Starting phenix.real_space_refine
on Sun Apr  5 00:17:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9p87_71367/04_2026/9p87_71367.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9p87_71367/04_2026/9p87_71367.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9p87_71367/04_2026/9p87_71367.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9p87_71367/04_2026/9p87_71367.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9p87_71367/04_2026/9p87_71367.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9p87_71367/04_2026/9p87_71367.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.028
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: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    4071      2.51       5
     N    1109      2.21       5
     O    1133      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6349
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2445
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 50}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 163
          Unresolved non-hydrogen angles: 204
          Unresolved non-hydrogen dihedrals: 124
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 8, 'GLN:plan1': 5, 'ARG:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 120
    Chain: "G"
      Number of atoms: 385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 385
          Classifications: {'peptide': 59}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 4, 'TRANS': 54}
          Unresolved non-hydrogen bonds: 68
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "L"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 58
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
    Chain: "R"
      Number of atoms: 1907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 1907
          Classifications: {'peptide': 290}
          Incomplete info: {'truncation_to_alanine': 126}
          Link IDs: {'PTRANS': 10, 'TRANS': 279}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 407
          Unresolved non-hydrogen angles: 521
          Unresolved non-hydrogen dihedrals: 320
          Unresolved non-hydrogen chiralities: 56
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'ASN:plan1': 7, 'TYR:plan': 3, 'PHE:plan': 5, 'HIS:plan': 4, 'ARG:plan': 9, 'GLN:plan1': 5}
          Unresolved non-hydrogen planarities: 191
    Chain: "A"
      Number of atoms: 1554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1554
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 72}
          Link IDs: {'PTRANS': 5, 'TRANS': 213}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 272
          Unresolved non-hydrogen angles: 339
          Unresolved non-hydrogen dihedrals: 210
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLU:plan': 16, 'ARG:plan': 11, 'ASN:plan1': 6, 'GLN:plan1': 5, 'ASP:plan': 11, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 202
  Time building chain proxies: 1.60, per 1000 atoms: 0.25
  Number of scatterers: 6349
  At special positions: 0
  Unit cell: (71.552, 97.344, 131.456, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1133      8.00
     N    1109      7.00
     C    4071      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 141 " - pdb=" SG  CYS R 224 " distance=2.03

  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: 0.71
  Conformation dependent library (CDL) restraints added in 267.7 milliseconds
  

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1732

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 9 sheets defined
      47.5% alpha, 18.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 4.255A  pdb=" N   GLN G  11 " --> pdb=" O   ALA G   7 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 59 through 88
    Processing helix  chain 'R' and resid 101 through 127
      Proline residue:  R 121  - end of helix
    Processing helix  chain 'R' and resid 139 through 172
      removed outlier: 4.336A  pdb=" N   GLY R 143 " --> pdb=" O   ALA R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 179
    Processing helix  chain 'R' and resid 181 through 206
      removed outlier: 3.777A  pdb=" N   ALA R 197 " --> pdb=" O   TRP R 193 " (cutoff:3.500A)
      Proline residue:  R 202  - end of helix
    Processing helix  chain 'R' and resid 229 through 245
    Processing helix  chain 'R' and resid 245 through 271
    Processing helix  chain 'R' and resid 281 through 329
      Proline residue:  R 318  - end of helix
    Processing helix  chain 'R' and resid 335 through 368
      removed outlier: 3.668A  pdb=" N   SER R 357 " --> pdb=" O   PHE R 353 " (cutoff:3.500A)
      Proline residue:  R 361  - end of helix
      removed outlier: 3.729A  pdb=" N   SER R 368 " --> pdb=" O   TYR R 364 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 368 through 374
    Processing helix  chain 'A' and resid 15 through 39
      removed outlier: 4.042A  pdb=" N   GLU A  39 " --> pdb=" O   ASP A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 63
    Processing helix  chain 'A' and resid 212 through 221
      removed outlier: 4.429A  pdb=" N   ILE A 217 " --> pdb=" O   ARG A 214 " (cutoff:3.500A)
      removed outlier: 5.774A  pdb=" N   HIS A 218 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 260
      removed outlier: 3.698A  pdb=" N   GLU A 250 " --> pdb=" O   ASN A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 265
      removed outlier: 3.649A  pdb=" N   GLN A 265 " --> pdb=" O   PRO A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 286
    Processing helix  chain 'A' and resid 301 through 315
    Processing helix  chain 'A' and resid 335 through 356
      removed outlier: 3.644A  pdb=" N   TYR A 356 " --> pdb=" O   ASN A 352 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.761A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.627A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 5.687A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.044A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.536A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.702A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.630A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'R' and resid 207 through 211
    Processing sheet with id=AA9, first strand: chain 'A' and resid 190 through 196
      removed outlier: 6.176A  pdb=" N   LEU A  40 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   VAL A 204 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   LEU A  42 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   SER A 225 " --> pdb=" O   LYS A  41 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   ILE A 226 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   PHE A 272 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   PHE A 228 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 7.456A  pdb=" N   ASN A 274 " --> pdb=" O   PHE A 228 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   VAL A 230 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   VAL A 269 " --> pdb=" O   TYR A 325 " (cutoff:3.500A)
      removed outlier: 8.190A  pdb=" N   HIS A 327 " --> pdb=" O   VAL A 269 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LEU A 271 " --> pdb=" O   HIS A 327 " (cutoff:3.500A)

    405 hydrogen bonds defined for protein.
    1179 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.97

  Time building geometry restraints manager: 0.89 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 1366
        1.33 -     1.45: 1484
        1.45 -     1.57: 3580
        1.57 -     1.69: 0
        1.69 -     1.82: 51
  Bond restraints: 6481
  Sorted by residual:
  bond pdb=" SD  MET A  59 "
       pdb=" CE  MET A  59 "
    ideal  model  delta    sigma   weight residual
    1.791  1.700  0.091 2.50e-02 1.60e+03 1.32e+01
  bond pdb=" N   ILE A 323 "
       pdb=" CA  ILE A 323 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 1.14e-02 7.69e+03 1.11e+01
  bond pdb=" N   ILE L  12 "
       pdb=" CA  ILE L  12 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.037 1.19e-02 7.06e+03 9.45e+00
  bond pdb=" N   TYR A 261 "
       pdb=" CA  TYR A 261 "
    ideal  model  delta    sigma   weight residual
    1.453  1.489 -0.035 1.16e-02 7.43e+03 9.20e+00
  bond pdb=" N   LYS A 322 "
       pdb=" CA  LYS A 322 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.035 1.31e-02 5.83e+03 7.33e+00
  ... (remaining 6476 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 8680
        1.90 -     3.81: 165
        3.81 -     5.71: 22
        5.71 -     7.61: 3
        7.61 -     9.51: 1
  Bond angle restraints: 8871
  Sorted by residual:
  angle pdb=" N   PRO A 318 "
        pdb=" CA  PRO A 318 "
        pdb=" CB  PRO A 318 "
      ideal   model   delta    sigma   weight residual
     103.25   99.38    3.87 1.05e+00 9.07e-01 1.36e+01
  angle pdb=" C   ARG L   9 "
        pdb=" CA  ARG L   9 "
        pdb=" CB  ARG L   9 "
      ideal   model   delta    sigma   weight residual
     109.67  103.74    5.93 1.65e+00 3.67e-01 1.29e+01
  angle pdb=" CA  PRO R 361 "
        pdb=" N   PRO R 361 "
        pdb=" CD  PRO R 361 "
      ideal   model   delta    sigma   weight residual
     112.00  107.08    4.92 1.40e+00 5.10e-01 1.23e+01
  angle pdb=" CA  LYS A 322 "
        pdb=" C   LYS A 322 "
        pdb=" O   LYS A 322 "
      ideal   model   delta    sigma   weight residual
     121.81  118.09    3.72 1.18e+00 7.18e-01 9.96e+00
  angle pdb=" CA  ILE L  12 "
        pdb=" C   ILE L  12 "
        pdb=" O   ILE L  12 "
      ideal   model   delta    sigma   weight residual
     121.36  118.01    3.35 1.10e+00 8.26e-01 9.27e+00
  ... (remaining 8866 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.98: 3361
       16.98 -    33.95: 282
       33.95 -    50.93: 95
       50.93 -    67.91: 19
       67.91 -    84.89: 5
  Dihedral angle restraints: 3762
    sinusoidal: 1098
      harmonic: 2664
  Sorted by residual:
  dihedral pdb=" CA  TYR A 356 "
           pdb=" C   TYR A 356 "
           pdb=" N   ASN A 357 "
           pdb=" CA  ASN A 357 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.06   19.94     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" C   ARG L   9 "
           pdb=" N   ARG L   9 "
           pdb=" CA  ARG L   9 "
           pdb=" CB  ARG L   9 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.31   -9.29     0      2.50e+00 1.60e-01 1.38e+01
  dihedral pdb=" CA  TRP B 339 "
           pdb=" C   TRP B 339 "
           pdb=" N   ASN B 340 "
           pdb=" CA  ASN B 340 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.73   17.27     0      5.00e+00 4.00e-02 1.19e+01
  ... (remaining 3759 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 880
       0.062 -    0.123: 171
       0.123 -    0.184: 9
       0.184 -    0.246: 2
       0.246 -    0.307: 1
  Chirality restraints: 1063
  Sorted by residual:
  chirality pdb=" CA  ARG L   9 "
            pdb=" N   ARG L   9 "
            pdb=" C   ARG L   9 "
            pdb=" CB  ARG L   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CG  LEU R 157 "
            pdb=" CB  LEU R 157 "
            pdb=" CD1 LEU R 157 "
            pdb=" CD2 LEU R 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  ILE A 323 "
            pdb=" N   ILE A 323 "
            pdb=" C   ILE A 323 "
            pdb=" CB  ILE A 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.24e-01
  ... (remaining 1060 not shown)

  Planarity restraints: 1136
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 360 "   -0.071 5.00e-02 4.00e+02   1.05e-01 1.77e+01
        pdb=" N   PRO R 361 "    0.182 5.00e-02 4.00e+02
        pdb=" CA  PRO R 361 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO R 361 "   -0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.038 5.00e-02 4.00e+02   5.71e-02 5.21e+00
        pdb=" N   PRO B 236 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 225 "   -0.032 5.00e-02 4.00e+02   4.87e-02 3.79e+00
        pdb=" N   PRO R 226 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO R 226 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO R 226 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1133 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 472
        2.74 -     3.28: 6311
        3.28 -     3.82: 11009
        3.82 -     4.36: 12254
        4.36 -     4.90: 21538
  Nonbonded interactions: 51584
  Sorted by model distance:
  nonbonded pdb=" O   SER R 253 "
            pdb=" OG1 THR R 257 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" O   ARG B  22 "
            pdb=" NE2 GLN B 259 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OD2 ASP B 228 "
            pdb=" NZ  LYS A 215 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" O   GLY A  46 "
            pdb=" OG  SER A  50 "
     model   vdw
     2.268 3.040
  ... (remaining 51579 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=1.00 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:             1.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.540
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:6.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
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      :  0.004   0.091   6482  Z= 0.234
  Angle     :  0.652   9.514   8873  Z= 0.385
  Chirality :  0.047   0.307   1063
  Planarity :  0.005   0.105   1136
  Dihedral  : 15.682  84.886   2027
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 29.37 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.28), residues: 893
  helix:  2.38 (0.26), residues: 410
  sheet:  0.26 (0.44), residues: 140
  loop : -1.13 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  27 
 TYR   0.018   0.002   TYR R 144 
 PHE   0.022   0.002   PHE A  55 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 6481)
  covalent geometry    : angle       0.65198 ( 8871)
  SS BOND              : bond        0.00021 (    1)
  SS BOND              : angle       1.45060 (    2)
  hydrogen bonds       : bond        0.13106 (  405)
  hydrogen bonds       : angle       5.42999 ( 1179)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 83
  average time/residue: 0.5064
  time to fit residues: 44.2643
Evaluate side-chains
  81 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain A residue  356 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:   40.0000
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.205050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.155595 restraints weight = 7445.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 2.34
r_work: 0.3589 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3462 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.0971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6482  Z= 0.169
  Angle     :  0.587   8.084   8873  Z= 0.311
  Chirality :  0.044   0.135   1063
  Planarity :  0.005   0.069   1136
  Dihedral  :  4.862  48.078    967
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 24.18 %
    Favored  : 71.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.28), residues: 893
  helix:  2.51 (0.25), residues: 405
  sheet:  0.22 (0.42), residues: 161
  loop : -0.99 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  27 
 TYR   0.018   0.002   TYR R 145 
 PHE   0.017   0.002   PHE B 151 
 TRP   0.013   0.002   TRP B 339 
 HIS   0.002   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 6481)
  covalent geometry    : angle       0.58678 ( 8871)
  SS BOND              : bond        0.00028 (    1)
  SS BOND              : angle       1.59890 (    2)
  hydrogen bonds       : bond        0.04690 (  405)
  hydrogen bonds       : angle       4.53962 ( 1179)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 0.260 
Fit side-chains
REVERT: B   22 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6882 (mtt180)
REVERT: B   46 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7531 (ttm110)
REVERT: A   57 LYS cc_start: 0.7856 (pttt) cc_final: 0.7392 (tttt)
REVERT: A  202 ARG cc_start: 0.8314 (mtt-85) cc_final: 0.8090 (mtp-110)
REVERT: A  333 ASP cc_start: 0.6868 (t70) cc_final: 0.6594 (t0)
REVERT: A  356 TYR cc_start: 0.6246 (OUTLIER) cc_final: 0.5908 (p90)
  outliers start: 25
  outliers final: 9
  residues processed: 107
  average time/residue: 0.4844
  time to fit residues: 54.7505
Evaluate side-chains
  100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  356 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0980
   chunk 6 optimal weight:    2.9990
   chunk 39 optimal weight:   40.0000
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
A  58 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.194157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.136489 restraints weight = 7375.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 2.11
r_work: 0.3465 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6482  Z= 0.167
  Angle     :  0.578   7.642   8873  Z= 0.305
  Chirality :  0.044   0.146   1063
  Planarity :  0.005   0.061   1136
  Dihedral  :  4.598  43.463    966
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 23.80 %
    Favored  : 70.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.28), residues: 893
  helix:  2.46 (0.25), residues: 407
  sheet:  0.19 (0.41), residues: 160
  loop : -0.96 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  27 
 TYR   0.016   0.002   TYR R  70 
 PHE   0.018   0.002   PHE B 151 
 TRP   0.013   0.002   TRP B 339 
 HIS   0.002   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 6481)
  covalent geometry    : angle       0.57761 ( 8871)
  SS BOND              : bond        0.00030 (    1)
  SS BOND              : angle       0.85806 (    2)
  hydrogen bonds       : bond        0.04572 (  405)
  hydrogen bonds       : angle       4.42814 ( 1179)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 89
  time to evaluate  : 0.195 
Fit side-chains
REVERT: B   22 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.6395 (mtt180)
REVERT: B   46 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7348 (ttm110)
REVERT: A  202 ARG cc_start: 0.8236 (mtt-85) cc_final: 0.7908 (mtp-110)
REVERT: A  356 TYR cc_start: 0.6274 (OUTLIER) cc_final: 0.5671 (p90)
  outliers start: 29
  outliers final: 13
  residues processed: 107
  average time/residue: 0.4600
  time to fit residues: 51.9887
Evaluate side-chains
  100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue  206 THR
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain R residue  363 LEU
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  356 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 34 optimal weight:    0.0070
   chunk 50 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0670
   chunk 55 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0970
   chunk 24 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.5936

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.197435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.140062 restraints weight = 7345.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 2.12
r_work: 0.3481 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3362 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6482  Z= 0.111
  Angle     :  0.508   6.275   8873  Z= 0.268
  Chirality :  0.041   0.130   1063
  Planarity :  0.004   0.057   1136
  Dihedral  :  4.314  45.653    966
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 24.76 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.29), residues: 893
  helix:  2.71 (0.25), residues: 406
  sheet:  0.47 (0.42), residues: 148
  loop : -1.03 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  27 
 TYR   0.015   0.001   TYR R 339 
 PHE   0.013   0.001   PHE B 151 
 TRP   0.010   0.001   TRP B 339 
 HIS   0.002   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 6481)
  covalent geometry    : angle       0.50781 ( 8871)
  SS BOND              : bond        0.00198 (    1)
  SS BOND              : angle       0.99810 (    2)
  hydrogen bonds       : bond        0.03861 (  405)
  hydrogen bonds       : angle       4.17451 ( 1179)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.235 
Fit side-chains
REVERT: B   22 ARG cc_start: 0.6585 (OUTLIER) cc_final: 0.6304 (mtt180)
REVERT: B   46 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7387 (ttm110)
REVERT: B   96 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.8027 (ttm170)
REVERT: A   40 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7055 (tt)
REVERT: A  202 ARG cc_start: 0.8231 (mtt-85) cc_final: 0.7931 (mtp-110)
REVERT: A  333 ASP cc_start: 0.7625 (t0) cc_final: 0.7180 (t0)
REVERT: A  356 TYR cc_start: 0.6161 (OUTLIER) cc_final: 0.5465 (p90)
  outliers start: 27
  outliers final: 8
  residues processed: 111
  average time/residue: 0.4688
  time to fit residues: 55.0825
Evaluate side-chains
  98 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain R residue  363 LEU
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  356 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 81 optimal weight:   30.0000
   chunk 42 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 7 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 66 optimal weight:    8.9990
   chunk 70 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.194288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.137117 restraints weight = 7427.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 2.08
r_work: 0.3473 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3349 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6482  Z= 0.158
  Angle     :  0.568   7.379   8873  Z= 0.297
  Chirality :  0.044   0.133   1063
  Planarity :  0.004   0.056   1136
  Dihedral  :  4.514  46.060    966
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 25.72 %
    Favored  : 68.91 %
  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 are not related in a simple way.
  whole:  1.38 (0.29), residues: 893
  helix:  2.62 (0.25), residues: 406
  sheet:  0.39 (0.42), residues: 144
  loop : -0.99 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  27 
 TYR   0.015   0.001   TYR R 342 
 PHE   0.018   0.002   PHE B 151 
 TRP   0.014   0.002   TRP B  82 
 HIS   0.002   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 6481)
  covalent geometry    : angle       0.56794 ( 8871)
  SS BOND              : bond        0.00182 (    1)
  SS BOND              : angle       0.81603 (    2)
  hydrogen bonds       : bond        0.04334 (  405)
  hydrogen bonds       : angle       4.30599 ( 1179)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 91
  time to evaluate  : 0.237 
Fit side-chains
REVERT: B   46 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7440 (ttm110)
REVERT: B   96 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.8040 (ttm170)
REVERT: A   40 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7305 (tt)
REVERT: A  202 ARG cc_start: 0.8240 (mtt-85) cc_final: 0.7930 (mtp-110)
REVERT: A  333 ASP cc_start: 0.7703 (t0) cc_final: 0.7162 (t0)
REVERT: A  356 TYR cc_start: 0.6064 (OUTLIER) cc_final: 0.5312 (p90)
  outliers start: 28
  outliers final: 12
  residues processed: 108
  average time/residue: 0.4809
  time to fit residues: 54.7793
Evaluate side-chains
  101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  356 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.196044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.138900 restraints weight = 7404.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.09
r_work: 0.3508 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6482  Z= 0.132
  Angle     :  0.554   9.420   8873  Z= 0.286
  Chirality :  0.043   0.132   1063
  Planarity :  0.004   0.058   1136
  Dihedral  :  4.389  47.408    966
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 26.49 %
    Favored  : 68.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.29), residues: 893
  helix:  2.68 (0.25), residues: 406
  sheet:  0.34 (0.43), residues: 144
  loop : -0.95 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G  27 
 TYR   0.014   0.001   TYR R 339 
 PHE   0.015   0.001   PHE B 151 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6481)
  covalent geometry    : angle       0.55386 ( 8871)
  SS BOND              : bond        0.00027 (    1)
  SS BOND              : angle       0.82651 (    2)
  hydrogen bonds       : bond        0.04008 (  405)
  hydrogen bonds       : angle       4.18517 ( 1179)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 91
  time to evaluate  : 0.229 
Fit side-chains
REVERT: B   46 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7401 (ttm110)
REVERT: B   96 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.7995 (ttm170)
REVERT: R  131 HIS cc_start: 0.6977 (OUTLIER) cc_final: 0.6223 (p-80)
REVERT: A   40 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.7047 (tt)
REVERT: A  202 ARG cc_start: 0.8198 (mtt-85) cc_final: 0.7878 (mtp-110)
REVERT: A  203 MET cc_start: 0.8188 (tpt) cc_final: 0.7756 (tpt)
REVERT: A  247 ARG cc_start: 0.7427 (ptp-110) cc_final: 0.7085 (ptp90)
REVERT: A  256 ARG cc_start: 0.7515 (tpp-160) cc_final: 0.7236 (tpp-160)
REVERT: A  261 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.5616 (t80)
REVERT: A  333 ASP cc_start: 0.7692 (t0) cc_final: 0.7219 (t0)
REVERT: A  356 TYR cc_start: 0.6019 (OUTLIER) cc_final: 0.5208 (p90)
  outliers start: 26
  outliers final: 10
  residues processed: 108
  average time/residue: 0.4857
  time to fit residues: 55.4718
Evaluate side-chains
  102 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  131 HIS
Chi-restraints excluded: chain R residue  206 THR
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  356 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 0 optimal weight:   50.0000
   chunk 56 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 80 optimal weight:    0.7980
   chunk 52 optimal weight:   10.0000
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.196306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.140762 restraints weight = 7385.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.44
r_work: 0.3382 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6482  Z= 0.126
  Angle     :  0.551   9.060   8873  Z= 0.282
  Chirality :  0.043   0.153   1063
  Planarity :  0.004   0.055   1136
  Dihedral  :  4.337  48.041    966
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 26.68 %
    Favored  : 68.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.29), residues: 893
  helix:  2.66 (0.25), residues: 407
  sheet:  0.40 (0.43), residues: 144
  loop : -0.91 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  27 
 TYR   0.018   0.001   TYR R 342 
 PHE   0.015   0.001   PHE B 151 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6481)
  covalent geometry    : angle       0.55105 ( 8871)
  SS BOND              : bond        0.00003 (    1)
  SS BOND              : angle       0.59597 (    2)
  hydrogen bonds       : bond        0.03919 (  405)
  hydrogen bonds       : angle       4.16132 ( 1179)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 88
  time to evaluate  : 0.195 
Fit side-chains
REVERT: B   46 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7458 (ttm110)
REVERT: B   96 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.8061 (ttm170)
REVERT: G   38 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7873 (ptm)
REVERT: R  131 HIS cc_start: 0.6956 (OUTLIER) cc_final: 0.6124 (p-80)
REVERT: A   57 LYS cc_start: 0.7774 (pttt) cc_final: 0.7375 (ttmt)
REVERT: A   58 GLN cc_start: 0.7340 (mt0) cc_final: 0.7025 (tp40)
REVERT: A  202 ARG cc_start: 0.8294 (mtt-85) cc_final: 0.7958 (mtp-110)
REVERT: A  203 MET cc_start: 0.8190 (tpt) cc_final: 0.7714 (tpt)
REVERT: A  247 ARG cc_start: 0.7459 (ptp-110) cc_final: 0.6930 (ptp90)
REVERT: A  261 TYR cc_start: 0.7438 (OUTLIER) cc_final: 0.5806 (t80)
REVERT: A  333 ASP cc_start: 0.7742 (t0) cc_final: 0.7471 (t0)
REVERT: A  356 TYR cc_start: 0.6023 (OUTLIER) cc_final: 0.5188 (p90)
  outliers start: 26
  outliers final: 11
  residues processed: 104
  average time/residue: 0.4838
  time to fit residues: 53.1902
Evaluate side-chains
  100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  131 HIS
Chi-restraints excluded: chain R residue  206 THR
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  356 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 0 optimal weight:   50.0000
   chunk 72 optimal weight:    0.4980
   chunk 17 optimal weight:    3.9990
   chunk 68 optimal weight:    9.9990
   chunk 39 optimal weight:   40.0000
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
B 293 ASN
** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.193785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.140181 restraints weight = 7400.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 2.50
r_work: 0.3348 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6482  Z= 0.170
  Angle     :  0.604  10.859   8873  Z= 0.310
  Chirality :  0.044   0.163   1063
  Planarity :  0.004   0.055   1136
  Dihedral  :  4.538  47.814    966
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 27.83 %
    Favored  : 67.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.29), residues: 893
  helix:  2.55 (0.25), residues: 407
  sheet:  0.30 (0.42), residues: 144
  loop : -0.96 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  27 
 TYR   0.019   0.002   TYR A 192 
 PHE   0.018   0.002   PHE B 151 
 TRP   0.013   0.002   TRP B  82 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 6481)
  covalent geometry    : angle       0.60400 ( 8871)
  SS BOND              : bond        0.00377 (    1)
  SS BOND              : angle       1.09011 (    2)
  hydrogen bonds       : bond        0.04363 (  405)
  hydrogen bonds       : angle       4.31417 ( 1179)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 86
  time to evaluate  : 0.258 
Fit side-chains
REVERT: B   46 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7452 (ttm110)
REVERT: B   96 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.8009 (ttm170)
REVERT: G   47 GLU cc_start: 0.8246 (pt0) cc_final: 0.7962 (pm20)
REVERT: R  131 HIS cc_start: 0.7025 (OUTLIER) cc_final: 0.6272 (p-80)
REVERT: A   57 LYS cc_start: 0.7780 (pttt) cc_final: 0.7400 (ttmt)
REVERT: A  202 ARG cc_start: 0.8238 (mtt-85) cc_final: 0.7914 (mtp-110)
REVERT: A  203 MET cc_start: 0.8307 (tpt) cc_final: 0.7799 (tpt)
REVERT: A  247 ARG cc_start: 0.7482 (ptp-110) cc_final: 0.6993 (ptp90)
REVERT: A  261 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.5758 (t80)
REVERT: A  333 ASP cc_start: 0.7867 (t0) cc_final: 0.7439 (t0)
REVERT: A  356 TYR cc_start: 0.6147 (OUTLIER) cc_final: 0.5205 (p90)
  outliers start: 25
  outliers final: 14
  residues processed: 100
  average time/residue: 0.4995
  time to fit residues: 52.7935
Evaluate side-chains
  101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  131 HIS
Chi-restraints excluded: chain R residue  206 THR
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  356 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0980
   chunk 71 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
R 256 ASN
A  58 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.196269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.138634 restraints weight = 7480.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 2.14
r_work: 0.3481 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3360 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6482  Z= 0.120
  Angle     :  0.553  11.764   8873  Z= 0.280
  Chirality :  0.042   0.140   1063
  Planarity :  0.004   0.055   1136
  Dihedral  :  4.274  48.585    966
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 28.02 %
    Favored  : 68.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.29), residues: 893
  helix:  2.69 (0.25), residues: 407
  sheet:  0.33 (0.42), residues: 149
  loop : -0.84 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G  27 
 TYR   0.018   0.001   TYR R 342 
 PHE   0.014   0.001   PHE B 151 
 TRP   0.009   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6481)
  covalent geometry    : angle       0.55246 ( 8871)
  SS BOND              : bond        0.00178 (    1)
  SS BOND              : angle       0.87059 (    2)
  hydrogen bonds       : bond        0.03809 (  405)
  hydrogen bonds       : angle       4.13897 ( 1179)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.178 
Fit side-chains
REVERT: B   46 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7465 (ttm110)
REVERT: B   96 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.8028 (ttm170)
REVERT: G   47 GLU cc_start: 0.8212 (pt0) cc_final: 0.7932 (pm20)
REVERT: R  131 HIS cc_start: 0.7038 (OUTLIER) cc_final: 0.6197 (p-80)
REVERT: A   57 LYS cc_start: 0.7779 (pttt) cc_final: 0.7420 (ttmt)
REVERT: A   58 GLN cc_start: 0.7361 (mt0) cc_final: 0.7006 (tp40)
REVERT: A  202 ARG cc_start: 0.8282 (mtt-85) cc_final: 0.7959 (mtp-110)
REVERT: A  247 ARG cc_start: 0.7465 (ptp-110) cc_final: 0.6967 (ptp90)
REVERT: A  261 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.5859 (t80)
REVERT: A  356 TYR cc_start: 0.6074 (OUTLIER) cc_final: 0.5191 (p90)
  outliers start: 20
  outliers final: 11
  residues processed: 99
  average time/residue: 0.5093
  time to fit residues: 53.2057
Evaluate side-chains
  97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  131 HIS
Chi-restraints excluded: chain R residue  206 THR
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  356 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 38 optimal weight:   20.0000
   chunk 12 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0980
   chunk 79 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0870
   chunk 29 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0970
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.199043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.142204 restraints weight = 7327.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 2.15
r_work: 0.3531 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3410 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6482  Z= 0.103
  Angle     :  0.540  12.959   8873  Z= 0.272
  Chirality :  0.041   0.130   1063
  Planarity :  0.004   0.056   1136
  Dihedral  :  4.037  49.315    966
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 28.79 %
    Favored  : 68.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.67 (0.29), residues: 893
  helix:  2.82 (0.26), residues: 407
  sheet:  0.36 (0.41), residues: 156
  loop : -0.76 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G  27 
 TYR   0.016   0.001   TYR R 339 
 PHE   0.014   0.001   PHE A 194 
 TRP   0.007   0.001   TRP B 339 
 HIS   0.002   0.001   HIS A 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 6481)
  covalent geometry    : angle       0.53964 ( 8871)
  SS BOND              : bond        0.00094 (    1)
  SS BOND              : angle       0.64839 (    2)
  hydrogen bonds       : bond        0.03452 (  405)
  hydrogen bonds       : angle       4.02355 ( 1179)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.233 
Fit side-chains
REVERT: B   46 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7361 (ttm110)
REVERT: B   96 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.8021 (ttm170)
REVERT: G   47 GLU cc_start: 0.8237 (pt0) cc_final: 0.7917 (pm20)
REVERT: A   57 LYS cc_start: 0.7728 (pttt) cc_final: 0.7397 (ttmt)
REVERT: A   58 GLN cc_start: 0.7227 (mt0) cc_final: 0.6899 (tp40)
REVERT: A  202 ARG cc_start: 0.8199 (mtt-85) cc_final: 0.7879 (mtp-110)
REVERT: A  247 ARG cc_start: 0.7447 (ptp-110) cc_final: 0.6945 (ptp90)
REVERT: A  256 ARG cc_start: 0.7523 (tpp-160) cc_final: 0.7118 (tpp-160)
REVERT: A  261 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.5957 (t80)
REVERT: A  356 TYR cc_start: 0.5973 (OUTLIER) cc_final: 0.5087 (p90)
  outliers start: 16
  outliers final: 10
  residues processed: 99
  average time/residue: 0.4992
  time to fit residues: 52.1583
Evaluate side-chains
  98 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  206 THR
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  356 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:    0.0170
   chunk 74 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 68 optimal weight:    9.9990
   overall best weight:    0.9220

-------------------------------------------------------------------------------
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 = 0.4241 r_free = 0.4241 target = 0.196247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.143346 restraints weight = 7387.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 2.69
r_work: 0.3406 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6482  Z= 0.129
  Angle     :  0.565   8.717   8873  Z= 0.289
  Chirality :  0.043   0.133   1063
  Planarity :  0.004   0.055   1136
  Dihedral  :  4.195  49.365    966
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 29.37 %
    Favored  : 67.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.29), residues: 893
  helix:  2.77 (0.25), residues: 407
  sheet:  0.23 (0.41), residues: 156
  loop : -0.83 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G  27 
 TYR   0.018   0.001   TYR R 342 
 PHE   0.016   0.001   PHE B 151 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6481)
  covalent geometry    : angle       0.56475 ( 8871)
  SS BOND              : bond        0.00065 (    1)
  SS BOND              : angle       0.61867 (    2)
  hydrogen bonds       : bond        0.03792 (  405)
  hydrogen bonds       : angle       4.11368 ( 1179)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2988.07 seconds
wall clock time: 51 minutes 22.74 seconds (3082.74 seconds total)