Starting phenix.real_space_refine
on Sat Oct 11 12:35:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wt9_37830/10_2025/8wt9_37830.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wt9_37830/10_2025/8wt9_37830.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wt9_37830/10_2025/8wt9_37830.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wt9_37830/10_2025/8wt9_37830.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wt9_37830/10_2025/8wt9_37830.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wt9_37830/10_2025/8wt9_37830.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.028
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     241      5.49       5
     Mg      2      5.21       5
     S      48      5.16       5
     C    8557      2.51       5
     N    2771      2.21       5
     O    3363      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14982
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 2530
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 319, 2515
          Classifications: {'peptide': 319}
          Link IDs: {'PTRANS': 12, 'TRANS': 306}
      Conformer: "B"
        Number of residues, atoms: 319, 2515
          Classifications: {'peptide': 319}
          Link IDs: {'PTRANS': 12, 'TRANS': 306}
          bond proxies already assigned to first conformer: 2547
    Chain: "B"
      Number of atoms: 2449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2449
          Classifications: {'peptide': 311}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 12, 'TRANS': 298}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 2517
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 318, 2506
          Classifications: {'peptide': 318}
          Link IDs: {'PTRANS': 12, 'TRANS': 305}
      Conformer: "B"
        Number of residues, atoms: 318, 2506
          Classifications: {'peptide': 318}
          Link IDs: {'PTRANS': 12, 'TRANS': 305}
          bond proxies already assigned to first conformer: 2543
    Chain: "D"
      Number of atoms: 2456
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 310, 2447
          Classifications: {'peptide': 310}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 297}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
      Conformer: "B"
        Number of residues, atoms: 310, 2447
          Classifications: {'peptide': 310}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 297}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
          bond proxies already assigned to first conformer: 2485
    Chain: "E"
      Number of atoms: 1249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 1249
          Classifications: {'RNA': 59}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 11, 'rna3p_pur': 22, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 14, 'rna3p': 44}
    Chain: "F"
      Number of atoms: 1442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 1442
          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: 580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 580
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
    Chain: "H"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 557
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 555
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "J"
      Number of atoms: 643
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 29, 602
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
      Conformer: "B"
        Number of residues, atoms: 29, 602
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 630
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "J"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 6
    residue:
      pdb=" N  AGLN A 139 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NE2BGLN A 139 " occ=0.50
    residue:
      pdb=" N  ASER A 241 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER A 241 " occ=0.50
    residue:
      pdb=" N  AARG C 237 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG C 237 " occ=0.50
    residue:
      pdb=" N  AGLN D 139 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NE2BGLN D 139 " occ=0.50
    residue:
      pdb=" P  A DT J  28 " occ=0.50
      ... (38 atoms not shown)
      pdb=" C6 B DT J  28 " occ=0.50
    residue:
      pdb=" P  A DA J  29 " occ=0.50
      ... (40 atoms not shown)
      pdb=" C4 B DA J  29 " occ=0.50
  Time building chain proxies: 5.15, per 1000 atoms: 0.34
  Number of scatterers: 14982
  At special positions: 0
  Unit cell: (122.84, 123.947, 116.2, 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     241     15.00
     Mg      2     11.99
     O    3363      8.00
     N    2771      7.00
     C    8557      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: 1.28
  Conformation dependent library (CDL) restraints added in 833.2 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2364

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 8 sheets defined
      67.2% alpha, 10.7% beta
      87 base pairs and 148 stacking pairs defined.
    Time for finding SS restraints: 2.16
  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: 3.627A  pdb=" N   GLY A  88 " --> pdb=" O   ASN A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 117
    Processing helix  chain 'A' and resid 125 through 155
      removed outlier: 4.162A  pdb=" N   GLU A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   THR A 154 " --> pdb=" O   ASN A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 188
      removed outlier: 3.656A  pdb=" N   ASP A 188 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 199
    Processing helix  chain 'A' and resid 205 through 217
    Processing helix  chain 'A' and resid 224 through 232
      removed outlier: 3.671A  pdb=" N   PHE A 228 " --> pdb=" O   HIS A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 263
      removed outlier: 3.756A  pdb=" N   LEU A 263 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 274
    Processing helix  chain 'A' and resid 274 through 287
      removed outlier: 3.532A  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
      removed outlier: 3.588A  pdb=" N   ARG A 320 " --> pdb=" O   ASP A 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 50
    Processing helix  chain 'B' and resid 63 through 65
      No H-bonds generated for 'chain 'B' and resid 63 through 65'
    Processing helix  chain 'B' and resid 66 through 77
    Processing helix  chain 'B' and resid 84 through 95
      removed outlier: 3.532A  pdb=" N   GLY B  88 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 117
    Processing helix  chain 'B' and resid 125 through 154
      removed outlier: 3.810A  pdb=" N   GLU B 153 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   THR B 154 " --> pdb=" O   ASN B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 188
      removed outlier: 3.624A  pdb=" N   ASP B 188 " --> pdb=" O   LEU B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 200
    Processing helix  chain 'B' and resid 205 through 217
    Processing helix  chain 'B' and resid 224 through 232
      removed outlier: 3.729A  pdb=" N   PHE B 228 " --> pdb=" O   HIS B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 263
    Processing helix  chain 'B' and resid 263 through 274
    Processing helix  chain 'B' and resid 274 through 287
      removed outlier: 3.714A  pdb=" N   ASN B 287 " --> pdb=" O   ARG B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 313
    Processing helix  chain 'B' and resid 317 through 321
    Processing helix  chain 'C' and resid 36 through 50
    Processing helix  chain 'C' and resid 66 through 77
    Processing helix  chain 'C' and resid 84 through 96
      removed outlier: 3.544A  pdb=" N   GLY C  88 " --> pdb=" O   ASN C  84 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY C  96 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 117
    Processing helix  chain 'C' and resid 125 through 153
      removed outlier: 3.912A  pdb=" N   GLU C 153 " --> pdb=" O   LEU C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 188
      removed outlier: 3.626A  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: 3.649A  pdb=" N   PHE C 228 " --> pdb=" O   HIS C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 256 through 262
      removed outlier: 3.596A  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
    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 49
    Processing helix  chain 'D' and resid 66 through 77
    Processing helix  chain 'D' and resid 84 through 95
    Processing helix  chain 'D' and resid 101 through 117
      removed outlier: 3.511A  pdb=" N   ALA D 110 " --> pdb=" O   ALA D 106 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 125 through 152
    Processing helix  chain 'D' and resid 159 through 188
      removed outlier: 3.653A  pdb=" N   ASP D 188 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 200
    Processing helix  chain 'D' and resid 205 through 216
    Processing helix  chain 'D' and resid 224 through 232
      removed outlier: 3.831A  pdb=" N   PHE D 228 " --> pdb=" O   HIS D 224 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 256 through 262
      removed outlier: 3.519A  pdb=" N   ALA D 262 " --> pdb=" O   SER D 258 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 263 through 274
    Processing helix  chain 'D' and resid 274 through 286
    Processing helix  chain 'D' and resid 290 through 313
    Processing helix  chain 'D' and resid 317 through 322
      removed outlier: 3.633A  pdb=" N   ASN D 322 " --> pdb=" O   SER D 319 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 34
      removed outlier: 6.540A  pdb=" N   HIS A   6 " --> pdb=" O   HIS A  56 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   CYS A  58 " --> pdb=" O   HIS A   6 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ILE A   8 " --> pdb=" O   CYS A  58 " (cutoff:3.500A)
      removed outlier: 8.517A  pdb=" N   GLU A  60 " --> pdb=" O   ILE A   8 " (cutoff:3.500A)
      removed outlier: 8.357A  pdb=" N   ILE A  10 " --> pdb=" O   GLU A  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 241
      removed outlier: 3.685A  pdb=" N   ARG A 250 " --> pdb=" O   ARG A 237 " (cutoff:3.500A)
      removed outlier: 5.855A  pdb=" N   TYR A 239 " --> pdb=" O   ALA A 248 " (cutoff:3.500A)
      removed outlier: 5.490A  pdb=" N   ALA A 248 " --> pdb=" O   TYR A 239 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N  ASER A 241 " --> pdb=" O   ARG A 246 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   ARG A 246 " --> pdb=" O  ASER A 241 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 34
      removed outlier: 4.434A  pdb=" N   GLU B  60 " --> pdb=" O   ILE B  10 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   THR B  12 " --> pdb=" O   GLU B  60 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 236 through 237
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 34
      removed outlier: 6.782A  pdb=" N   HIS C   6 " --> pdb=" O   HIS C  56 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   CYS C  58 " --> pdb=" O   HIS C   6 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ILE C   8 " --> pdb=" O   CYS C  58 " (cutoff:3.500A)
      removed outlier: 8.496A  pdb=" N   GLU C  60 " --> pdb=" O   ILE C   8 " (cutoff:3.500A)
      removed outlier: 8.392A  pdb=" N   ILE C  10 " --> pdb=" O   GLU C  60 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 236 through 241
      removed outlier: 3.915A  pdb=" N   ARG C 250 " --> pdb=" O  AARG C 237 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   TYR C 239 " --> pdb=" O   ALA C 248 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   ALA C 248 " --> pdb=" O   TYR C 239 " (cutoff:3.500A)
      removed outlier: 7.862A  pdb=" N   SER C 241 " --> pdb=" O   ARG C 246 " (cutoff:3.500A)
      removed outlier: 5.447A  pdb=" N   ARG C 246 " --> pdb=" O   SER C 241 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 34
      removed outlier: 6.664A  pdb=" N   HIS D   6 " --> pdb=" O   HIS D  56 " (cutoff:3.500A)
      removed outlier: 7.956A  pdb=" N   CYS D  58 " --> pdb=" O   HIS D   6 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   ILE D   8 " --> pdb=" O   CYS D  58 " (cutoff:3.500A)
      removed outlier: 8.576A  pdb=" N   GLU D  60 " --> pdb=" O   ILE D   8 " (cutoff:3.500A)
      removed outlier: 8.372A  pdb=" N   ILE D  10 " --> pdb=" O   GLU D  60 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 236 through 237

    680 hydrogen bonds defined for protein.
    2003 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      222 hydrogen bonds
      438 hydrogen bond angles
      0 basepair planarities
      87 basepair parallelities
      150 stacking parallelities
  Total time for adding SS restraints: 2.65

  Time building geometry restraints manager: 1.73 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: 3485
        1.34 -     1.46: 5386
        1.46 -     1.58: 6336
        1.58 -     1.69: 475
        1.69 -     1.81: 84
  Bond restraints: 15766
  Sorted by residual:
  bond pdb=" P     A F 110 "
       pdb=" OP2   A F 110 "
    ideal  model  delta    sigma   weight residual
    1.485  1.560 -0.075 2.00e-02 2.50e+03 1.41e+01
  bond pdb=" P     A F 110 "
       pdb=" OP1   A F 110 "
    ideal  model  delta    sigma   weight residual
    1.485  1.559 -0.074 2.00e-02 2.50e+03 1.37e+01
  bond pdb=" P     A F 110 "
       pdb=" O5'   A F 110 "
    ideal  model  delta    sigma   weight residual
    1.593  1.633 -0.040 1.50e-02 4.44e+03 7.07e+00
  bond pdb=" C   THR D 235 "
       pdb=" N   PRO D 236 "
    ideal  model  delta    sigma   weight residual
    1.329  1.358 -0.029 1.20e-02 6.94e+03 5.98e+00
  bond pdb=" C   ILE A 201 "
       pdb=" N   PRO A 202 "
    ideal  model  delta    sigma   weight residual
    1.333  1.357 -0.024 1.01e-02 9.80e+03 5.58e+00
  ... (remaining 15761 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 19710
        2.10 -     4.19: 2427
        4.19 -     6.29: 216
        6.29 -     8.38: 14
        8.38 -    10.48: 2
  Bond angle restraints: 22369
  Sorted by residual:
  angle pdb=" O3'  DC G  15 "
        pdb=" P    DC G  16 "
        pdb=" O5'  DC G  16 "
      ideal   model   delta    sigma   weight residual
     104.00   94.68    9.32 1.50e+00 4.44e-01 3.86e+01
  angle pdb=" O3'   U F 159 "
        pdb=" P     U F 160 "
        pdb=" O5'   U F 160 "
      ideal   model   delta    sigma   weight residual
     104.00   95.77    8.23 1.50e+00 4.44e-01 3.01e+01
  angle pdb=" O3'  DC G  23 "
        pdb=" P    DC G  24 "
        pdb=" O5'  DC G  24 "
      ideal   model   delta    sigma   weight residual
     104.00   96.79    7.21 1.50e+00 4.44e-01 2.31e+01
  angle pdb=" CG  MET D 108 "
        pdb=" SD  MET D 108 "
        pdb=" CE  MET D 108 "
      ideal   model   delta    sigma   weight residual
     100.90  111.38  -10.48 2.20e+00 2.07e-01 2.27e+01
  angle pdb=" O3'   U F 168 "
        pdb=" P     G F 169 "
        pdb=" O5'   G F 169 "
      ideal   model   delta    sigma   weight residual
     104.00  111.04   -7.04 1.50e+00 4.44e-01 2.20e+01
  ... (remaining 22364 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.07: 8729
       34.07 -    68.13: 676
       68.13 -   102.20: 52
      102.20 -   136.26: 0
      136.26 -   170.33: 1
  Dihedral angle restraints: 9458
    sinusoidal: 5803
      harmonic: 3655
  Sorted by residual:
  dihedral pdb=" C5'   C E  95 "
           pdb=" C4'   C E  95 "
           pdb=" C3'   C E  95 "
           pdb=" O3'   C E  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   86.35   60.65     1      8.00e+00 1.56e-02 7.65e+01
  dihedral pdb=" O4'   C E  95 "
           pdb=" C4'   C E  95 "
           pdb=" C3'   C E  95 "
           pdb=" C2'   C E  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -32.53   56.53     1      8.00e+00 1.56e-02 6.73e+01
  dihedral pdb=" O4'   U F 159 "
           pdb=" C1'   U F 159 "
           pdb=" N1    U F 159 "
           pdb=" C2    U F 159 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   61.67  170.33     1      1.70e+01 3.46e-03 6.60e+01
  ... (remaining 9455 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.148: 2386
       0.148 -    0.297: 199
       0.297 -    0.445: 0
       0.445 -    0.594: 1
       0.594 -    0.742: 5
  Chirality restraints: 2591
  Sorted by residual:
  chirality pdb=" P     A F 110 "
            pdb=" OP1   A F 110 "
            pdb=" OP2   A F 110 "
            pdb=" O5'   A F 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -3.15   -0.74 2.00e-01 2.50e+01 1.38e+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   -0.65 2.00e-01 2.50e+01 1.05e+01
  chirality pdb=" P    DG I   5 "
            pdb=" OP1  DG I   5 "
            pdb=" OP2  DG I   5 "
            pdb=" O5'  DG I   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.96   -0.62 2.00e-01 2.50e+01 9.57e+00
  ... (remaining 2588 not shown)

  Planarity restraints: 2007
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F 157 "   -0.037 2.00e-02 2.50e+03   1.49e-02 6.10e+00
        pdb=" N9    A F 157 "    0.022 2.00e-02 2.50e+03
        pdb=" C8    A F 157 "    0.008 2.00e-02 2.50e+03
        pdb=" N7    A F 157 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    A F 157 "    0.005 2.00e-02 2.50e+03
        pdb=" C6    A F 157 "   -0.010 2.00e-02 2.50e+03
        pdb=" N6    A F 157 "   -0.014 2.00e-02 2.50e+03
        pdb=" N1    A F 157 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    A F 157 "    0.007 2.00e-02 2.50e+03
        pdb=" N3    A F 157 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    A F 157 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA J  35 "   -0.031 2.00e-02 2.50e+03   1.31e-02 4.72e+00
        pdb=" N9   DA J  35 "    0.027 2.00e-02 2.50e+03
        pdb=" C8   DA J  35 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DA J  35 "    0.000 2.00e-02 2.50e+03
        pdb=" C5   DA J  35 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DA J  35 "   -0.005 2.00e-02 2.50e+03
        pdb=" N6   DA J  35 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DA J  35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA J  35 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DA J  35 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DA J  35 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U F 168 "   -0.024 2.00e-02 2.50e+03   1.35e-02 4.11e+00
        pdb=" N1    U F 168 "    0.031 2.00e-02 2.50e+03
        pdb=" C2    U F 168 "    0.003 2.00e-02 2.50e+03
        pdb=" O2    U F 168 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    U F 168 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    U F 168 "   -0.005 2.00e-02 2.50e+03
        pdb=" O4    U F 168 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    U F 168 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    U F 168 "    0.004 2.00e-02 2.50e+03
  ... (remaining 2004 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.27: 9
        2.27 -     2.92: 5260
        2.92 -     3.58: 22496
        3.58 -     4.24: 40738
        4.24 -     4.90: 62012
  Nonbonded interactions: 130515
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 241 "
            pdb=" P    DC H  18 "
     model   vdw
     1.607 3.400
  nonbonded pdb=" OG BSER A 241 "
            pdb=" P  B DA J  29 "
     model   vdw
     1.608 3.400
  nonbonded pdb="MG    MG B 401 "
            pdb=" O   HOH B 502 "
     model   vdw
     2.065 2.170
  nonbonded pdb="MG    MG B 401 "
            pdb=" O   HOH B 501 "
     model   vdw
     2.072 2.170
  nonbonded pdb=" OE1 GLU B  60 "
            pdb="MG    MG B 401 "
     model   vdw
     2.086 2.170
  ... (remaining 130510 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 138 or resid 140 through 236 or (resid 238 throu \ 
gh 239 and (name N or name CA or name C or name O or name CB )) or resid 248 thr \ 
ough 322))
  selection = (chain 'B' and (resid 5 through 138 or resid 140 through 236 or resid 238 throug \ 
h 322))
  selection = (chain 'C' and (resid 5 through 138 or resid 140 through 236 or (resid 238 throu \ 
gh 239 and (name N or name CA or name C or name O or name CB )) or resid 248 thr \ 
ough 322))
  selection = (chain 'D' and (resid 5 through 138 or resid 140 through 236 or (resid 238 throu \ 
gh 248 and (name N or name CA or name C or name O or name CB )) or resid 249 thr \ 
ough 322))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.99
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:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.070
  Set scattering table:                    0.020
  Process input model:                     17.880
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.040
  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:8.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
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   0.075  15766  Z= 0.477
  Angle     :  1.362  10.479  22369  Z= 0.878
  Chirality :  0.080   0.742   2591
  Planarity :  0.003   0.029   2007
  Dihedral  : 20.155 170.329   7094
  Min Nonbonded Distance : 1.607

Molprobity Statistics.
  All-atom Clashscore : 0.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  2.44 %
    Favored  : 96.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.19), residues: 1258
  helix: -0.66 (0.15), residues: 794
  sheet: -1.40 (0.34), residues: 153
  loop : -1.36 (0.29), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.002   ARG C 300 
 TYR   0.017   0.002   TYR B  78 
 PHE   0.017   0.003   PHE D 231 
 TRP   0.022   0.006   TRP B 169 
 HIS   0.006   0.002   HIS D 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00793 (15766)
  covalent geometry    : angle       1.36173 (22369)
  hydrogen bonds       : bond        0.20347 (  902)
  hydrogen bonds       : angle       6.71794 ( 2441)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.494 
Fit side-chains
REVERT: A   66 MET cc_start: 0.8236 (ppp) cc_final: 0.7997 (pp-130)
REVERT: B  273 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8471 (mttm)
REVERT: C  298 MET cc_start: 0.8201 (tpt) cc_final: 0.7879 (tpt)
REVERT: D  287 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8324 (t0)
  outliers start: 10
  outliers final: 0
  residues processed: 112
  average time/residue: 0.9119
  time to fit residues: 108.7977
Evaluate side-chains
  77 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  273 LYS
Chi-restraints excluded: chain D residue  287 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.6980
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 139 GLN
C  93 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 = 0.3277 r_free = 0.3277 target = 0.091115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.057983 restraints weight = 84254.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.2668 rms_B_bonded: 3.24
r_work: 0.2434 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2434
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2444
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2444 r_free = 0.2444    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2444 r_free = 0.2444    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2444
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15766  Z= 0.158
  Angle     :  0.606   7.501  22369  Z= 0.340
  Chirality :  0.039   0.204   2591
  Planarity :  0.004   0.053   2007
  Dihedral  : 22.134 162.320   4647
  Min Nonbonded Distance : 1.831

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  5.96 %
    Favored  : 93.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.23), residues: 1258
  helix:  2.01 (0.17), residues: 797
  sheet: -0.88 (0.36), residues: 165
  loop : -0.82 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 129 
 TYR   0.019   0.002   TYR A  74 
 PHE   0.012   0.002   PHE B 280 
 TRP   0.022   0.002   TRP D 276 
 HIS   0.006   0.001   HIS D 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (15766)
  covalent geometry    : angle       0.60642 (22369)
  hydrogen bonds       : bond        0.05372 (  902)
  hydrogen bonds       : angle       4.03130 ( 2441)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.416 
Fit side-chains
REVERT: D  191 MET cc_start: 0.9040 (mmm) cc_final: 0.8714 (mtp)
REVERT: D  275 GLU cc_start: 0.8289 (pm20) cc_final: 0.8086 (pm20)
REVERT: D  287 ASN cc_start: 0.9030 (t0) cc_final: 0.8718 (m110)
  outliers start: 6
  outliers final: 2
  residues processed: 83
  average time/residue: 0.7379
  time to fit residues: 66.3837
Evaluate side-chains
  70 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain D residue   38 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 126 optimal weight:    7.9990
   chunk 67 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 106 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 150 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.087848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.054593 restraints weight = 87493.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.2645 rms_B_bonded: 3.33
r_work: 0.2408 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.2408
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2420
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2420 r_free = 0.2420    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2420 r_free = 0.2420    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2420
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  15766  Z= 0.255
  Angle     :  0.589   6.118  22369  Z= 0.327
  Chirality :  0.041   0.203   2591
  Planarity :  0.005   0.042   2007
  Dihedral  : 22.274 162.868   4641
  Min Nonbonded Distance : 1.856

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  6.65 %
    Favored  : 92.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.24), residues: 1258
  helix:  2.33 (0.18), residues: 803
  sheet: -0.73 (0.37), residues: 165
  loop : -0.70 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 129 
 TYR   0.024   0.002   TYR A  74 
 PHE   0.015   0.002   PHE C 112 
 TRP   0.020   0.002   TRP C  46 
 HIS   0.005   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00576 (15766)
  covalent geometry    : angle       0.58854 (22369)
  hydrogen bonds       : bond        0.05540 (  902)
  hydrogen bonds       : angle       3.81262 ( 2441)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.411 
Fit side-chains
REVERT: D  191 MET cc_start: 0.8938 (mmm) cc_final: 0.8683 (mtp)
REVERT: D  287 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8777 (m110)
  outliers start: 9
  outliers final: 3
  residues processed: 72
  average time/residue: 0.7001
  time to fit residues: 54.8451
Evaluate side-chains
  67 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain D residue  287 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 117 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9980
   chunk 128 optimal weight:    5.9990
   chunk 116 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 85 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 104 optimal weight:    0.0870
   chunk 19 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.6758

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.091462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.058651 restraints weight = 104984.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.2689 rms_B_bonded: 3.48
r_work: 0.2450 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2450
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2459
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2459 r_free = 0.2459    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2459 r_free = 0.2459    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
r_final: 0.2459
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15766  Z= 0.123
  Angle     :  0.513   6.248  22369  Z= 0.286
  Chirality :  0.035   0.188   2591
  Planarity :  0.004   0.039   2007
  Dihedral  : 22.159 164.366   4641
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  7.04 %
    Favored  : 92.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.31 (0.24), residues: 1258
  helix:  2.66 (0.18), residues: 805
  sheet: -0.34 (0.40), residues: 147
  loop : -0.63 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 129 
 TYR   0.017   0.001   TYR A  74 
 PHE   0.009   0.001   PHE A 280 
 TRP   0.013   0.002   TRP D 276 
 HIS   0.004   0.001   HIS B 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (15766)
  covalent geometry    : angle       0.51286 (22369)
  hydrogen bonds       : bond        0.04108 (  902)
  hydrogen bonds       : angle       3.59075 ( 2441)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.456 
Fit side-chains
REVERT: D   54 HIS cc_start: 0.8711 (m90) cc_final: 0.8480 (m90)
REVERT: D  191 MET cc_start: 0.8917 (mmm) cc_final: 0.8669 (mtp)
REVERT: D  275 GLU cc_start: 0.8204 (pm20) cc_final: 0.7971 (pm20)
REVERT: D  287 ASN cc_start: 0.9116 (t0) cc_final: 0.8849 (m110)
REVERT: D  299 MET cc_start: 0.9081 (mtp) cc_final: 0.8791 (mtp)
  outliers start: 5
  outliers final: 2
  residues processed: 80
  average time/residue: 0.6665
  time to fit residues: 58.2859
Evaluate side-chains
  70 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  284 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 107 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 67 optimal weight:    6.9990
   chunk 130 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 96 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    3.1788

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.087518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.054565 restraints weight = 100718.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.2602 rms_B_bonded: 3.44
r_work: 0.2360 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2360
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2414
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2414 r_free = 0.2414    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2414 r_free = 0.2414    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
r_final: 0.2414
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053  15766  Z= 0.298
  Angle     :  0.579   5.873  22369  Z= 0.317
  Chirality :  0.042   0.202   2591
  Planarity :  0.004   0.041   2007
  Dihedral  : 22.235 163.133   4641
  Min Nonbonded Distance : 1.877

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  7.43 %
    Favored  : 91.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.18 (0.24), residues: 1258
  helix:  2.59 (0.18), residues: 804
  sheet: -0.68 (0.37), residues: 163
  loop : -0.56 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 129 
 TYR   0.016   0.002   TYR D 215 
 PHE   0.016   0.002   PHE C 112 
 TRP   0.015   0.002   TRP A  46 
 HIS   0.004   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00678 (15766)
  covalent geometry    : angle       0.57945 (22369)
  hydrogen bonds       : bond        0.05185 (  902)
  hydrogen bonds       : angle       3.70404 ( 2441)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.458 
Fit side-chains
REVERT: D  191 MET cc_start: 0.8927 (mmm) cc_final: 0.8706 (mtp)
REVERT: D  287 ASN cc_start: 0.9060 (t0) cc_final: 0.8808 (m110)
  outliers start: 8
  outliers final: 2
  residues processed: 69
  average time/residue: 0.7304
  time to fit residues: 55.0255
Evaluate side-chains
  66 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  284 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 122 optimal weight:    0.6980
   chunk 120 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9980
   chunk 110 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.090691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.058348 restraints weight = 76385.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.2681 rms_B_bonded: 3.09
r_work: 0.2454 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2454
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2464
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2464 r_free = 0.2464    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2464 r_free = 0.2464    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
r_final: 0.2464
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15766  Z= 0.140
  Angle     :  0.512   6.134  22369  Z= 0.283
  Chirality :  0.035   0.188   2591
  Planarity :  0.004   0.041   2007
  Dihedral  : 22.175 164.510   4641
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  7.92 %
    Favored  : 91.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.47 (0.24), residues: 1258
  helix:  2.77 (0.18), residues: 805
  sheet: -0.47 (0.39), residues: 161
  loop : -0.40 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 129 
 TYR   0.012   0.001   TYR C 307 
 PHE   0.010   0.001   PHE A 280 
 TRP   0.013   0.002   TRP A  46 
 HIS   0.004   0.001   HIS B 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (15766)
  covalent geometry    : angle       0.51152 (22369)
  hydrogen bonds       : bond        0.04151 (  902)
  hydrogen bonds       : angle       3.52231 ( 2441)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.462 
Fit side-chains
REVERT: D  191 MET cc_start: 0.8915 (mmm) cc_final: 0.8668 (mtp)
REVERT: D  275 GLU cc_start: 0.8174 (pm20) cc_final: 0.7938 (pm20)
REVERT: D  287 ASN cc_start: 0.9124 (t0) cc_final: 0.8854 (m110)
  outliers start: 7
  outliers final: 2
  residues processed: 75
  average time/residue: 0.6360
  time to fit residues: 52.5739
Evaluate side-chains
  71 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 69
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  284 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 138 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 86 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9980
   chunk 102 optimal weight:    7.9990
   chunk 79 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.3586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.090032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.057505 restraints weight = 80793.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.2665 rms_B_bonded: 3.15
r_work: 0.2434 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2434
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2487
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2487 r_free = 0.2487    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2487 r_free = 0.2487    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
r_final: 0.2487
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  15766  Z= 0.162
  Angle     :  0.508   5.763  22369  Z= 0.281
  Chirality :  0.036   0.189   2591
  Planarity :  0.004   0.040   2007
  Dihedral  : 22.169 165.574   4641
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  8.11 %
    Favored  : 91.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.55 (0.24), residues: 1258
  helix:  2.83 (0.18), residues: 805
  sheet: -0.50 (0.38), residues: 163
  loop : -0.30 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 129 
 TYR   0.021   0.001   TYR A  74 
 PHE   0.011   0.002   PHE D 112 
 TRP   0.013   0.002   TRP A  46 
 HIS   0.004   0.001   HIS D 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (15766)
  covalent geometry    : angle       0.50756 (22369)
  hydrogen bonds       : bond        0.04280 (  902)
  hydrogen bonds       : angle       3.50263 ( 2441)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.456 
Fit side-chains
REVERT: D  191 MET cc_start: 0.8919 (mmm) cc_final: 0.8672 (mtp)
REVERT: D  275 GLU cc_start: 0.8206 (pm20) cc_final: 0.7978 (pm20)
REVERT: D  287 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8751 (m110)
  outliers start: 6
  outliers final: 2
  residues processed: 73
  average time/residue: 0.6733
  time to fit residues: 53.9204
Evaluate side-chains
  72 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain D residue  287 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 106 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 133 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 110 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 96 optimal weight:    7.9990
   overall best weight:    1.0782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.090607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.058053 restraints weight = 80406.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.2681 rms_B_bonded: 3.14
r_work: 0.2451 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2451
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2461
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2461 r_free = 0.2461    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2461 r_free = 0.2461    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
r_final: 0.2461
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15766  Z= 0.142
  Angle     :  0.498   6.012  22369  Z= 0.275
  Chirality :  0.035   0.191   2591
  Planarity :  0.004   0.038   2007
  Dihedral  : 22.159 165.473   4641
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  8.02 %
    Favored  : 91.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.63 (0.24), residues: 1258
  helix:  2.88 (0.18), residues: 805
  sheet: -0.28 (0.40), residues: 149
  loop : -0.37 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 129 
 TYR   0.020   0.001   TYR A  74 
 PHE   0.011   0.001   PHE D 112 
 TRP   0.013   0.001   TRP A  46 
 HIS   0.003   0.001   HIS D 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (15766)
  covalent geometry    : angle       0.49784 (22369)
  hydrogen bonds       : bond        0.04105 (  902)
  hydrogen bonds       : angle       3.49064 ( 2441)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.427 
Fit side-chains
REVERT: D  144 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8737 (mtp)
REVERT: D  191 MET cc_start: 0.8918 (mmm) cc_final: 0.8687 (mtp)
REVERT: D  275 GLU cc_start: 0.8210 (pm20) cc_final: 0.7992 (pm20)
REVERT: D  287 ASN cc_start: 0.9089 (OUTLIER) cc_final: 0.8755 (m110)
  outliers start: 5
  outliers final: 2
  residues processed: 71
  average time/residue: 0.6499
  time to fit residues: 50.6215
Evaluate side-chains
  72 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain D residue  144 MET
Chi-restraints excluded: chain D residue  287 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 125 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 113 optimal weight:    0.7980
   chunk 103 optimal weight:    6.9990
   chunk 85 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 140 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
C 322 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.091274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.058839 restraints weight = 77870.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.2698 rms_B_bonded: 3.11
r_work: 0.2469 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2469
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2479
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2479 r_free = 0.2479    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2479 r_free = 0.2479    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
r_final: 0.2479
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15766  Z= 0.130
  Angle     :  0.490   6.936  22369  Z= 0.271
  Chirality :  0.035   0.195   2591
  Planarity :  0.004   0.037   2007
  Dihedral  : 22.151 166.072   4641
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  8.70 %
    Favored  : 90.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.71 (0.24), residues: 1258
  helix:  2.92 (0.18), residues: 805
  sheet: -0.22 (0.40), residues: 149
  loop : -0.31 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 129 
 TYR   0.019   0.001   TYR A  74 
 PHE   0.011   0.001   PHE D 112 
 TRP   0.012   0.001   TRP A  46 
 HIS   0.003   0.001   HIS D 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (15766)
  covalent geometry    : angle       0.49009 (22369)
  hydrogen bonds       : bond        0.03966 (  902)
  hydrogen bonds       : angle       3.45871 ( 2441)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.467 
Fit side-chains
REVERT: D  144 MET cc_start: 0.9057 (tpp) cc_final: 0.8810 (mtp)
REVERT: D  191 MET cc_start: 0.8917 (mmm) cc_final: 0.8678 (mtp)
REVERT: D  275 GLU cc_start: 0.8214 (pm20) cc_final: 0.8000 (pm20)
REVERT: D  287 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8756 (m110)
  outliers start: 4
  outliers final: 2
  residues processed: 71
  average time/residue: 0.6788
  time to fit residues: 52.8672
Evaluate side-chains
  72 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain D residue  287 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 104 optimal weight:    0.8980
   chunk 106 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   chunk 43 optimal weight:    0.2980
   chunk 10 optimal weight:    0.9980
   chunk 24 optimal weight:    9.9990
   chunk 127 optimal weight:    8.9990
   chunk 125 optimal weight:    5.9990
   overall best weight:    1.0182

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.091369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.059125 restraints weight = 68562.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.2705 rms_B_bonded: 2.96
r_work: 0.2482 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2482
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2490
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2490 r_free = 0.2490    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2490 r_free = 0.2490    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
r_final: 0.2490
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  15766  Z= 0.138
  Angle     :  0.493   7.555  22369  Z= 0.272
  Chirality :  0.035   0.196   2591
  Planarity :  0.004   0.041   2007
  Dihedral  : 22.138 166.562   4641
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  8.70 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.78 (0.24), residues: 1258
  helix:  2.98 (0.18), residues: 805
  sheet: -0.19 (0.40), residues: 149
  loop : -0.28 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 129 
 TYR   0.019   0.001   TYR A  74 
 PHE   0.011   0.001   PHE D 112 
 TRP   0.012   0.001   TRP A  46 
 HIS   0.003   0.001   HIS D 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (15766)
  covalent geometry    : angle       0.49267 (22369)
  hydrogen bonds       : bond        0.03972 (  902)
  hydrogen bonds       : angle       3.44510 ( 2441)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.451 
Fit side-chains
REVERT: D  191 MET cc_start: 0.8919 (mmm) cc_final: 0.8685 (mtp)
REVERT: D  275 GLU cc_start: 0.8246 (pm20) cc_final: 0.8038 (pm20)
REVERT: D  287 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8765 (m110)
  outliers start: 3
  outliers final: 2
  residues processed: 72
  average time/residue: 0.6864
  time to fit residues: 53.9161
Evaluate side-chains
  70 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain D residue  287 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 123 optimal weight:    0.0070
   chunk 121 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 138 optimal weight:    5.9990
   chunk 110 optimal weight:    0.5980
   chunk 60 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.0802

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

Flipped N/Q/H residues before XYZ refinement:
C 322 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.091418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.059065 restraints weight = 73579.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.2701 rms_B_bonded: 3.04
r_work: 0.2475 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2475
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2485
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2485 r_free = 0.2485    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2485 r_free = 0.2485    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2485
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15766  Z= 0.140
  Angle     :  0.489   5.914  22369  Z= 0.270
  Chirality :  0.035   0.196   2591
  Planarity :  0.004   0.040   2007
  Dihedral  : 22.134 166.408   4641
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  8.90 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.79 (0.24), residues: 1258
  helix:  2.97 (0.18), residues: 805
  sheet: -0.18 (0.40), residues: 149
  loop : -0.25 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 129 
 TYR   0.019   0.001   TYR A  74 
 PHE   0.011   0.001   PHE D 112 
 TRP   0.012   0.001   TRP A  46 
 HIS   0.003   0.001   HIS D 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (15766)
  covalent geometry    : angle       0.48920 (22369)
  hydrogen bonds       : bond        0.03968 (  902)
  hydrogen bonds       : angle       3.43733 ( 2441)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4381.82 seconds
wall clock time: 75 minutes 30.39 seconds (4530.39 seconds total)