Starting phenix.real_space_refine
on Thu Feb 13 01:09:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cz5_30505/02_2025/7cz5_30505.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cz5_30505/02_2025/7cz5_30505.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cz5_30505/02_2025/7cz5_30505.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cz5_30505/02_2025/7cz5_30505.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cz5_30505/02_2025/7cz5_30505.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cz5_30505/02_2025/7cz5_30505.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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      46      5.16       5
     C    5304      2.51       5
     N    1444      2.21       5
     O    1542      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8336
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "R"
      Number of atoms: 2155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 2155
          Classifications: {'peptide': 269}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 259}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 1893
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1893
          Classifications: {'peptide': 228}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 3
    Chain: "P"
      Number of atoms: 224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 224
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119}
    Chain: "R"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 46
          Unusual residues: {'CLR': 1, 'PLM': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 18
          Unusual residues: {'PLM': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 5.09, per 1000 atoms: 0.61
  Number of scatterers: 8336
  At special positions: 0
  Unit cell: (97.344, 97.344, 135.876, 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      46     16.00
     O    1542      8.00
     N    1444      7.00
     C    5304      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 202 " - pdb=" SG  CYS R 272 " distance=2.02

  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: 2.10
  Conformation dependent library (CDL) restraints added in 959.6 milliseconds
  

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 10 sheets defined
      41.4% alpha, 19.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'R' and resid 119 through 154
    Processing helix  chain 'R' and resid 155 through 158
      removed outlier: 3.758A  pdb=" N   HIS R 158 " --> pdb=" O   ARG R 155 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 155 through 158'
    Processing helix  chain 'R' and resid 159 through 187
      removed outlier: 3.501A  pdb=" N   TYR R 163 " --> pdb=" O   CYS R 159 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   VAL R 164 " --> pdb=" O   PRO R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 199 through 233
    Processing helix  chain 'R' and resid 239 through 268
      removed outlier: 3.620A  pdb=" N   TRP R 243 " --> pdb=" O   ARG R 239 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   TRP R 250 " --> pdb=" O   VAL R 246 " (cutoff:3.500A)
      Proline residue:  R 253  - end of helix
      removed outlier: 3.509A  pdb=" N   PHE R 267 " --> pdb=" O   CYS R 263 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 274
      removed outlier: 3.672A  pdb=" N   ASP R 274 " --> pdb=" O   ALA R 271 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 282 through 309
      Proline residue:  R 288  - end of helix
      removed outlier: 3.515A  pdb=" N   GLY R 298 " --> pdb=" O   GLY R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 324 through 339
      Proline residue:  R 336  - end of helix
    Processing helix  chain 'R' and resid 340 through 343
    Processing helix  chain 'R' and resid 353 through 363
      removed outlier: 3.698A  pdb=" N   LEU R 358 " --> pdb=" O   LEU R 354 " (cutoff:3.500A)
      Proline residue:  R 359  - end of helix
    Processing helix  chain 'R' and resid 364 through 366
      No H-bonds generated for 'chain 'R' and resid 364 through 366'
    Processing helix  chain 'R' and resid 367 through 377
    Processing helix  chain 'R' and resid 380 through 393
      removed outlier: 3.737A  pdb=" N   ARG R 384 " --> pdb=" O   ASN R 380 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   GLU R 386 " --> pdb=" O   GLU R 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 10 through 39
      removed outlier: 3.693A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 58
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.707A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.742A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.597A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'P' and resid 2 through 28
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.503A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 22
      removed outlier: 4.274A  pdb=" N   ALA G  12 " --> pdb=" O   SER G   8 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.691A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
      removed outlier: 3.555A  pdb=" N   LYS N  65 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 62 through 65'
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.759A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.376A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.201A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.534A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.558A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.681A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.662A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.995A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.682A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.784A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.615A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.528A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.675A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.561A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    409 hydrogen bonds defined for protein.
    1173 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: 2.50

  Time building geometry restraints manager: 2.39 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2565
        1.34 -     1.46: 2200
        1.46 -     1.59: 3680
        1.59 -     1.72: 0
        1.72 -     1.84: 62
  Bond restraints: 8507
  Sorted by residual:
  bond pdb=" C1  PLM A 401 "
       pdb=" O1  PLM A 401 "
    ideal  model  delta    sigma   weight residual
    1.249  1.342 -0.093 2.00e-02 2.50e+03 2.15e+01
  bond pdb=" C1  PLM R 601 "
       pdb=" O1  PLM R 601 "
    ideal  model  delta    sigma   weight residual
    1.249  1.342 -0.093 2.00e-02 2.50e+03 2.15e+01
  bond pdb=" C1  PLM R 601 "
       pdb=" O2  PLM R 601 "
    ideal  model  delta    sigma   weight residual
    1.249  1.208  0.041 2.00e-02 2.50e+03 4.19e+00
  bond pdb=" C1  PLM A 401 "
       pdb=" O2  PLM A 401 "
    ideal  model  delta    sigma   weight residual
    1.249  1.209  0.040 2.00e-02 2.50e+03 4.05e+00
  bond pdb=" C1  PLM A 401 "
       pdb=" C2  PLM A 401 "
    ideal  model  delta    sigma   weight residual
    1.542  1.505  0.037 2.00e-02 2.50e+03 3.38e+00
  ... (remaining 8502 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 11111
        1.54 -     3.07: 311
        3.07 -     4.61: 63
        4.61 -     6.14: 24
        6.14 -     7.68: 7
  Bond angle restraints: 11516
  Sorted by residual:
  angle pdb=" CA  TYR R 133 "
        pdb=" CB  TYR R 133 "
        pdb=" CG  TYR R 133 "
      ideal   model   delta    sigma   weight residual
     113.90  119.99   -6.09 1.80e+00 3.09e-01 1.14e+01
  angle pdb=" C   ILE R 132 "
        pdb=" N   TYR R 133 "
        pdb=" CA  TYR R 133 "
      ideal   model   delta    sigma   weight residual
     121.14  115.26    5.88 1.75e+00 3.27e-01 1.13e+01
  angle pdb=" N   TYR R 226 "
        pdb=" CA  TYR R 226 "
        pdb=" C   TYR R 226 "
      ideal   model   delta    sigma   weight residual
     111.28  114.82   -3.54 1.09e+00 8.42e-01 1.06e+01
  angle pdb=" CA  TRP B  99 "
        pdb=" CB  TRP B  99 "
        pdb=" CG  TRP B  99 "
      ideal   model   delta    sigma   weight residual
     113.60  107.64    5.96 1.90e+00 2.77e-01 9.84e+00
  angle pdb=" CA  TRP R 219 "
        pdb=" CB  TRP R 219 "
        pdb=" CG  TRP R 219 "
      ideal   model   delta    sigma   weight residual
     113.60  108.30    5.30 1.90e+00 2.77e-01 7.78e+00
  ... (remaining 11511 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 4651
       17.38 -    34.76: 370
       34.76 -    52.14: 49
       52.14 -    69.52: 16
       69.52 -    86.90: 6
  Dihedral angle restraints: 5092
    sinusoidal: 2059
      harmonic: 3033
  Sorted by residual:
  dihedral pdb=" CB  CYS R 202 "
           pdb=" SG  CYS R 202 "
           pdb=" SG  CYS R 272 "
           pdb=" CB  CYS R 272 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   51.17   41.83     1      1.00e+01 1.00e-02 2.45e+01
  dihedral pdb=" CA  ILE R 270 "
           pdb=" C   ILE R 270 "
           pdb=" N   ALA R 271 "
           pdb=" CA  ALA R 271 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.89   20.11     0      5.00e+00 4.00e-02 1.62e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.32   19.68     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 5089 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 1222
       0.095 -    0.190: 66
       0.190 -    0.285: 1
       0.285 -    0.380: 1
       0.380 -    0.475: 1
  Chirality restraints: 1291
  Sorted by residual:
  chirality pdb=" C14 CLR R 602 "
            pdb=" C13 CLR R 602 "
            pdb=" C15 CLR R 602 "
            pdb=" C8  CLR R 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.79    0.48 2.00e-01 2.50e+01 5.65e+00
  chirality pdb=" C10 CLR R 602 "
            pdb=" C1  CLR R 602 "
            pdb=" C5  CLR R 602 "
            pdb=" C9  CLR R 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.52   -0.33 2.00e-01 2.50e+01 2.70e+00
  chirality pdb=" C17 CLR R 602 "
            pdb=" C13 CLR R 602 "
            pdb=" C16 CLR R 602 "
            pdb=" C20 CLR R 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.81   -0.25 2.00e-01 2.50e+01 1.60e+00
  ... (remaining 1288 not shown)

  Planarity restraints: 1459
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  99 "   -0.021 2.00e-02 2.50e+03   1.14e-02 3.27e+00
        pdb=" CG  TRP B  99 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  99 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  99 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  99 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  99 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  99 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  99 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  99 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  99 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "   -0.027 5.00e-02 4.00e+02   4.17e-02 2.78e+00
        pdb=" N   PRO G  49 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR P   1 "    0.012 2.00e-02 2.50e+03   1.16e-02 2.69e+00
        pdb=" CG  TYR P   1 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR P   1 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR P   1 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR P   1 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR P   1 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR P   1 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR P   1 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1456 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 510
        2.73 -     3.27: 8139
        3.27 -     3.81: 13353
        3.81 -     4.36: 17137
        4.36 -     4.90: 29252
  Nonbonded interactions: 68391
  Sorted by model distance:
  nonbonded pdb=" O   GLY N   8 "
            pdb=" OG1 THR N 122 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" OD1 ASN R 380 "
            pdb=" O   HOH R 701 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   GLY B 310 "
            pdb=" NZ  LYS B 337 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" NH1 ARG A 228 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" ND2 ASN R 380 "
            pdb=" OE2 GLU R 382 "
     model   vdw
     2.304 3.120
  ... (remaining 68386 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:             0.700
  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:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     21.400
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
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   0.093   8507  Z= 0.280
  Angle     :  0.686   7.677  11516  Z= 0.368
  Chirality :  0.049   0.475   1291
  Planarity :  0.004   0.042   1459
  Dihedral  : 13.226  86.899   3125
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.24), residues: 1026
  helix: -0.70 (0.24), residues: 413
  sheet: -0.89 (0.32), residues: 218
  loop : -2.23 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B  99 
 HIS   0.014   0.001   HIS A 357 
 PHE   0.019   0.002   PHE B 151 
 TYR   0.027   0.002   TYR P   1 
 ARG   0.003   0.000   ARG G  13 

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.7050 (mmpt) cc_final: 0.6848 (mttp)
REVERT: A  230 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7686 (mt-10)
REVERT: A  378 ASP cc_start: 0.7294 (m-30) cc_final: 0.7038 (m-30)
REVERT: P   27 MET cc_start: 0.2554 (mmm) cc_final: 0.1770 (tmt)
REVERT: B  197 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7744 (mtt-85)
REVERT: B  337 LYS cc_start: 0.8763 (mttt) cc_final: 0.8466 (mttt)
REVERT: G   21 MET cc_start: 0.6371 (tpp) cc_final: 0.5388 (mpt)
REVERT: G   29 LYS cc_start: 0.8418 (mmtm) cc_final: 0.8094 (mptm)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 1.4314
  time to fit residues: 205.5431
Evaluate side-chains
  104 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9990
   chunk 42 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 78 optimal weight:    5.9990
   chunk 30 optimal weight:    8.9990
   chunk 47 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   chunk 90 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
R 323 GLN
A  14 ASN
A 267 GLN
A 292 ASN
P   8 ASN
B  35 ASN
B  91 HIS
G  18 GLN
G  24 ASN
N   3 GLN
N  84 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.176683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.132618 restraints weight = 9151.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 1.98
r_work: 0.3586 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3467 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8507  Z= 0.177
  Angle     :  0.565   8.805  11516  Z= 0.300
  Chirality :  0.043   0.200   1291
  Planarity :  0.004   0.044   1459
  Dihedral  :  6.706  53.557   1228
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  8.63 %
    Favored  : 90.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.25), residues: 1026
  helix:  0.44 (0.26), residues: 415
  sheet: -0.44 (0.34), residues: 205
  loop : -1.77 (0.28), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP R 219 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.035   0.001   TYR R 133 
 ARG   0.006   0.000   ARG A 283 

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
REVERT: R  270 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7468 (mp)
REVERT: R  364 LEU cc_start: 0.7831 (tp) cc_final: 0.7575 (tt)
REVERT: A   24 LYS cc_start: 0.7315 (mmpt) cc_final: 0.7073 (ttmm)
REVERT: A  378 ASP cc_start: 0.7957 (m-30) cc_final: 0.7633 (m-30)
REVERT: P   27 MET cc_start: 0.2599 (mmm) cc_final: 0.1800 (tmt)
REVERT: B   45 MET cc_start: 0.9382 (mtt) cc_final: 0.8721 (mtt)
REVERT: B   59 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.8302 (t80)
REVERT: B  175 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7928 (mm110)
REVERT: G   42 GLU cc_start: 0.7738 (mp0) cc_final: 0.7438 (mp0)
REVERT: G   62 ARG cc_start: 0.6329 (OUTLIER) cc_final: 0.5947 (tpp-160)
  outliers start: 12
  outliers final: 2
  residues processed: 113
  average time/residue: 1.4423
  time to fit residues: 172.4115
Evaluate side-chains
  105 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  202 CYS
Chi-restraints excluded: chain R residue  270 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain G residue   62 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 21 optimal weight:    0.2980
   chunk 41 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 78 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 93 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 80 optimal weight:    7.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B  75 GLN
B 340 ASN
N 120 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.176881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.132480 restraints weight = 9338.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 2.02
r_work: 0.3588 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3466 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8507  Z= 0.179
  Angle     :  0.538   8.625  11516  Z= 0.287
  Chirality :  0.043   0.186   1291
  Planarity :  0.004   0.045   1459
  Dihedral  :  6.543  53.869   1228
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  :  9.98 %
    Favored  : 88.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.26), residues: 1026
  helix:  1.04 (0.27), residues: 405
  sheet: -0.20 (0.33), residues: 207
  loop : -1.57 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 219 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.030   0.001   TYR R 133 
 ARG   0.005   0.000   ARG A 317 

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
REVERT: R  364 LEU cc_start: 0.7805 (tp) cc_final: 0.7562 (tt)
REVERT: A   24 LYS cc_start: 0.7373 (mmpt) cc_final: 0.7090 (ttmm)
REVERT: A  378 ASP cc_start: 0.7976 (m-30) cc_final: 0.7657 (m-30)
REVERT: P   27 MET cc_start: 0.2574 (mmm) cc_final: 0.1854 (tmt)
REVERT: B   44 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8502 (mt0)
REVERT: B   45 MET cc_start: 0.9396 (mtt) cc_final: 0.8688 (mtt)
REVERT: B   59 TYR cc_start: 0.9180 (OUTLIER) cc_final: 0.8286 (t80)
REVERT: G   62 ARG cc_start: 0.6324 (OUTLIER) cc_final: 0.5972 (tpp-160)
  outliers start: 17
  outliers final: 6
  residues processed: 115
  average time/residue: 1.3754
  time to fit residues: 168.0692
Evaluate side-chains
  101 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain R residue  202 CYS
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain G residue   62 ARG
Chi-restraints excluded: chain N residue   25 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0060
   chunk 72 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 89 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   overall best weight:    1.1400

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

Flipped N/Q/H residues before XYZ refinement:
R 165 HIS
A 292 ASN
B  75 GLN
B 175 GLN
B 266 HIS
B 268 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.176512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.132286 restraints weight = 9264.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 2.00
r_work: 0.3575 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3453 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8507  Z= 0.196
  Angle     :  0.537   8.078  11516  Z= 0.286
  Chirality :  0.043   0.170   1291
  Planarity :  0.004   0.047   1459
  Dihedral  :  6.487  53.817   1228
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 10.76 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.26), residues: 1026
  helix:  1.24 (0.27), residues: 408
  sheet: -0.05 (0.33), residues: 210
  loop : -1.48 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 219 
 HIS   0.009   0.001   HIS A 357 
 PHE   0.025   0.001   PHE P   6 
 TYR   0.028   0.001   TYR R 133 
 ARG   0.004   0.000   ARG A 317 

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.810 
Fit side-chains
REVERT: R  364 LEU cc_start: 0.7820 (tp) cc_final: 0.7588 (tt)
REVERT: A   24 LYS cc_start: 0.7362 (mmpt) cc_final: 0.7055 (ttmm)
REVERT: A  292 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8618 (m-40)
REVERT: A  378 ASP cc_start: 0.7903 (m-30) cc_final: 0.7560 (m-30)
REVERT: P   27 MET cc_start: 0.2509 (mmm) cc_final: 0.1888 (tmt)
REVERT: B   44 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8511 (mt0)
REVERT: B   59 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.8301 (t80)
REVERT: G   21 MET cc_start: 0.6493 (tpp) cc_final: 0.5134 (mpt)
REVERT: G   42 GLU cc_start: 0.7754 (mp0) cc_final: 0.7402 (mp0)
REVERT: G   62 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.5993 (tpp-160)
  outliers start: 19
  outliers final: 7
  residues processed: 110
  average time/residue: 1.3876
  time to fit residues: 161.6776
Evaluate side-chains
  103 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  133 TYR
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain R residue  202 CYS
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain G residue   62 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 15 optimal weight:   20.0000
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
R 210 HIS
A  59 GLN
A 292 ASN
B  75 GLN
B 175 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.173359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.128766 restraints weight = 9205.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 1.98
r_work: 0.3520 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3399 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8507  Z= 0.331
  Angle     :  0.617  10.367  11516  Z= 0.327
  Chirality :  0.046   0.177   1291
  Planarity :  0.005   0.046   1459
  Dihedral  :  6.835  57.623   1228
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 12.11 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.26), residues: 1026
  helix:  1.07 (0.26), residues: 408
  sheet:  0.06 (0.34), residues: 206
  loop : -1.43 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 219 
 HIS   0.013   0.001   HIS A 357 
 PHE   0.019   0.002   PHE B 199 
 TYR   0.030   0.002   TYR R 133 
 ARG   0.006   0.001   ARG A 317 

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.7627 (mmpt) cc_final: 0.7218 (ttmm)
REVERT: A  292 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8672 (m-40)
REVERT: A  378 ASP cc_start: 0.8037 (m-30) cc_final: 0.7754 (m-30)
REVERT: P   27 MET cc_start: 0.2694 (mmm) cc_final: 0.1784 (tmt)
REVERT: B   44 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8549 (mt0)
REVERT: B   45 MET cc_start: 0.9354 (mtt) cc_final: 0.8696 (mtt)
REVERT: B   59 TYR cc_start: 0.9185 (OUTLIER) cc_final: 0.8327 (t80)
REVERT: G   62 ARG cc_start: 0.6381 (OUTLIER) cc_final: 0.5995 (tpp-160)
  outliers start: 26
  outliers final: 17
  residues processed: 112
  average time/residue: 1.3951
  time to fit residues: 165.3904
Evaluate side-chains
  114 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  128 THR
Chi-restraints excluded: chain R residue  133 TYR
Chi-restraints excluded: chain R residue  135 VAL
Chi-restraints excluded: chain R residue  157 LEU
Chi-restraints excluded: chain R residue  174 LEU
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain R residue  202 CYS
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   62 ARG
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   25 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 40 optimal weight:    0.3980
   chunk 67 optimal weight:    0.9980
   chunk 98 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B  75 GLN
B 175 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.177029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.132853 restraints weight = 9209.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 1.99
r_work: 0.3581 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3465 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8507  Z= 0.166
  Angle     :  0.525   8.653  11516  Z= 0.278
  Chirality :  0.042   0.163   1291
  Planarity :  0.004   0.046   1459
  Dihedral  :  6.396  56.015   1228
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.79 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.26), residues: 1026
  helix:  1.43 (0.27), residues: 408
  sheet: -0.05 (0.33), residues: 217
  loop : -1.28 (0.29), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 219 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.015   0.001   PHE P   6 
 TYR   0.026   0.001   TYR R 133 
 ARG   0.005   0.000   ARG A 317 

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.933 
Fit side-chains
REVERT: R  270 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7545 (mp)
REVERT: A   24 LYS cc_start: 0.7442 (mmpt) cc_final: 0.7070 (ttmm)
REVERT: A  343 ASP cc_start: 0.8184 (m-30) cc_final: 0.7856 (m-30)
REVERT: A  378 ASP cc_start: 0.7886 (m-30) cc_final: 0.7550 (m-30)
REVERT: P   27 MET cc_start: 0.2534 (mmm) cc_final: 0.1778 (tmt)
REVERT: B   45 MET cc_start: 0.9387 (mtt) cc_final: 0.8729 (mtt)
REVERT: B   59 TYR cc_start: 0.9165 (OUTLIER) cc_final: 0.8285 (t80)
REVERT: B  188 MET cc_start: 0.8718 (mmm) cc_final: 0.8501 (mmm)
REVERT: G   21 MET cc_start: 0.6541 (tpp) cc_final: 0.5177 (mpt)
REVERT: G   62 ARG cc_start: 0.6363 (OUTLIER) cc_final: 0.5991 (tpp-160)
  outliers start: 16
  outliers final: 8
  residues processed: 107
  average time/residue: 1.5313
  time to fit residues: 173.3659
Evaluate side-chains
  103 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  133 TYR
Chi-restraints excluded: chain R residue  174 LEU
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain R residue  202 CYS
Chi-restraints excluded: chain R residue  270 ILE
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain G residue   62 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0170
   chunk 67 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 79 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   overall best weight:    0.9622

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.177277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.133203 restraints weight = 9268.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 1.99
r_work: 0.3579 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3459 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8507  Z= 0.175
  Angle     :  0.527   8.442  11516  Z= 0.278
  Chirality :  0.042   0.164   1291
  Planarity :  0.004   0.046   1459
  Dihedral  :  6.276  58.643   1228
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.24 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.26), residues: 1026
  helix:  1.54 (0.27), residues: 409
  sheet:  0.05 (0.33), residues: 215
  loop : -1.18 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 219 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.026   0.001   TYR R 133 
 ARG   0.007   0.000   ARG A 317 

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.946 
Fit side-chains
REVERT: A   24 LYS cc_start: 0.7408 (mmpt) cc_final: 0.7038 (ttmm)
REVERT: A  343 ASP cc_start: 0.8236 (m-30) cc_final: 0.7908 (m-30)
REVERT: A  378 ASP cc_start: 0.7910 (m-30) cc_final: 0.7566 (m-30)
REVERT: P   27 MET cc_start: 0.2530 (mmm) cc_final: 0.1757 (tmt)
REVERT: B   45 MET cc_start: 0.9384 (mtt) cc_final: 0.8739 (mtt)
REVERT: B   59 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.8244 (t80)
REVERT: B  314 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7755 (ttt180)
REVERT: G   21 MET cc_start: 0.6433 (tpp) cc_final: 0.5035 (mpt)
REVERT: G   46 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8074 (tppp)
  outliers start: 17
  outliers final: 9
  residues processed: 107
  average time/residue: 1.4443
  time to fit residues: 163.0773
Evaluate side-chains
  103 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 1.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  133 TYR
Chi-restraints excluded: chain R residue  174 LEU
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain R residue  202 CYS
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue   25 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0870
   chunk 92 optimal weight:    0.7980
   chunk 89 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 84 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0040
   overall best weight:    0.5772

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

Flipped N/Q/H residues before XYZ refinement:
P   8 ASN
B  17 GLN
B  75 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.179034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.134950 restraints weight = 9338.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 2.02
r_work: 0.3608 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3490 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
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      :  0.002   0.035   8507  Z= 0.140
  Angle     :  0.502   9.033  11516  Z= 0.264
  Chirality :  0.041   0.160   1291
  Planarity :  0.004   0.046   1459
  Dihedral  :  5.952  56.876   1228
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.57 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.26), residues: 1026
  helix:  1.75 (0.27), residues: 409
  sheet:  0.03 (0.33), residues: 217
  loop : -1.06 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 219 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.025   0.001   TYR R 133 
 ARG   0.005   0.000   ARG A 317 

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.939 
Fit side-chains
REVERT: A   24 LYS cc_start: 0.7353 (mmpt) cc_final: 0.6986 (ttmm)
REVERT: A  343 ASP cc_start: 0.8158 (m-30) cc_final: 0.7764 (m-30)
REVERT: A  356 ARG cc_start: 0.7162 (ptt180) cc_final: 0.6367 (ptt180)
REVERT: P   27 MET cc_start: 0.2701 (mmm) cc_final: 0.1891 (tmt)
REVERT: B   17 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7451 (tm-30)
REVERT: B   45 MET cc_start: 0.9401 (mtt) cc_final: 0.8966 (mtt)
REVERT: B   59 TYR cc_start: 0.9168 (OUTLIER) cc_final: 0.8221 (t80)
REVERT: B  314 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7598 (ttt180)
REVERT: G   21 MET cc_start: 0.6492 (tpp) cc_final: 0.5049 (mpt)
REVERT: G   46 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8074 (tppp)
  outliers start: 17
  outliers final: 8
  residues processed: 112
  average time/residue: 1.5038
  time to fit residues: 177.5666
Evaluate side-chains
  107 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  133 TYR
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain R residue  202 CYS
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue   25 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 63 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0470
   chunk 26 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0970
   chunk 45 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.0080

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
B  17 GLN
B  75 GLN
N   3 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.178165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.133981 restraints weight = 9397.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 2.01
r_work: 0.3593 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3479 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8507  Z= 0.179
  Angle     :  0.528   9.205  11516  Z= 0.277
  Chirality :  0.042   0.162   1291
  Planarity :  0.004   0.045   1459
  Dihedral  :  5.967  56.125   1228
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 15.13 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.26), residues: 1026
  helix:  1.73 (0.26), residues: 408
  sheet:  0.11 (0.33), residues: 215
  loop : -1.00 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 219 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.026   0.001   TYR R 133 
 ARG   0.005   0.000   ARG A 317 

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.872 
Fit side-chains
REVERT: A   24 LYS cc_start: 0.7403 (mmpt) cc_final: 0.7040 (ttmm)
REVERT: A  343 ASP cc_start: 0.8210 (m-30) cc_final: 0.7846 (m-30)
REVERT: A  356 ARG cc_start: 0.7242 (ptt180) cc_final: 0.6431 (ptt180)
REVERT: P   27 MET cc_start: 0.2665 (mmm) cc_final: 0.1832 (tmt)
REVERT: B   45 MET cc_start: 0.9377 (mtt) cc_final: 0.8923 (mtt)
REVERT: B   59 TYR cc_start: 0.9192 (OUTLIER) cc_final: 0.8235 (t80)
REVERT: B  314 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7798 (ttt180)
REVERT: G   21 MET cc_start: 0.6492 (tpp) cc_final: 0.5101 (mpt)
REVERT: G   46 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8089 (tppp)
  outliers start: 14
  outliers final: 9
  residues processed: 104
  average time/residue: 1.5520
  time to fit residues: 170.3456
Evaluate side-chains
  103 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  133 TYR
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain R residue  202 CYS
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue   25 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    4.9990
   chunk 59 optimal weight:    0.3980
   chunk 3 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 99 optimal weight:    0.0770
   chunk 67 optimal weight:    0.0970
   overall best weight:    0.7140

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
A 390 GLN
B  17 GLN
B  75 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.178860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.134914 restraints weight = 9265.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 2.01
r_work: 0.3610 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3490 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8507  Z= 0.152
  Angle     :  0.514   8.920  11516  Z= 0.271
  Chirality :  0.042   0.160   1291
  Planarity :  0.004   0.045   1459
  Dihedral  :  5.779  53.928   1228
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.47 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.26), residues: 1026
  helix:  1.77 (0.26), residues: 408
  sheet:  0.04 (0.33), residues: 217
  loop : -0.95 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 219 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.025   0.001   TYR R 133 
 ARG   0.005   0.000   ARG A 317 

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.910 
Fit side-chains
REVERT: A   24 LYS cc_start: 0.7379 (mmpt) cc_final: 0.7002 (ttmm)
REVERT: A  343 ASP cc_start: 0.8206 (m-30) cc_final: 0.7825 (m-30)
REVERT: A  356 ARG cc_start: 0.7109 (ptt180) cc_final: 0.6374 (ptt180)
REVERT: P   27 MET cc_start: 0.2489 (mmm) cc_final: 0.1825 (tmt)
REVERT: B   45 MET cc_start: 0.9383 (mtt) cc_final: 0.8942 (mtt)
REVERT: B   59 TYR cc_start: 0.9180 (OUTLIER) cc_final: 0.8214 (t80)
REVERT: B  314 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7607 (ttt180)
REVERT: G   21 MET cc_start: 0.6433 (tpp) cc_final: 0.5008 (mpt)
REVERT: G   46 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8079 (tppp)
  outliers start: 15
  outliers final: 8
  residues processed: 108
  average time/residue: 1.4535
  time to fit residues: 165.6774
Evaluate side-chains
  106 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  133 TYR
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue   25 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0970
   chunk 74 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 84 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
B  17 GLN
B  75 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.178141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.133812 restraints weight = 9417.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 2.03
r_work: 0.3592 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3472 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8507  Z= 0.172
  Angle     :  0.524   9.251  11516  Z= 0.276
  Chirality :  0.042   0.169   1291
  Planarity :  0.004   0.045   1459
  Dihedral  :  5.724  52.591   1228
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.47 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.26), residues: 1026
  helix:  1.82 (0.26), residues: 407
  sheet:  0.12 (0.33), residues: 215
  loop : -0.96 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 219 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.025   0.001   TYR R 133 
 ARG   0.007   0.000   ARG A 317 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7024.42 seconds
wall clock time: 124 minutes 22.85 seconds (7462.85 seconds total)