Starting phenix.real_space_refine
on Fri May 16 12:55:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wt6_37827/05_2025/8wt6_37827.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wt6_37827/05_2025/8wt6_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wt6_37827/05_2025/8wt6_37827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wt6_37827/05_2025/8wt6_37827.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wt6_37827/05_2025/8wt6_37827.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wt6_37827/05_2025/8wt6_37827.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.57, per 1000 atoms: 0.78
  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: 4.16
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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: 6.66
  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: 6.11

  Time building geometry restraints manager: 4.86 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=" 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
  bond pdb=" O5'   C F 176 "
       pdb=" C5'   C F 176 "
    ideal  model  delta    sigma   weight residual
    1.420  1.458 -0.038 1.50e-02 4.44e+03 6.31e+00
  bond pdb=" O5'   G E  53 "
       pdb=" C5'   G E  53 "
    ideal  model  delta    sigma   weight residual
    1.420  1.457 -0.037 1.50e-02 4.44e+03 6.16e+00
  bond pdb=" O5'   G E  41 "
       pdb=" C5'   G E  41 "
    ideal  model  delta    sigma   weight residual
    1.420  1.456 -0.036 1.50e-02 4.44e+03 5.84e+00
  bond pdb=" C   ILE D 201 "
       pdb=" N   PRO D 202 "
    ideal  model  delta    sigma   weight residual
    1.333  1.358 -0.024 1.01e-02 9.80e+03 5.70e+00
  ... (remaining 15499 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 19192
        2.01 -     4.02: 2510
        4.02 -     6.03: 252
        6.03 -     8.04: 22
        8.04 -    10.05: 4
  Bond angle restraints: 21980
  Sorted by residual:
  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
  angle pdb=" O3'  DA G  26 "
        pdb=" P    DC G  27 "
        pdb=" O5'  DC G  27 "
      ideal   model   delta    sigma   weight residual
     104.00   96.69    7.31 1.50e+00 4.44e-01 2.37e+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 -    0.130: 2253
       0.130 -    0.261: 288
       0.261 -    0.391: 0
       0.391 -    0.521: 0
       0.521 -    0.652: 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       2.35   -3.00   -0.65 2.00e-01 2.50e+01 1.06e+01
  chirality pdb=" P    DG I   5 "
            pdb=" OP1  DG I   5 "
            pdb=" OP2  DG I   5 "
            pdb=" O5'  DG I   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.99   -0.64 2.00e-01 2.50e+01 1.04e+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       2.35   -2.99   -0.64 2.00e-01 2.50e+01 1.03e+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:             1.060
  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:             0.020
  Extract box with map and model:          0.660
  Check model and map are aligned:         0.130
  Set scattering table:                    0.160
  Process input model:                     44.660
  Find NCS groups from input model:        0.610
  Set up NCS constraints:                  0.060
  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:11.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   58.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8773
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   0.043  15504  Z= 0.482
  Angle     :  1.365  10.051  21980  Z= 0.875
  Chirality :  0.083   0.652   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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (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
 TRP   0.037   0.009   TRP D 169 
 HIS   0.012   0.002   HIS D 256 
 PHE   0.024   0.004   PHE A 231 
 TYR   0.024   0.003   TYR B 264 
 ARG   0.021   0.003   ARG A 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20172 (  892)
  hydrogen bonds       : angle       6.42089 ( 2398)
  covalent geometry    : bond        0.00795 (15504)
  covalent geometry    : angle       1.36474 (21980)

*********************** 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  : 1.259 
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: 1.9306
  time to fit residues: 218.5800
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  : 1.314 
-------------------------------------------------------------------------------
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 119 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 72 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 128 optimal weight:    5.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3167 r_free = 0.3167 target = 0.082770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.055311 restraints weight = 48820.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.2601 rms_B_bonded: 2.48
r_work: 0.2406 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2406
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2415
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2415 r_free = 0.2415    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 = 0.2415 r_free = 0.2415    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2415
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15504  Z= 0.153
  Angle     :  0.578   7.338  21980  Z= 0.326
  Chirality :  0.039   0.229   2549
  Planarity :  0.004   0.039   1975
  Dihedral  : 22.020 174.412   4558
  Min Nonbonded Distance : 1.771

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  7.11 %
    Favored  : 92.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.23), residues: 1237
  helix:  2.01 (0.17), residues: 794
  sheet: -0.27 (0.39), residues: 164
  loop : -0.46 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D  46 
 HIS   0.004   0.001   HIS D 256 
 PHE   0.015   0.001   PHE C 280 
 TYR   0.016   0.002   TYR B 215 
 ARG   0.005   0.001   ARG D  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05765 (  892)
  hydrogen bonds       : angle       3.96827 ( 2398)
  covalent geometry    : bond        0.00306 (15504)
  covalent geometry    : angle       0.57830 (21980)

*********************** 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
  91 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 1.414 
Fit side-chains
   revert: symmetry clash
REVERT: A  221 ARG cc_start: 0.8524 (ttp80) cc_final: 0.8272 (ttm-80)
REVERT: A  258 SER cc_start: 0.9333 (m) cc_final: 0.8967 (t)
REVERT: B   51 LYS cc_start: 0.9403 (mttm) cc_final: 0.9198 (mtmm)
REVERT: D  105 ASP cc_start: 0.7726 (t70) cc_final: 0.7155 (p0)
REVERT: D  287 ASN cc_start: 0.8776 (t0) cc_final: 0.8498 (t160)
  outliers start: 7
  outliers final: 0
  residues processed: 87
  average time/residue: 1.6679
  time to fit residues: 157.1709
Evaluate side-chains
  74 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 1.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 127 optimal weight:   10.0000
   chunk 54 optimal weight:    6.9990
   chunk 123 optimal weight:    6.9990
   chunk 31 optimal weight:    7.9990
   chunk 87 optimal weight:    3.9990
   chunk 138 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 130 optimal weight:   10.0000
   chunk 78 optimal weight:    3.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
B 139 GLN
C 150 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 = 0.3103 r_free = 0.3103 target = 0.078665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2577 r_free = 0.2577 target = 0.051405 restraints weight = 47689.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.2550 rms_B_bonded: 2.43
r_work: 0.2350 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2212 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2223
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2223 r_free = 0.2223    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2222 r_free = 0.2222    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2222
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.1791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049  15504  Z= 0.324
  Angle     :  0.604   7.408  21980  Z= 0.338
  Chirality :  0.044   0.264   2549
  Planarity :  0.005   0.044   1975
  Dihedral  : 22.037 172.359   4554
  Min Nonbonded Distance : 1.718

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  8.40 %
    Favored  : 90.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.24), residues: 1237
  helix:  2.36 (0.18), residues: 793
  sheet: -0.34 (0.37), residues: 176
  loop : -0.22 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP D  46 
 HIS   0.005   0.001   HIS D 256 
 PHE   0.017   0.002   PHE B 112 
 TYR   0.015   0.002   TYR B 307 
 ARG   0.006   0.000   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06467 (  892)
  hydrogen bonds       : angle       3.86361 ( 2398)
  covalent geometry    : bond        0.00728 (15504)
  covalent geometry    : angle       0.60440 (21980)

*********************** 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
  81 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 1.426 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8730 (ttp80) cc_final: 0.8334 (ttm-80)
REVERT: A  258 SER cc_start: 0.9339 (m) cc_final: 0.8998 (t)
REVERT: B   51 LYS cc_start: 0.9411 (mttm) cc_final: 0.9188 (mtmm)
REVERT: D  103 THR cc_start: 0.8730 (m) cc_final: 0.8522 (t)
REVERT: D  105 ASP cc_start: 0.8074 (t70) cc_final: 0.7381 (p0)
REVERT: D  287 ASN cc_start: 0.8840 (t0) cc_final: 0.8502 (t160)
  outliers start: 7
  outliers final: 0
  residues processed: 77
  average time/residue: 1.8255
  time to fit residues: 151.9864
Evaluate side-chains
  69 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 1.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 71 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 88 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 87 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B  93 GLN
B 139 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.083025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.055791 restraints weight = 46981.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.2628 rms_B_bonded: 2.42
r_work: 0.2433 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2433
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2441
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2441 r_free = 0.2441    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2441 r_free = 0.2441    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2441
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15504  Z= 0.136
  Angle     :  0.502   7.470  21980  Z= 0.285
  Chirality :  0.036   0.227   2549
  Planarity :  0.004   0.046   1975
  Dihedral  : 21.919 172.887   4554
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  9.19 %
    Favored  : 90.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.51 (0.24), residues: 1237
  helix:  2.64 (0.18), residues: 794
  sheet: -0.04 (0.39), residues: 164
  loop : -0.15 (0.37), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D  46 
 HIS   0.004   0.001   HIS D 256 
 PHE   0.012   0.001   PHE C 280 
 TYR   0.013   0.001   TYR B 307 
 ARG   0.010   0.000   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04518 (  892)
  hydrogen bonds       : angle       3.62674 ( 2398)
  covalent geometry    : bond        0.00286 (15504)
  covalent geometry    : angle       0.50157 (21980)

*********************** 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
  87 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 1.297 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8263 (ttm-80)
REVERT: A  258 SER cc_start: 0.9263 (m) cc_final: 0.8917 (t)
REVERT: B   27 ARG cc_start: 0.8321 (mtm-85) cc_final: 0.8036 (mtp-110)
REVERT: B   51 LYS cc_start: 0.9274 (mttm) cc_final: 0.9061 (mtmm)
  outliers start: 7
  outliers final: 1
  residues processed: 83
  average time/residue: 1.8760
  time to fit residues: 167.9375
Evaluate side-chains
  75 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 1.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 12 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 117 optimal weight:    3.9990
   chunk 121 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 110 optimal weight:    0.0980
   chunk 44 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 102 optimal weight:    6.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3140 r_free = 0.3140 target = 0.080637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.053335 restraints weight = 45087.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.2569 rms_B_bonded: 2.37
r_work: 0.2375 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2239 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2239
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2277
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2277 r_free = 0.2277    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2277 r_free = 0.2277    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2277
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  15504  Z= 0.215
  Angle     :  0.524   6.536  21980  Z= 0.295
  Chirality :  0.039   0.242   2549
  Planarity :  0.004   0.045   1975
  Dihedral  : 21.892 173.095   4554
  Min Nonbonded Distance : 1.808

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  9.39 %
    Favored  : 90.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.56 (0.24), residues: 1237
  helix:  2.71 (0.18), residues: 794
  sheet: -0.09 (0.38), residues: 162
  loop : -0.16 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D  46 
 HIS   0.005   0.001   HIS D 256 
 PHE   0.014   0.002   PHE B 112 
 TYR   0.014   0.001   TYR B 307 
 ARG   0.009   0.000   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05160 (  892)
  hydrogen bonds       : angle       3.64625 ( 2398)
  covalent geometry    : bond        0.00482 (15504)
  covalent geometry    : angle       0.52368 (21980)

*********************** 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
  78 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 1.262 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8773 (ttp80) cc_final: 0.8358 (ttm-80)
REVERT: A  258 SER cc_start: 0.9268 (m) cc_final: 0.8945 (t)
REVERT: B   27 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.7742 (mtm110)
REVERT: B   51 LYS cc_start: 0.9396 (mttm) cc_final: 0.9178 (mtmm)
  outliers start: 5
  outliers final: 1
  residues processed: 76
  average time/residue: 1.5948
  time to fit residues: 131.6718
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  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  150 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 111 optimal weight:    0.5980
   chunk 122 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 93 optimal weight:    8.9990
   chunk 135 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 132 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    3.9188

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3100 r_free = 0.3100 target = 0.078331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2569 r_free = 0.2569 target = 0.050813 restraints weight = 50377.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.2544 rms_B_bonded: 2.52
r_work: 0.2343 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2343
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2353
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2353 r_free = 0.2353    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2353 r_free = 0.2353    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2353
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.055  15504  Z= 0.349
  Angle     :  0.595   6.409  21980  Z= 0.330
  Chirality :  0.044   0.265   2549
  Planarity :  0.005   0.047   1975
  Dihedral  : 22.006 172.867   4554
  Min Nonbonded Distance : 1.778

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 10.08 %
    Favored  : 89.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.37 (0.24), residues: 1237
  helix:  2.55 (0.18), residues: 794
  sheet: -0.11 (0.38), residues: 162
  loop : -0.27 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D  46 
 HIS   0.007   0.001   HIS D 256 
 PHE   0.019   0.002   PHE B 112 
 TYR   0.017   0.002   TYR B  74 
 ARG   0.008   0.000   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06279 (  892)
  hydrogen bonds       : angle       3.76537 ( 2398)
  covalent geometry    : bond        0.00786 (15504)
  covalent geometry    : angle       0.59495 (21980)

*********************** 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
  80 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 1.254 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8676 (ttp80) cc_final: 0.8290 (ttm-80)
REVERT: A  258 SER cc_start: 0.9318 (m) cc_final: 0.8962 (t)
REVERT: B   27 ARG cc_start: 0.8365 (mtm-85) cc_final: 0.7698 (mtm110)
REVERT: B   51 LYS cc_start: 0.9383 (mttm) cc_final: 0.9156 (mtmm)
  outliers start: 5
  outliers final: 2
  residues processed: 77
  average time/residue: 1.5862
  time to fit residues: 132.6433
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  : 1.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 12 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 125 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 134 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 122 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3139 r_free = 0.3139 target = 0.080537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.053243 restraints weight = 47089.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.2566 rms_B_bonded: 2.40
r_work: 0.2371 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2234 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2272
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2272 r_free = 0.2272    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2272 r_free = 0.2272    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2272
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.2226

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= 0.157
  Angle     :  0.525   6.544  21980  Z= 0.298
  Chirality :  0.038   0.236   2549
  Planarity :  0.004   0.046   1975
  Dihedral  : 22.031 173.154   4554
  Min Nonbonded Distance : 1.828

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 10.47 %
    Favored  : 89.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.24), residues: 1237
  helix:  2.65 (0.18), residues: 794
  sheet: -0.09 (0.38), residues: 161
  loop : -0.21 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D  46 
 HIS   0.004   0.001   HIS D 256 
 PHE   0.010   0.002   PHE B 112 
 TYR   0.013   0.001   TYR D 307 
 ARG   0.008   0.000   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05163 (  892)
  hydrogen bonds       : angle       3.66251 ( 2398)
  covalent geometry    : bond        0.00333 (15504)
  covalent geometry    : angle       0.52508 (21980)

*********************** 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
  78 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 1.453 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8754 (ttp80) cc_final: 0.8376 (ttm-80)
REVERT: A  258 SER cc_start: 0.9300 (m) cc_final: 0.8960 (t)
REVERT: B   27 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.7733 (mtm110)
REVERT: B   51 LYS cc_start: 0.9396 (mttm) cc_final: 0.9171 (mtmm)
  outliers start: 4
  outliers final: 0
  residues processed: 76
  average time/residue: 1.6383
  time to fit residues: 135.6589
Evaluate side-chains
  73 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 107 optimal weight:    0.5980
   chunk 51 optimal weight:    0.2980
   chunk 138 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9990
   chunk 96 optimal weight:    3.9990
   chunk 114 optimal weight:    2.9990
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3203 r_free = 0.3203 target = 0.084085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.057644 restraints weight = 35268.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.2669 rms_B_bonded: 2.08
r_work: 0.2491 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2357 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2357
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2392
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2392 r_free = 0.2392    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2392 r_free = 0.2392    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2392
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  15504  Z= 0.118
  Angle     :  0.486   6.992  21980  Z= 0.276
  Chirality :  0.035   0.220   2549
  Planarity :  0.004   0.046   1975
  Dihedral  : 21.861 173.130   4554
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 10.28 %
    Favored  : 89.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.74 (0.24), residues: 1237
  helix:  2.81 (0.18), residues: 795
  sheet:  0.13 (0.38), residues: 160
  loop : -0.09 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  46 
 HIS   0.005   0.000   HIS D 256 
 PHE   0.011   0.001   PHE B 112 
 TYR   0.013   0.001   TYR B 307 
 ARG   0.007   0.000   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04033 (  892)
  hydrogen bonds       : angle       3.50197 ( 2398)
  covalent geometry    : bond        0.00246 (15504)
  covalent geometry    : angle       0.48580 (21980)

*********************** 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
  84 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 1.395 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8811 (ttp80) cc_final: 0.8383 (ttm-80)
REVERT: A  258 SER cc_start: 0.9289 (m) cc_final: 0.8966 (t)
REVERT: B   27 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.8015 (mtp-110)
REVERT: B   51 LYS cc_start: 0.9300 (mttm) cc_final: 0.9084 (mtmm)
  outliers start: 4
  outliers final: 0
  residues processed: 82
  average time/residue: 1.6361
  time to fit residues: 145.6518
Evaluate side-chains
  76 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 1.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
B 139 GLN
D  99 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.081300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.053810 restraints weight = 49947.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.2614 rms_B_bonded: 2.47
r_work: 0.2414 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2414
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2424
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2424 r_free = 0.2424    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2424 r_free = 0.2424    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2424
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  15504  Z= 0.201
  Angle     :  0.519   8.082  21980  Z= 0.291
  Chirality :  0.038   0.236   2549
  Planarity :  0.004   0.046   1975
  Dihedral  : 21.855 173.136   4554
  Min Nonbonded Distance : 1.793

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 11.26 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.72 (0.24), residues: 1237
  helix:  2.80 (0.18), residues: 795
  sheet:  0.05 (0.38), residues: 162
  loop : -0.08 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D  46 
 HIS   0.006   0.001   HIS D 256 
 PHE   0.014   0.002   PHE B 112 
 TYR   0.017   0.001   TYR B  74 
 ARG   0.007   0.000   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04923 (  892)
  hydrogen bonds       : angle       3.55105 ( 2398)
  covalent geometry    : bond        0.00447 (15504)
  covalent geometry    : angle       0.51869 (21980)

*********************** 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
  80 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 1.270 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8719 (ttp80) cc_final: 0.8358 (ttm-80)
REVERT: A  258 SER cc_start: 0.9228 (m) cc_final: 0.8887 (t)
REVERT: B   27 ARG cc_start: 0.8303 (mtm-85) cc_final: 0.7585 (mtm110)
  outliers start: 3
  outliers final: 1
  residues processed: 78
  average time/residue: 1.6234
  time to fit residues: 137.2722
Evaluate side-chains
  76 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 4 optimal weight:    2.9990
   chunk 63 optimal weight:    6.9990
   chunk 120 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 135 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 122 optimal weight:   10.0000
   chunk 103 optimal weight:    0.6980
   chunk 44 optimal weight:    4.9990
   overall best weight:    1.7386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.081640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.054333 restraints weight = 49138.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.2618 rms_B_bonded: 2.44
r_work: 0.2419 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2419
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2427
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2427 r_free = 0.2427    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2427 r_free = 0.2427    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2427
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15504  Z= 0.183
  Angle     :  0.513   8.690  21980  Z= 0.287
  Chirality :  0.037   0.228   2549
  Planarity :  0.004   0.048   1975
  Dihedral  : 21.865 173.229   4554
  Min Nonbonded Distance : 1.802

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 11.76 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.70 (0.24), residues: 1237
  helix:  2.80 (0.18), residues: 794
  sheet:  0.03 (0.38), residues: 162
  loop : -0.13 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  46 
 HIS   0.007   0.001   HIS D 256 
 PHE   0.013   0.002   PHE B 112 
 TYR   0.014   0.001   TYR B 307 
 ARG   0.007   0.000   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04819 (  892)
  hydrogen bonds       : angle       3.54709 ( 2398)
  covalent geometry    : bond        0.00407 (15504)
  covalent geometry    : angle       0.51324 (21980)

********************** 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
  78 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 1.349 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8730 (ttp80) cc_final: 0.8366 (ttm-80)
REVERT: A  258 SER cc_start: 0.9224 (m) cc_final: 0.8881 (t)
REVERT: B   27 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7581 (mtm110)
  outliers start: 2
  outliers final: 3
  residues processed: 77
  average time/residue: 1.6321
  time to fit residues: 136.5054
Evaluate side-chains
  79 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 1.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  150 ASN
Chi-restraints excluded: chain C residue  298 MET
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 81 optimal weight:    0.9990
   chunk 125 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 112 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 115 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
B 139 GLN
D 139 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.082146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.054841 restraints weight = 47478.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.2631 rms_B_bonded: 2.40
r_work: 0.2433 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2433
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2443
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2443 r_free = 0.2443    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2443 r_free = 0.2443    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2443
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.2510

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= 0.140
  Angle     :  0.504   8.051  21980  Z= 0.283
  Chirality :  0.036   0.225   2549
  Planarity :  0.004   0.045   1975
  Dihedral  : 21.881 173.368   4554
  Min Nonbonded Distance : 1.817

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 11.96 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.75 (0.24), residues: 1237
  helix:  2.84 (0.18), residues: 794
  sheet:  0.03 (0.38), residues: 162
  loop : -0.10 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  46 
 HIS   0.007   0.001   HIS D 256 
 PHE   0.010   0.001   PHE B 112 
 TYR   0.017   0.001   TYR B  74 
 ARG   0.007   0.000   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04652 (  892)
  hydrogen bonds       : angle       3.53675 ( 2398)
  covalent geometry    : bond        0.00302 (15504)
  covalent geometry    : angle       0.50398 (21980)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10197.30 seconds
wall clock time: 176 minutes 4.96 seconds (10564.96 seconds total)