunk 107 optimal weight:    0.5980
   chunk 89 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN
B 139 GLN
C 287 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.081695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.054558 restraints weight = 44416.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.2626 rms_B_bonded: 2.34
r_work: 0.2430 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2294 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2294
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2303
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2303 r_free = 0.2303    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2303 r_free = 0.2303    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2303
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  15504  Z= 0.129
  Angle     :  0.489   6.407  21980  Z= 0.294
  Chirality :  0.038   0.235   2549
  Planarity :  0.004   0.049   1975
  Dihedral  : 22.007 174.726   4554
  Min Nonbonded Distance : 1.807

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  9.98 %
    Favored  : 89.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.67 (0.24), residues: 1237
  helix:  2.76 (0.18), residues: 794
  sheet: -0.03 (0.38), residues: 161
  loop : -0.05 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 151 
 TYR   0.014   0.001   TYR C 307 
 PHE   0.011   0.002   PHE B 112 
 TRP   0.013   0.001   TRP D  46 
 HIS   0.004   0.001   HIS D 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.13 (15504)
  covalent geometry    : angle       0.48913 /  0.29 (21980)
  hydrogen bonds       : bond        0.04936 /  3.28 (  892)
  hydrogen bonds       : angle       3.62419 /  2.63 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.450 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8769 (ttp80) cc_final: 0.8342 (ttm-80)
REVERT: A  258 SER cc_start: 0.9258 (m) cc_final: 0.8936 (t)
REVERT: B   27 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7804 (mtm110)
REVERT: D  105 ASP cc_start: 0.7787 (t0) cc_final: 0.7415 (m-30)
  outliers start: 8
  outliers final: 3
  residues processed: 79
  average time/residue: 0.7755
  time to fit residues: 66.3826
Evaluate side-chains
  74 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   60 GLU
Chi-restraints excluded: chain C residue  150 ASN
Chi-restraints excluded: chain D residue  158 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 121 optimal weight:    2.9990
   chunk 140 optimal weight:   10.0000
   chunk 110 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   chunk 81 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 109 optimal weight:    0.8980
   chunk 123 optimal weight:   10.0000
   overall best weight:    1.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN
B 139 GLN
C 287 ASN
D 287 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.081616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.054240 restraints weight = 47662.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.2621 rms_B_bonded: 2.43
r_work: 0.2424 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2424
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2405
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2405 r_free = 0.2405    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2405 r_free = 0.2405    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2405
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15504  Z= 0.158
  Angle     :  0.493   6.527  21980  Z= 0.293
  Chirality :  0.038   0.234   2549
  Planarity :  0.004   0.048   1975
  Dihedral  : 21.972 174.715   4554
  Min Nonbonded Distance : 1.804

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 10.57 %
    Favored  : 88.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.72 (0.24), residues: 1237
  helix:  2.78 (0.18), residues: 794
  sheet:  0.07 (0.39), residues: 162
  loop : -0.03 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 129 
 TYR   0.013   0.001   TYR C 307 
 PHE   0.012   0.002   PHE B 112 
 TRP   0.013   0.001   TRP D  46 
 HIS   0.006   0.001   HIS D 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.16 (15504)
  covalent geometry    : angle       0.49312 /  0.29 (21980)
  hydrogen bonds       : bond        0.04924 /  3.26 (  892)
  hydrogen bonds       : angle       3.59089 /  2.61 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8304 (ttm-80)
REVERT: A  258 SER cc_start: 0.9214 (m) cc_final: 0.8881 (t)
REVERT: D  105 ASP cc_start: 0.7653 (t0) cc_final: 0.7372 (m-30)
  outliers start: 5
  outliers final: 2
  residues processed: 77
  average time/residue: 0.7134
  time to fit residues: 59.3285
Evaluate side-chains
  74 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  150 ASN
Chi-restraints excluded: chain D residue  158 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 122 optimal weight:   20.0000
   chunk 67 optimal weight:    0.6980
   chunk 75 optimal weight:    0.5980
   chunk 133 optimal weight:   20.0000
   chunk 14 optimal weight:    3.9990
   chunk 119 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 102 optimal weight:    0.0670
   overall best weight:    1.2722

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN
B 139 GLN
C 287 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.082392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.055003 restraints weight = 53332.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.2610 rms_B_bonded: 2.54
r_work: 0.2410 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2410
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2420
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2420 r_free = 0.2420    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2420 r_free = 0.2420    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2420
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15504  Z= 0.141
  Angle     :  0.480   8.485  21980  Z= 0.286
  Chirality :  0.037   0.229   2549
  Planarity :  0.004   0.053   1975
  Dihedral  : 21.970 174.744   4554
  Min Nonbonded Distance : 1.839

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 11.36 %
    Favored  : 88.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.78 (0.24), residues: 1237
  helix:  2.83 (0.18), residues: 794
  sheet:  0.08 (0.38), residues: 162
  loop :  0.03 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B  27 
 TYR   0.014   0.001   TYR C 307 
 PHE   0.011   0.001   PHE B 112 
 TRP   0.013   0.001   TRP D  46 
 HIS   0.007   0.001   HIS D 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.14 (15504)
  covalent geometry    : angle       0.47987 /  0.29 (21980)
  hydrogen bonds       : bond        0.04676 /  3.10 (  892)
  hydrogen bonds       : angle       3.55270 /  2.58 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8313 (ttm-80)
REVERT: A  258 SER cc_start: 0.9234 (m) cc_final: 0.8906 (t)
REVERT: B   27 ARG cc_start: 0.8380 (mtm-85) cc_final: 0.7874 (mtm110)
REVERT: D  105 ASP cc_start: 0.7654 (t0) cc_final: 0.7390 (m-30)
  outliers start: 2
  outliers final: 2
  residues processed: 78
  average time/residue: 0.7730
  time to fit residues: 65.4961
Evaluate side-chains
  77 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  150 ASN
Chi-restraints excluded: chain D residue  158 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 111 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 121 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0470
   overall best weight:    1.2882

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN
B 139 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.082482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2669 r_free = 0.2669 target = 0.055114 restraints weight = 47428.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.2642 rms_B_bonded: 2.43
r_work: 0.2447 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2447
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2457
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2457 r_free = 0.2457    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2457 r_free = 0.2457    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2457
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15504  Z= 0.144
  Angle     :  0.478   7.644  21980  Z= 0.284
  Chirality :  0.037   0.226   2549
  Planarity :  0.004   0.048   1975
  Dihedral  : 21.952 174.673   4554
  Min Nonbonded Distance : 1.826

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 11.66 %
    Favored  : 88.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.82 (0.24), residues: 1237
  helix:  2.86 (0.18), residues: 794
  sheet:  0.17 (0.39), residues: 160
  loop : -0.02 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  27 
 TYR   0.013   0.001   TYR B 307 
 PHE   0.012   0.001   PHE B 112 
 TRP   0.012   0.001   TRP D  46 
 HIS   0.006   0.001   HIS D 256 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.14 (15504)
  covalent geometry    : angle       0.47781 /  0.28 (21980)
  hydrogen bonds       : bond        0.04686 /  3.10 (  892)
  hydrogen bonds       : angle       3.53007 /  2.56 ( 2398)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4804.11 seconds
wall clock time: 82 minutes 41.14 seconds (4961.14 seconds total)