Starting phenix.real_space_refine
on Wed Feb 12 02:50:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cr2_16802/02_2025/8cr2_16802.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cr2_16802/02_2025/8cr2_16802.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cr2_16802/02_2025/8cr2_16802.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cr2_16802/02_2025/8cr2_16802.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cr2_16802/02_2025/8cr2_16802.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cr2_16802/02_2025/8cr2_16802.cif"
  }
  resolution = 4.2
  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=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 306 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      51      5.16       5
     C    4419      2.51       5
     N    1133      2.21       5
     O    1234      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6838
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 2113
          Classifications: {'peptide': 268}
          Link IDs: {'PTRANS': 16, 'TRANS': 251}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2066
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 2066
          Classifications: {'peptide': 262}
          Link IDs: {'PTRANS': 16, 'TRANS': 245}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 1, 'TRANS': 95}
    Chain: "D"
      Number of atoms: 1856
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1856
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 4, 'TRANS': 223}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1658  SG  CYS A 289      37.717  41.793  15.466  1.00 88.42           S
  ATOM   1681  SG  CYS A 292      36.187  44.539  16.689  1.00 83.88           S
  ATOM   3724  SG  CYS B 289      39.158  45.820  14.919  1.00 94.34           S
  ATOM   3747  SG  CYS B 292      40.200  43.439  17.412  1.00 83.96           S

  Time building chain proxies: 4.74, per 1000 atoms: 0.69
  Number of scatterers: 6838
  At special positions: 0
  Unit cell: (74.37, 96.57, 135.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      51     16.00
     O    1234      8.00
     N    1133      7.00
     C    4419      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 208 " - pdb=" SG  CYS D 284 " 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: 1.47
  Conformation dependent library (CDL) restraints added in 946.9 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 401 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS B 292 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS A 292 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS A 289 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS B 289 "
      Number of angles added : 6


  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1642

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 4 sheets defined
      69.0% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 34
    Processing helix  chain 'A' and resid 49 through 65
      removed outlier: 3.949A  pdb=" N   LYS A  63 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   GLY A  64 " --> pdb=" O   GLN A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 84
      removed outlier: 3.922A  pdb=" N   ASP A  81 " --> pdb=" O   HIS A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 158
      removed outlier: 4.132A  pdb=" N   MET A 158 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 176
    Processing helix  chain 'A' and resid 177 through 192
    Processing helix  chain 'A' and resid 217 through 238
      Proline residue:  A 227  - end of helix
      removed outlier: 3.532A  pdb=" N   GLU A 234 " --> pdb=" O   ARG A 230 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   GLN A 235 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   PHE A 236 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 268
    Processing helix  chain 'A' and resid 290 through 310
      removed outlier: 3.562A  pdb=" N   HIS A 296 " --> pdb=" O   CYS A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 340
    Processing helix  chain 'B' and resid 28 through 33
    Processing helix  chain 'B' and resid 49 through 65
      removed outlier: 3.868A  pdb=" N   LYS B  63 " --> pdb=" O   VAL B  59 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   GLY B  64 " --> pdb=" O   GLN B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 84
      removed outlier: 3.775A  pdb=" N   ASP B  81 " --> pdb=" O   HIS B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 159
      removed outlier: 4.105A  pdb=" N   ALA B 145 " --> pdb=" O   GLY B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 178
      removed outlier: 4.092A  pdb=" N   LEU B 176 " --> pdb=" O   HIS B 172 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU B 177 " --> pdb=" O   THR B 173 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ASN B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 172 through 178'
    Processing helix  chain 'B' and resid 178 through 190
      removed outlier: 3.974A  pdb=" N   ILE B 182 " --> pdb=" O   ASN B 178 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU B 190 " --> pdb=" O   GLY B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 238
      Proline residue:  B 227  - end of helix
      removed outlier: 4.137A  pdb=" N   VAL B 232 " --> pdb=" O   VAL B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 268
    Processing helix  chain 'B' and resid 290 through 310
    Processing helix  chain 'B' and resid 327 through 337
      removed outlier: 3.681A  pdb=" N   LEU B 337 " --> pdb=" O   THR B 333 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1029 through 1039
    Processing helix  chain 'C' and resid 1039 through 1062
      removed outlier: 3.820A  pdb=" N   SER C1047 " --> pdb=" O   ALA C1043 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1068 through 1124
    Processing helix  chain 'D' and resid 190 through 207
    Processing helix  chain 'D' and resid 208 through 210
      No H-bonds generated for 'chain 'D' and resid 208 through 210'
    Processing helix  chain 'D' and resid 214 through 234
      removed outlier: 3.520A  pdb=" N   GLY D 226 " --> pdb=" O   LEU D 222 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   PHE D 231 " --> pdb=" O   LEU D 227 " (cutoff:3.500A)
      Proline residue:  D 232  - end of helix
    Processing helix  chain 'D' and resid 255 through 284
      removed outlier: 3.925A  pdb=" N   PHE D 281 " --> pdb=" O   TYR D 277 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE D 282 " --> pdb=" O   PHE D 278 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   PHE D 283 " --> pdb=" O   PHE D 279 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   CYS D 284 " --> pdb=" O   THR D 280 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 285 through 291
    Processing helix  chain 'D' and resid 1006 through 1035
      removed outlier: 3.969A  pdb=" N   VAL D1014 " --> pdb=" O   ALA D1010 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   LEU D1015 " --> pdb=" O   TRP D1011 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER D1016 " --> pdb=" O   LEU D1012 " (cutoff:3.500A)
      Proline residue:  D1029  - end of helix
    Processing helix  chain 'D' and resid 1035 through 1062
      removed outlier: 4.559A  pdb=" N   LYS D1041 " --> pdb=" O   ARG D1037 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   GLN D1045 " --> pdb=" O   LYS D1041 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   THR D1062 " --> pdb=" O   GLN D1058 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1068 through 1123
      removed outlier: 4.752A  pdb=" N   LYS D1099 " --> pdb=" O   ALA D1095 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1150 through 1161
    Processing helix  chain 'D' and resid 1162 through 1171
    Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70
      removed outlier: 3.565A  pdb=" N   LEU A  69 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL A 164 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
      removed outlier: 10.597A  pdb=" N   THR A 242 " --> pdb=" O   THR A 272 " (cutoff:3.500A)
      removed outlier: 9.744A  pdb=" N   ASN A 274 " --> pdb=" O   THR A 242 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   PHE A 244 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   ILE A 276 " --> pdb=" O   PHE A 244 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   CYS A 246 " --> pdb=" O   ILE A 276 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   HIS A 273 " --> pdb=" O   HIS A 314 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   VAL A 316 " --> pdb=" O   HIS A 273 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ILE A 275 " --> pdb=" O   VAL A 316 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 93
    Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72
      removed outlier: 6.963A  pdb=" N   ILE B  40 " --> pdb=" O   PHE B 165 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   TRP B  39 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   ILE B 245 " --> pdb=" O   TRP B  39 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   PHE B  41 " --> pdb=" O   ILE B 245 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   VAL B 247 " --> pdb=" O   PHE B  41 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   GLY B  43 " --> pdb=" O   VAL B 247 " (cutoff:3.500A)
      removed outlier: 8.521A  pdb=" N   ILE B 249 " --> pdb=" O   GLY B  43 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   THR B 272 " --> pdb=" O   THR B 242 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   PHE B 244 " --> pdb=" O   THR B 272 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ASN B 274 " --> pdb=" O   PHE B 244 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   HIS B 273 " --> pdb=" O   HIS B 314 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   VAL B 316 " --> pdb=" O   HIS B 273 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   ILE B 275 " --> pdb=" O   VAL B 316 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 69
      removed outlier: 6.008A  pdb=" N   VAL B  68 " --> pdb=" O   PHE B 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    429 hydrogen bonds defined for protein.
    1278 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: 1.91

  Time building geometry restraints manager: 1.77 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: 1313
        1.33 -     1.45: 1584
        1.45 -     1.57: 3997
        1.57 -     1.70: 0
        1.70 -     1.82: 81
  Bond restraints: 6975
  Sorted by residual:
  bond pdb=" CA  HIS A 323 "
       pdb=" C   HIS A 323 "
    ideal  model  delta    sigma   weight residual
    1.522  1.562 -0.041 1.72e-02 3.38e+03 5.62e+00
  bond pdb=" CG  GLN A 235 "
       pdb=" CD  GLN A 235 "
    ideal  model  delta    sigma   weight residual
    1.516  1.473  0.043 2.50e-02 1.60e+03 2.90e+00
  bond pdb=" CG  GLN D1112 "
       pdb=" CD  GLN D1112 "
    ideal  model  delta    sigma   weight residual
    1.516  1.474  0.042 2.50e-02 1.60e+03 2.88e+00
  bond pdb=" CG  GLU C1076 "
       pdb=" CD  GLU C1076 "
    ideal  model  delta    sigma   weight residual
    1.516  1.479  0.037 2.50e-02 1.60e+03 2.23e+00
  bond pdb=" CG1 ILE B 249 "
       pdb=" CD1 ILE B 249 "
    ideal  model  delta    sigma   weight residual
    1.513  1.456  0.057 3.90e-02 6.57e+02 2.12e+00
  ... (remaining 6970 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.09: 9190
        3.09 -     6.18: 194
        6.18 -     9.28: 20
        9.28 -    12.37: 8
       12.37 -    15.46: 1
  Bond angle restraints: 9413
  Sorted by residual:
  angle pdb=" CA  HIS A 323 "
        pdb=" C   HIS A 323 "
        pdb=" N   GLU A 324 "
      ideal   model   delta    sigma   weight residual
     118.59  129.17  -10.58 1.63e+00 3.76e-01 4.21e+01
  angle pdb=" N   GLU C1076 "
        pdb=" CA  GLU C1076 "
        pdb=" CB  GLU C1076 "
      ideal   model   delta    sigma   weight residual
     110.12  118.20   -8.08 1.47e+00 4.63e-01 3.02e+01
  angle pdb=" N   GLN D1112 "
        pdb=" CA  GLN D1112 "
        pdb=" CB  GLN D1112 "
      ideal   model   delta    sigma   weight residual
     110.30  118.33   -8.03 1.54e+00 4.22e-01 2.72e+01
  angle pdb=" CB  MET D1116 "
        pdb=" CG  MET D1116 "
        pdb=" SD  MET D1116 "
      ideal   model   delta    sigma   weight residual
     112.70  128.16  -15.46 3.00e+00 1.11e-01 2.66e+01
  angle pdb=" CA  GLU C1076 "
        pdb=" CB  GLU C1076 "
        pdb=" CG  GLU C1076 "
      ideal   model   delta    sigma   weight residual
     114.10  123.54   -9.44 2.00e+00 2.50e-01 2.23e+01
  ... (remaining 9408 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 3863
       17.96 -    35.93: 337
       35.93 -    53.89: 48
       53.89 -    71.85: 4
       71.85 -    89.82: 6
  Dihedral angle restraints: 4258
    sinusoidal: 1745
      harmonic: 2513
  Sorted by residual:
  dihedral pdb=" CB  CYS D 208 "
           pdb=" SG  CYS D 208 "
           pdb=" SG  CYS D 284 "
           pdb=" CB  CYS D 284 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -175.82   89.82     1      1.00e+01 1.00e-02 9.57e+01
  dihedral pdb=" N   GLU C1076 "
           pdb=" C   GLU C1076 "
           pdb=" CA  GLU C1076 "
           pdb=" CB  GLU C1076 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.72   -9.92     0      2.50e+00 1.60e-01 1.57e+01
  dihedral pdb=" CA  HIS A 273 "
           pdb=" C   HIS A 273 "
           pdb=" N   ASN A 274 "
           pdb=" CA  ASN A 274 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.34  -17.66     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 4255 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 788
       0.056 -    0.111: 220
       0.111 -    0.167: 60
       0.167 -    0.222: 10
       0.222 -    0.278: 3
  Chirality restraints: 1081
  Sorted by residual:
  chirality pdb=" CA  PRO B 169 "
            pdb=" N   PRO B 169 "
            pdb=" C   PRO B 169 "
            pdb=" CB  PRO B 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CA  GLU C1076 "
            pdb=" N   GLU C1076 "
            pdb=" C   GLU C1076 "
            pdb=" CB  GLU C1076 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" CA  GLN A 235 "
            pdb=" N   GLN A 235 "
            pdb=" C   GLN A 235 "
            pdb=" CB  GLN A 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 1078 not shown)

  Planarity restraints: 1172
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D1158 "   -0.030 2.00e-02 2.50e+03   3.06e-02 2.34e+01
        pdb=" CG  TRP D1158 "    0.083 2.00e-02 2.50e+03
        pdb=" CD1 TRP D1158 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD2 TRP D1158 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP D1158 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP D1158 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP D1158 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D1158 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D1158 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP D1158 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D1011 "   -0.027 2.00e-02 2.50e+03   2.84e-02 2.01e+01
        pdb=" CG  TRP D1011 "    0.077 2.00e-02 2.50e+03
        pdb=" CD1 TRP D1011 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD2 TRP D1011 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP D1011 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP D1011 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP D1011 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D1011 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D1011 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP D1011 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 220 "   -0.022 2.00e-02 2.50e+03   4.43e-02 1.96e+01
        pdb=" C   LEU D 220 "    0.077 2.00e-02 2.50e+03
        pdb=" O   LEU D 220 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   GLN D 221 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 1169 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 43
        2.51 -     3.11: 5613
        3.11 -     3.71: 10443
        3.71 -     4.30: 14029
        4.30 -     4.90: 21621
  Nonbonded interactions: 51749
  Sorted by model distance:
  nonbonded pdb=" O   PHE B  83 "
            pdb=" OD1 ASP B  84 "
     model   vdw
     1.914 3.040
  nonbonded pdb=" O   LYS D1101 "
            pdb=" OG  SER D1105 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   GLN A 235 "
            pdb=" OG1 THR A 242 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   TYR D 277 "
            pdb=" OG1 THR D 280 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OE1 GLN A 263 "
            pdb=" NH2 ARG D1077 "
     model   vdw
     2.241 3.120
  ... (remaining 51744 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 23 through 190 or resid 220 through 344))
  selection = (chain 'B' and resid 23 through 344)
}

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 group one per residue
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:             0.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.190
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.020
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3059
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   0.057   6975  Z= 0.281
  Angle     :  1.068  15.462   9413  Z= 0.593
  Chirality :  0.057   0.278   1081
  Planarity :  0.007   0.058   1172
  Dihedral  : 13.243  87.522   2613
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 20.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.18 (0.27), residues: 833
  helix: -1.65 (0.19), residues: 535
  sheet: -3.24 (0.52), residues: 81
  loop : -2.24 (0.44), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.083   0.005   TRP D1158 
 HIS   0.020   0.002   HIS B 172 
 PHE   0.036   0.002   PHE D1019 
 TYR   0.052   0.002   TYR D 224 
 ARG   0.013   0.001   ARG D1093 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 MET cc_start: -0.2862 (mmm) cc_final: -0.4250 (ptm)
REVERT: A  291 MET cc_start: 0.6140 (ptp) cc_final: 0.5606 (ptp)
REVERT: B  158 MET cc_start: 0.6750 (mpp) cc_final: 0.6458 (mpp)
REVERT: B  326 ARG cc_start: 0.3648 (tpt90) cc_final: 0.1145 (mmp80)
REVERT: C 1116 MET cc_start: 0.4065 (ttt) cc_final: 0.3604 (ttt)
REVERT: D  222 LEU cc_start: 0.7355 (pp) cc_final: 0.7115 (tp)
REVERT: D  259 ARG cc_start: 0.3986 (mtt180) cc_final: 0.2349 (mpt-90)
REVERT: D  261 MET cc_start: 0.2969 (ptt) cc_final: 0.1806 (tmm)
REVERT: D  270 VAL cc_start: 0.6126 (m) cc_final: 0.4950 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 218
  average time/residue: 0.2539
  time to fit residues: 67.9581
Evaluate side-chains
  122 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 34 optimal weight:    0.0870
   chunk 21 optimal weight:    6.9990
   chunk 42 optimal weight:    0.4980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 39 optimal weight:    8.9990
   chunk 48 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.6360

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A 241 GLN
B 159 ASN
B 274 ASN
** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1045 GLN
D1054 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.216748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.155232 restraints weight = 9345.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.159450 restraints weight = 6800.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.162444 restraints weight = 5399.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5110
moved from start:          0.5467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6975  Z= 0.278
  Angle     :  0.836  11.792   9413  Z= 0.435
  Chirality :  0.051   0.191   1081
  Planarity :  0.006   0.055   1172
  Dihedral  :  4.817  19.889    908
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  7.99 %
    Favored  : 91.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.71 (0.28), residues: 833
  helix:  0.35 (0.21), residues: 534
  sheet: -2.53 (0.50), residues: 85
  loop : -1.39 (0.44), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.004   TRP D1158 
 HIS   0.006   0.002   HIS A 172 
 PHE   0.028   0.003   PHE D1108 
 TYR   0.026   0.002   TYR D 230 
 ARG   0.006   0.001   ARG C1037 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 175
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.5324 (tp-100) cc_final: 0.4902 (tp-100)
REVERT: A  332 ASN cc_start: 0.7284 (m-40) cc_final: 0.6988 (p0)
REVERT: B  326 ARG cc_start: 0.4481 (tpt90) cc_final: 0.2154 (tpp-160)
REVERT: C 1035 MET cc_start: 0.7738 (mmp) cc_final: 0.7443 (ptt)
REVERT: D  217 PHE cc_start: 0.7397 (m-80) cc_final: 0.6669 (m-80)
REVERT: D  224 TYR cc_start: 0.7218 (t80) cc_final: 0.6915 (t80)
REVERT: D  258 ASN cc_start: 0.7665 (t0) cc_final: 0.7303 (m-40)
REVERT: D  259 ARG cc_start: 0.3229 (mtt180) cc_final: 0.2891 (ttm170)
REVERT: D  261 MET cc_start: 0.4615 (ptt) cc_final: 0.3712 (tmm)
REVERT: D  270 VAL cc_start: 0.6379 (m) cc_final: 0.6169 (p)
REVERT: D  290 TYR cc_start: 0.2981 (t80) cc_final: 0.1384 (t80)
REVERT: D 1022 ASN cc_start: 0.8923 (m110) cc_final: 0.8579 (m-40)
REVERT: D 1079 ILE cc_start: 0.8385 (pt) cc_final: 0.8128 (pt)
  outliers start: 6
  outliers final: 0
  residues processed: 178
  average time/residue: 0.1960
  time to fit residues: 45.8183
Evaluate side-chains
  119 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 32 optimal weight:    0.4980
   chunk 27 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0370
   chunk 67 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0770
   chunk 73 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0980
   chunk 37 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.3016

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
A 241 GLN
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 172 HIS
B 274 ASN
B 305 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.217665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.156748 restraints weight = 9460.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.160281 restraints weight = 7308.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.162094 restraints weight = 5920.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5342
moved from start:          0.6500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6975  Z= 0.202
  Angle     :  0.694   7.639   9413  Z= 0.361
  Chirality :  0.044   0.159   1081
  Planarity :  0.005   0.083   1172
  Dihedral  :  4.330  17.515    908
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.41 %
    Favored  : 96.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.29), residues: 833
  helix:  0.75 (0.21), residues: 551
  sheet: -2.06 (0.54), residues: 77
  loop : -0.96 (0.46), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.003   TRP D1011 
 HIS   0.005   0.001   HIS B 323 
 PHE   0.029   0.002   PHE D1108 
 TYR   0.025   0.001   TYR D 230 
 ARG   0.006   0.000   ARG B 153 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 158
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 THR cc_start: 0.8126 (m) cc_final: 0.7918 (m)
REVERT: A   87 PHE cc_start: 0.7149 (m-10) cc_final: 0.6862 (m-10)
REVERT: B  326 ARG cc_start: 0.4765 (tpt90) cc_final: 0.2447 (tpp-160)
REVERT: B  332 ASN cc_start: 0.7206 (m110) cc_final: 0.6968 (m110)
REVERT: C 1035 MET cc_start: 0.7727 (mmp) cc_final: 0.7442 (ptt)
REVERT: D  221 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8660 (mm-40)
REVERT: D  258 ASN cc_start: 0.7591 (t0) cc_final: 0.7252 (t0)
REVERT: D  259 ARG cc_start: 0.3484 (mtt180) cc_final: 0.2153 (mtt180)
REVERT: D  261 MET cc_start: 0.4606 (ptt) cc_final: 0.3625 (tmm)
REVERT: D  283 PHE cc_start: 0.8427 (m-80) cc_final: 0.8118 (m-80)
REVERT: D 1019 PHE cc_start: 0.7588 (m-80) cc_final: 0.7133 (t80)
REVERT: D 1022 ASN cc_start: 0.8853 (m110) cc_final: 0.8508 (m-40)
REVERT: D 1079 ILE cc_start: 0.8491 (pt) cc_final: 0.7982 (pt)
REVERT: D 1082 MET cc_start: 0.7716 (tpt) cc_final: 0.6851 (mmt)
  outliers start: 2
  outliers final: 1
  residues processed: 160
  average time/residue: 0.2027
  time to fit residues: 42.5594
Evaluate side-chains
  116 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0370
   chunk 63 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0770
   overall best weight:    0.9820

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

Flipped N/Q/H residues before XYZ refinement:
** A  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 299 GLN
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4622 r_free = 0.4622 target = 0.216655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.177353 restraints weight = 9539.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.175229 restraints weight = 13077.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.176719 restraints weight = 11003.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.4250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6142
moved from start:          0.9629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6975  Z= 0.270
  Angle     :  0.816  12.163   9413  Z= 0.429
  Chirality :  0.049   0.184   1081
  Planarity :  0.005   0.055   1172
  Dihedral  :  4.943  21.349    908
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 14.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  6.68 %
    Favored  : 93.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.29), residues: 833
  helix:  0.69 (0.21), residues: 544
  sheet: -2.48 (0.49), residues: 92
  loop : -1.28 (0.44), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.065   0.004   TRP D1011 
 HIS   0.010   0.002   HIS A  77 
 PHE   0.031   0.003   PHE A 313 
 TYR   0.020   0.002   TYR A 148 
 ARG   0.009   0.001   ARG B 153 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 162
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LEU cc_start: 0.7201 (tt) cc_final: 0.6654 (tp)
REVERT: B   55 CYS cc_start: 0.8246 (m) cc_final: 0.7156 (p)
REVERT: B  275 ILE cc_start: 0.8480 (mp) cc_final: 0.8218 (mt)
REVERT: B  338 LEU cc_start: 0.3482 (mt) cc_final: 0.2816 (mp)
REVERT: D  217 PHE cc_start: 0.5495 (m-80) cc_final: 0.5140 (m-10)
REVERT: D  259 ARG cc_start: 0.4338 (mtt180) cc_final: 0.2258 (mtt180)
REVERT: D  261 MET cc_start: 0.4544 (ptt) cc_final: 0.3514 (tmm)
REVERT: D 1079 ILE cc_start: 0.8435 (pt) cc_final: 0.8102 (pt)
  outliers start: 2
  outliers final: 0
  residues processed: 164
  average time/residue: 0.2045
  time to fit residues: 43.3274
Evaluate side-chains
  106 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 62 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 69 optimal weight:   20.0000
   chunk 72 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A  77 HIS
** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 299 GLN
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 HIS
** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.211159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.186838 restraints weight = 9534.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.179058 restraints weight = 10558.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.175836 restraints weight = 10011.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.4245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6224
moved from start:          1.0475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6975  Z= 0.227
  Angle     :  0.739  10.422   9413  Z= 0.378
  Chirality :  0.046   0.175   1081
  Planarity :  0.005   0.054   1172
  Dihedral  :  4.429  16.709    908
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.28 %
    Favored  : 96.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.29), residues: 833
  helix:  1.06 (0.21), residues: 533
  sheet: -2.37 (0.50), residues: 91
  loop : -1.00 (0.44), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.077   0.004   TRP D1158 
 HIS   0.006   0.001   HIS B 323 
 PHE   0.020   0.002   PHE D1108 
 TYR   0.025   0.002   TYR D 224 
 ARG   0.008   0.001   ARG B 153 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LEU cc_start: 0.6851 (tt) cc_final: 0.6330 (tt)
REVERT: A  240 GLU cc_start: 0.6089 (pp20) cc_final: 0.5232 (tm-30)
REVERT: A  264 GLU cc_start: 0.6613 (pt0) cc_final: 0.6375 (pt0)
REVERT: B  230 ARG cc_start: 0.7755 (tpp80) cc_final: 0.7285 (tpm170)
REVERT: B  275 ILE cc_start: 0.8645 (mp) cc_final: 0.8444 (mt)
REVERT: C 1065 MET cc_start: 0.8115 (mmp) cc_final: 0.7890 (mmp)
REVERT: D  259 ARG cc_start: 0.4469 (mtt180) cc_final: 0.2265 (mtt180)
REVERT: D  261 MET cc_start: 0.4599 (ptt) cc_final: 0.3593 (tmm)
REVERT: D 1048 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.5665 (pp30)
REVERT: D 1079 ILE cc_start: 0.8638 (pt) cc_final: 0.8431 (pt)
REVERT: D 1082 MET cc_start: 0.7405 (mmm) cc_final: 0.6870 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 153
  average time/residue: 0.1906
  time to fit residues: 38.3273
Evaluate side-chains
  113 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 39 optimal weight:    0.0020
   chunk 62 optimal weight:    7.9990
   chunk 49 optimal weight:    0.0070
   chunk 7 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 81 optimal weight:    0.7980
   chunk 40 optimal weight:    8.9990
   chunk 64 optimal weight:    3.9990
   chunk 73 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9980
   chunk 80 optimal weight:    8.9990
   overall best weight:    0.4606

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 HIS
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 323 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.207045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 100)---------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.157758 restraints weight = 9524.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.157941 restraints weight = 8704.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.157669 restraints weight = 8208.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.4013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6550
moved from start:          1.1032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6975  Z= 0.193
  Angle     :  0.712   8.727   9413  Z= 0.368
  Chirality :  0.045   0.152   1081
  Planarity :  0.004   0.054   1172
  Dihedral  :  4.263  19.318    908
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.83 %
    Favored  : 98.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.29), residues: 833
  helix:  1.12 (0.22), residues: 538
  sheet: -1.82 (0.52), residues: 94
  loop : -1.15 (0.44), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.083   0.004   TRP D1158 
 HIS   0.007   0.001   HIS B 323 
 PHE   0.019   0.001   PHE D1031 
 TYR   0.022   0.002   TYR D 230 
 ARG   0.005   0.000   ARG D1050 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 LEU cc_start: 0.7102 (tt) cc_final: 0.6461 (tt)
REVERT: A  240 GLU cc_start: 0.5711 (pp20) cc_final: 0.5341 (tm-30)
REVERT: A  260 ARG cc_start: 0.8361 (tmm-80) cc_final: 0.8092 (tmm-80)
REVERT: A  264 GLU cc_start: 0.7059 (pt0) cc_final: 0.6789 (pt0)
REVERT: B  230 ARG cc_start: 0.7809 (tpp80) cc_final: 0.7427 (tpm170)
REVERT: C 1065 MET cc_start: 0.8328 (mmp) cc_final: 0.7897 (mmp)
REVERT: D  259 ARG cc_start: 0.4109 (mtt180) cc_final: 0.2202 (mtt180)
REVERT: D  261 MET cc_start: 0.4693 (ptt) cc_final: 0.3672 (tmm)
REVERT: D  267 MET cc_start: 0.1831 (mmm) cc_final: 0.0995 (mpp)
REVERT: D 1022 ASN cc_start: 0.8356 (m-40) cc_final: 0.8155 (m110)
REVERT: D 1079 ILE cc_start: 0.8697 (pt) cc_final: 0.8407 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1985
  time to fit residues: 37.0999
Evaluate side-chains
  110 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0060
   chunk 25 optimal weight:    0.8980
   chunk 63 optimal weight:   10.0000
   chunk 11 optimal weight:    0.0570
   chunk 80 optimal weight:    0.8980
   chunk 54 optimal weight:    4.9990
   chunk 62 optimal weight:    8.9990
   chunk 44 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.5514

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 172 HIS
B 235 GLN
** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 323 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.206802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 118)---------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.157349 restraints weight = 9877.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.154951 restraints weight = 12199.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.156943 restraints weight = 11714.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6659
moved from start:          1.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6975  Z= 0.199
  Angle     :  0.730   9.745   9413  Z= 0.375
  Chirality :  0.045   0.169   1081
  Planarity :  0.004   0.053   1172
  Dihedral  :  4.204  18.120    908
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.29), residues: 833
  helix:  1.08 (0.22), residues: 545
  sheet: -1.69 (0.53), residues: 95
  loop : -1.00 (0.45), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.089   0.004   TRP D1158 
 HIS   0.007   0.001   HIS B 323 
 PHE   0.021   0.002   PHE D 279 
 TYR   0.026   0.002   TYR D 210 
 ARG   0.006   0.001   ARG D1074 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 ILE cc_start: 0.9040 (mp) cc_final: 0.8788 (mt)
REVERT: A  240 GLU cc_start: 0.5733 (pp20) cc_final: 0.5361 (tm-30)
REVERT: A  260 ARG cc_start: 0.8486 (tmm-80) cc_final: 0.8225 (tmm-80)
REVERT: A  264 GLU cc_start: 0.6981 (pt0) cc_final: 0.6750 (pt0)
REVERT: B  230 ARG cc_start: 0.7680 (tpp80) cc_final: 0.7297 (tpm170)
REVERT: C 1065 MET cc_start: 0.8506 (mmp) cc_final: 0.7961 (mmp)
REVERT: D  259 ARG cc_start: 0.4058 (mtt180) cc_final: 0.2109 (mtt180)
REVERT: D  261 MET cc_start: 0.5130 (ptt) cc_final: 0.3867 (tmm)
REVERT: D  267 MET cc_start: 0.1906 (mmm) cc_final: 0.0950 (mpp)
REVERT: D 1079 ILE cc_start: 0.8717 (pt) cc_final: 0.8503 (pt)
REVERT: D 1082 MET cc_start: 0.7388 (mmm) cc_final: 0.7021 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1917
  time to fit residues: 37.2038
Evaluate side-chains
  111 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0050
   chunk 74 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0270
   chunk 52 optimal weight:    0.2980
   chunk 26 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 76 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0970
   overall best weight:    0.2250

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 HIS
** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 323 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.207765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 109)---------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.153292 restraints weight = 9511.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.154824 restraints weight = 8680.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.153029 restraints weight = 8473.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6701
moved from start:          1.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6975  Z= 0.187
  Angle     :  0.744   9.294   9413  Z= 0.388
  Chirality :  0.045   0.172   1081
  Planarity :  0.005   0.061   1172
  Dihedral  :  4.106  19.333    908
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.49 (0.29), residues: 833
  helix:  1.12 (0.22), residues: 539
  sheet: -1.39 (0.55), residues: 92
  loop : -0.79 (0.45), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.073   0.003   TRP D1158 
 HIS   0.009   0.001   HIS B 323 
 PHE   0.035   0.001   PHE D 271 
 TYR   0.023   0.002   TYR D 230 
 ARG   0.006   0.000   ARG D1074 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 ILE cc_start: 0.9068 (mp) cc_final: 0.8804 (mt)
REVERT: A  174 LEU cc_start: 0.6669 (tp) cc_final: 0.6180 (tp)
REVERT: A  240 GLU cc_start: 0.5538 (pp20) cc_final: 0.5200 (tm-30)
REVERT: A  260 ARG cc_start: 0.8512 (tmm-80) cc_final: 0.8277 (tmm-80)
REVERT: A  304 ASP cc_start: 0.7597 (m-30) cc_final: 0.7262 (m-30)
REVERT: B  230 ARG cc_start: 0.7607 (tpp80) cc_final: 0.7284 (tpm170)
REVERT: C 1065 MET cc_start: 0.8328 (mmp) cc_final: 0.7606 (mmp)
REVERT: D  261 MET cc_start: 0.5152 (ptt) cc_final: 0.3840 (tmm)
REVERT: D 1079 ILE cc_start: 0.8846 (pt) cc_final: 0.8532 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1976
  time to fit residues: 37.7149
Evaluate side-chains
  115 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 25 optimal weight:    0.1980
   chunk 18 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 32 optimal weight:    0.2980
   chunk 81 optimal weight:    4.9990
   chunk 68 optimal weight:   20.0000
   chunk 30 optimal weight:    0.0570
   chunk 48 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0670
   overall best weight:    0.2436

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 305 GLN
A 323 HIS
** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1022 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.207712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.167463 restraints weight = 9526.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.155095 restraints weight = 11227.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.155826 restraints weight = 12574.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6640
moved from start:          1.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6975  Z= 0.187
  Angle     :  0.742   9.526   9413  Z= 0.389
  Chirality :  0.045   0.169   1081
  Planarity :  0.004   0.053   1172
  Dihedral  :  4.055  22.128    908
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.29), residues: 833
  helix:  1.08 (0.22), residues: 551
  sheet: -1.10 (0.56), residues: 92
  loop : -0.70 (0.46), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.097   0.005   TRP D1158 
 HIS   0.002   0.001   HIS B 314 
 PHE   0.016   0.001   PHE D 279 
 TYR   0.030   0.002   TYR C1072 
 ARG   0.011   0.001   ARG A  65 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.6409 (mp) cc_final: 0.6136 (mp)
REVERT: A   70 ILE cc_start: 0.8949 (mp) cc_final: 0.8706 (mt)
REVERT: A  103 MET cc_start: 0.7459 (tpt) cc_final: 0.7013 (tpp)
REVERT: A  174 LEU cc_start: 0.6661 (tp) cc_final: 0.6165 (tp)
REVERT: A  230 ARG cc_start: 0.8522 (ptm160) cc_final: 0.8283 (ptm-80)
REVERT: A  240 GLU cc_start: 0.5460 (pp20) cc_final: 0.5151 (tm-30)
REVERT: A  304 ASP cc_start: 0.7582 (m-30) cc_final: 0.7192 (m-30)
REVERT: B  230 ARG cc_start: 0.7542 (tpp80) cc_final: 0.7323 (tpm170)
REVERT: D  259 ARG cc_start: 0.3935 (mtt180) cc_final: 0.2061 (mtt180)
REVERT: D  261 MET cc_start: 0.5195 (ptt) cc_final: 0.3900 (tmm)
REVERT: D 1082 MET cc_start: 0.7595 (mmm) cc_final: 0.6825 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1905
  time to fit residues: 35.0321
Evaluate side-chains
  116 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 62 optimal weight:   20.0000
   chunk 3 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0070
   chunk 67 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 HIS
B 235 GLN
** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.203940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.176895 restraints weight = 9594.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.169505 restraints weight = 12049.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.167288 restraints weight = 11036.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.4160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6464
moved from start:          1.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6975  Z= 0.219
  Angle     :  0.769   8.580   9413  Z= 0.405
  Chirality :  0.047   0.170   1081
  Planarity :  0.005   0.053   1172
  Dihedral  :  4.226  22.363    908
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.29), residues: 833
  helix:  1.03 (0.22), residues: 549
  sheet: -1.20 (0.56), residues: 95
  loop : -0.78 (0.46), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.096   0.004   TRP D1158 
 HIS   0.004   0.001   HIS B 314 
 PHE   0.020   0.002   PHE D1108 
 TYR   0.035   0.002   TYR C1072 
 ARG   0.007   0.001   ARG D1050 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.6055 (mp) cc_final: 0.5852 (mp)
REVERT: A   61 LEU cc_start: 0.6717 (tp) cc_final: 0.6278 (tp)
REVERT: A   70 ILE cc_start: 0.9015 (mp) cc_final: 0.8790 (mt)
REVERT: A  174 LEU cc_start: 0.6835 (tp) cc_final: 0.6334 (tp)
REVERT: A  240 GLU cc_start: 0.5670 (pp20) cc_final: 0.5237 (tm-30)
REVERT: C 1035 MET cc_start: 0.6094 (pmm) cc_final: 0.5885 (pmm)
REVERT: C 1076 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6468 (mt-10)
REVERT: D  261 MET cc_start: 0.4796 (ptt) cc_final: 0.3807 (tmm)
REVERT: D  265 SER cc_start: 0.5103 (p) cc_final: 0.4820 (p)
REVERT: D  267 MET cc_start: 0.2560 (mmm) cc_final: 0.1827 (mpp)
REVERT: D 1079 ILE cc_start: 0.8957 (pt) cc_final: 0.8755 (pt)
REVERT: D 1082 MET cc_start: 0.7296 (mmm) cc_final: 0.6708 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1736
  time to fit residues: 33.3239
Evaluate side-chains
  115 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 64 optimal weight:    0.3980
   chunk 75 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 20 optimal weight:    0.3980
   chunk 35 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0030
   overall best weight:    0.4390

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 305 GLN
** B 299 GLN ** 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 = 0.4512 r_free = 0.4512 target = 0.205047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.170295 restraints weight = 9502.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.163647 restraints weight = 12032.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.161084 restraints weight = 10727.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.4087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6567
moved from start:          1.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6975  Z= 0.198
  Angle     :  0.762   8.907   9413  Z= 0.397
  Chirality :  0.046   0.172   1081
  Planarity :  0.005   0.053   1172
  Dihedral  :  4.181  22.764    908
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.29), residues: 833
  helix:  1.13 (0.22), residues: 544
  sheet: -1.15 (0.58), residues: 93
  loop : -0.65 (0.45), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.088   0.004   TRP D1158 
 HIS   0.002   0.001   HIS B 172 
 PHE   0.016   0.001   PHE D 271 
 TYR   0.034   0.002   TYR C1072 
 ARG   0.008   0.001   ARG D1050 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2463.40 seconds
wall clock time: 44 minutes 42.46 seconds (2682.46 seconds total)