Starting phenix.real_space_refine
on Wed Mar 12 02:32:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cr2_16802/03_2025/8cr2_16802.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cr2_16802/03_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_16802/03_2025/8cr2_16802.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cr2_16802/03_2025/8cr2_16802.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cr2_16802/03_2025/8cr2_16802.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cr2_16802/03_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-5624/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: 4.44, per 1000 atoms: 0.65
  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: 1.80
  Conformation dependent library (CDL) restraints added in 950.9 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: 0.67
  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: 1.78

  Time building geometry restraints manager: 2.14 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:             0.990
  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:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.820
  Find NCS groups from input model:        0.210
  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:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.390
-------------------------------------------------------------------------------
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  : 0.734 
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: 0.2481
  time to fit residues: 66.6096
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  : 0.690 
-------------------------------------------------------------------------------
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 = 0.216761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.155398 restraints weight = 9345.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.159534 restraints weight = 6802.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.161990 restraints weight = 5450.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5118
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  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.5322 (tp-100) cc_final: 0.4898 (tp-100)
REVERT: A  332 ASN cc_start: 0.7307 (m-40) cc_final: 0.6999 (p0)
REVERT: B  326 ARG cc_start: 0.4488 (tpt90) cc_final: 0.2154 (tpp-160)
REVERT: C 1035 MET cc_start: 0.7757 (mmp) cc_final: 0.7448 (ptt)
REVERT: D  217 PHE cc_start: 0.7394 (m-80) cc_final: 0.6665 (m-80)
REVERT: D  224 TYR cc_start: 0.7196 (t80) cc_final: 0.6888 (t80)
REVERT: D  258 ASN cc_start: 0.7668 (t0) cc_final: 0.7307 (m-40)
REVERT: D  259 ARG cc_start: 0.3236 (mtt180) cc_final: 0.2899 (ttm170)
REVERT: D  261 MET cc_start: 0.4622 (ptt) cc_final: 0.3716 (tmm)
REVERT: D  270 VAL cc_start: 0.6374 (m) cc_final: 0.6163 (p)
REVERT: D  290 TYR cc_start: 0.2978 (t80) cc_final: 0.1380 (t80)
REVERT: D 1022 ASN cc_start: 0.8915 (m110) cc_final: 0.8572 (m-40)
REVERT: D 1079 ILE cc_start: 0.8386 (pt) cc_final: 0.8130 (pt)
  outliers start: 6
  outliers final: 0
  residues processed: 178
  average time/residue: 0.2044
  time to fit residues: 48.1785
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  : 0.742 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0470
   chunk 67 optimal weight:    7.9990
   chunk 28 optimal weight:    0.1980
   chunk 47 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 25 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0670
   overall best weight:    0.3216

-------------------------------------------------------------------------------
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 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 = 0.4588 r_free = 0.4588 target = 0.217149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.164199 restraints weight = 9441.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.164908 restraints weight = 7295.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.164051 restraints weight = 5700.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5338
moved from start:          0.6548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6975  Z= 0.205
  Angle     :  0.698   7.802   9413  Z= 0.365
  Chirality :  0.045   0.159   1081
  Planarity :  0.006   0.100   1172
  Dihedral  :  4.346  17.829    908
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.41 %
    Favored  : 96.46 %
  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:  0.01 (0.29), residues: 833
  helix:  0.77 (0.21), residues: 551
  sheet: -2.07 (0.55), residues: 77
  loop : -0.98 (0.46), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP D1011 
 HIS   0.005   0.001   HIS B 323 
 PHE   0.030   0.002   PHE D1108 
 TYR   0.023   0.002   TYR D 228 
 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
  162 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 0.698 
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   87 PHE cc_start: 0.7202 (m-10) cc_final: 0.6923 (m-10)
REVERT: B  326 ARG cc_start: 0.4679 (tpt90) cc_final: 0.2414 (tpp-160)
REVERT: B  332 ASN cc_start: 0.7280 (m110) cc_final: 0.7011 (m110)
REVERT: D  221 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8645 (mm-40)
REVERT: D  258 ASN cc_start: 0.7724 (t0) cc_final: 0.7426 (t0)
REVERT: D  261 MET cc_start: 0.4706 (ptt) cc_final: 0.3660 (tmm)
REVERT: D  283 PHE cc_start: 0.8307 (m-80) cc_final: 0.8092 (m-80)
REVERT: D 1019 PHE cc_start: 0.7303 (m-80) cc_final: 0.7091 (t80)
REVERT: D 1022 ASN cc_start: 0.8695 (m110) cc_final: 0.8365 (m-40)
REVERT: D 1079 ILE cc_start: 0.8458 (pt) cc_final: 0.7921 (pt)
  outliers start: 1
  outliers final: 1
  residues processed: 162
  average time/residue: 0.1922
  time to fit residues: 40.9527
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  : 0.746 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 63 optimal weight:   10.0000
   chunk 6 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 75 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   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 ** both conformations clash, **PLEASE CHECK MANUALLY**
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.214863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 114)---------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.159069 restraints weight = 9532.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.159367 restraints weight = 8686.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.160197 restraints weight = 7785.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.4059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6336
moved from start:          0.8858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6975  Z= 0.250
  Angle     :  0.772  11.075   9413  Z= 0.401
  Chirality :  0.047   0.191   1081
  Planarity :  0.005   0.054   1172
  Dihedral  :  4.589  18.704    908
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  4.85 %
    Favored  : 94.76 %
  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: -0.11 (0.29), residues: 833
  helix:  0.82 (0.21), residues: 545
  sheet: -2.33 (0.49), residues: 92
  loop : -1.20 (0.46), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.003   TRP D1011 
 HIS   0.010   0.002   HIS A  77 
 PHE   0.021   0.002   PHE D1108 
 TYR   0.014   0.001   TYR A 148 
 ARG   0.007   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
  161 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 158
  time to evaluate  : 0.798 
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: symmetry clash
REVERT: A  174 LEU cc_start: 0.7047 (tt) cc_final: 0.6608 (tp)
REVERT: B  158 MET cc_start: 0.7087 (mtm) cc_final: 0.6703 (mtm)
REVERT: B  338 LEU cc_start: 0.3238 (mt) cc_final: 0.2836 (mt)
REVERT: D  261 MET cc_start: 0.4695 (ptt) cc_final: 0.3634 (tmm)
REVERT: D  283 PHE cc_start: 0.8629 (m-80) cc_final: 0.8305 (m-80)
REVERT: D 1022 ASN cc_start: 0.8881 (m110) cc_final: 0.8601 (m110)
REVERT: D 1048 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6070 (pp30)
REVERT: D 1049 MET cc_start: 0.7782 (ptp) cc_final: 0.7296 (ptp)
REVERT: D 1052 GLU cc_start: 0.8683 (pm20) cc_final: 0.8364 (pm20)
REVERT: D 1079 ILE cc_start: 0.8593 (pt) cc_final: 0.8374 (pt)
REVERT: D 1082 MET cc_start: 0.7430 (mmm) cc_final: 0.6942 (mmt)
REVERT: D 1116 MET cc_start: 0.9147 (mtp) cc_final: 0.8924 (mtm)
  outliers start: 3
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1951
  time to fit residues: 41.1623
Evaluate side-chains
  117 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 30 optimal weight:    0.0970
   chunk 80 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.7178

-------------------------------------------------------------------------------
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
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 HIS
B 323 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.213203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.184628 restraints weight = 9418.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.181489 restraints weight = 11627.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.178610 restraints weight = 9815.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.4265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6060
moved from start:          0.9834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6975  Z= 0.217
  Angle     :  0.705   9.061   9413  Z= 0.366
  Chirality :  0.045   0.156   1081
  Planarity :  0.005   0.054   1172
  Dihedral  :  4.341  17.314    908
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  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:  0.20 (0.29), residues: 833
  helix:  1.03 (0.22), residues: 534
  sheet: -2.04 (0.53), residues: 91
  loop : -0.97 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.003   TRP D1011 
 HIS   0.006   0.001   HIS B 323 
 PHE   0.022   0.002   PHE A  87 
 TYR   0.034   0.002   TYR D 210 
 ARG   0.008   0.000   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
  157 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 155
  time to evaluate  : 0.812 
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   87 PHE cc_start: 0.7433 (m-10) cc_final: 0.7213 (m-10)
REVERT: A  103 MET cc_start: 0.7261 (tpt) cc_final: 0.6585 (tpp)
REVERT: A  174 LEU cc_start: 0.6919 (tt) cc_final: 0.6340 (tt)
REVERT: A  240 GLU cc_start: 0.5826 (pp20) cc_final: 0.4921 (tm-30)
REVERT: A  264 GLU cc_start: 0.6596 (pt0) cc_final: 0.6233 (pt0)
REVERT: A  272 THR cc_start: 0.8286 (t) cc_final: 0.8062 (m)
REVERT: B   55 CYS cc_start: 0.8165 (m) cc_final: 0.6973 (p)
REVERT: B  158 MET cc_start: 0.7046 (mtm) cc_final: 0.6756 (mtm)
REVERT: B  230 ARG cc_start: 0.7732 (tpp80) cc_final: 0.7333 (tpm170)
REVERT: C 1035 MET cc_start: 0.6536 (ptt) cc_final: 0.6285 (ptt)
REVERT: D  261 MET cc_start: 0.4308 (ptt) cc_final: 0.3416 (tmm)
REVERT: D 1079 ILE cc_start: 0.8714 (pt) cc_final: 0.8428 (pt)
REVERT: D 1096 GLN cc_start: 0.6726 (OUTLIER) cc_final: 0.6138 (tp-100)
  outliers start: 2
  outliers final: 1
  residues processed: 156
  average time/residue: 0.2047
  time to fit residues: 42.6041
Evaluate side-chains
  122 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 120
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
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:    0.0370
   chunk 62 optimal weight:    4.9990
   chunk 49 optimal weight:    0.3980
   chunk 7 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 75 optimal weight:    0.0670
   chunk 80 optimal weight:    6.9990
   overall best weight:    1.3000

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
** A  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 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 314 HIS
B 323 HIS
D1008 HIS
D1022 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.200304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 114)---------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.138622 restraints weight = 9625.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.137728 restraints weight = 9446.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.137653 restraints weight = 9539.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7022
moved from start:          1.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   6975  Z= 0.309
  Angle     :  0.843   9.647   9413  Z= 0.447
  Chirality :  0.050   0.222   1081
  Planarity :  0.005   0.052   1172
  Dihedral  :  4.913  18.334    908
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 14.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  4.19 %
    Favored  : 95.67 %
  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: -0.39 (0.28), residues: 833
  helix:  0.48 (0.21), residues: 538
  sheet: -2.11 (0.52), residues: 95
  loop : -0.98 (0.44), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.076   0.005   TRP D1158 
 HIS   0.005   0.002   HIS B 323 
 PHE   0.030   0.003   PHE A 313 
 TYR   0.022   0.002   TYR D 230 
 ARG   0.013   0.001   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
  158 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.770 
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  103 MET cc_start: 0.7990 (tpt) cc_final: 0.7563 (tpp)
REVERT: A  240 GLU cc_start: 0.6282 (pp20) cc_final: 0.5433 (tm-30)
REVERT: B  230 ARG cc_start: 0.7807 (tpp80) cc_final: 0.7243 (tpm170)
REVERT: B  291 MET cc_start: 0.8716 (ppp) cc_final: 0.8325 (ppp)
REVERT: C 1059 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7497 (mt-10)
REVERT: D  261 MET cc_start: 0.4836 (ptt) cc_final: 0.3716 (tmm)
REVERT: D  267 MET cc_start: 0.2116 (mmm) cc_final: 0.1340 (mpp)
REVERT: D 1022 ASN cc_start: 0.9163 (m-40) cc_final: 0.8939 (m110)
REVERT: D 1065 MET cc_start: 0.8358 (tpp) cc_final: 0.8157 (mmm)
REVERT: D 1082 MET cc_start: 0.7804 (mmm) cc_final: 0.7507 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1989
  time to fit residues: 41.0478
Evaluate side-chains
  120 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0050
   chunk 25 optimal weight:    4.9990
   chunk 63 optimal weight:   20.0000
   chunk 11 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 44 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.7598

-------------------------------------------------------------------------------
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 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 235 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 = 0.4498 r_free = 0.4498 target = 0.203238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 118)---------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.149145 restraints weight = 9532.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.149027 restraints weight = 8757.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.148512 restraints weight = 8484.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6885
moved from start:          1.2489

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= 0.227
  Angle     :  0.746  10.099   9413  Z= 0.385
  Chirality :  0.046   0.178   1081
  Planarity :  0.005   0.053   1172
  Dihedral  :  4.477  22.504    908
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  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:  0.09 (0.29), residues: 833
  helix:  0.92 (0.22), residues: 535
  sheet: -1.87 (0.54), residues: 96
  loop : -1.03 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.002   TRP D1158 
 HIS   0.004   0.001   HIS A 273 
 PHE   0.026   0.002   PHE D 279 
 TYR   0.016   0.001   TYR C1072 
 ARG   0.006   0.001   ARG A 153 

*********************** 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
  148 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 ILE cc_start: 0.9033 (tt) cc_final: 0.8820 (mt)
REVERT: A  156 LYS cc_start: 0.8053 (ptmm) cc_final: 0.7792 (tttp)
REVERT: A  174 LEU cc_start: 0.7013 (tp) cc_final: 0.6496 (tp)
REVERT: A  240 GLU cc_start: 0.5997 (pp20) cc_final: 0.5540 (tm-30)
REVERT: A  332 ASN cc_start: 0.6872 (m-40) cc_final: 0.6629 (p0)
REVERT: D  221 GLN cc_start: 0.8437 (tp-100) cc_final: 0.7900 (mm-40)
REVERT: D  261 MET cc_start: 0.5168 (ptt) cc_final: 0.3849 (tmm)
REVERT: D  267 MET cc_start: 0.2673 (mmm) cc_final: 0.1887 (mpp)
REVERT: D 1049 MET cc_start: 0.7591 (ptp) cc_final: 0.6699 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.1878
  time to fit residues: 36.8380
Evaluate side-chains
  117 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 32 optimal weight:    0.2980
   chunk 74 optimal weight:    0.0470
   chunk 28 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0870
   chunk 52 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0870
   chunk 76 optimal weight:    0.6980
   chunk 39 optimal weight:    8.9990
   overall best weight:    0.2434

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 273 HIS
A 305 GLN
A 323 HIS
B 172 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.206249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 109)---------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.146410 restraints weight = 9440.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.147537 restraints weight = 9289.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.147227 restraints weight = 8644.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6887
moved from start:          1.2679

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= 0.184
  Angle     :  0.744  11.285   9413  Z= 0.380
  Chirality :  0.045   0.200   1081
  Planarity :  0.005   0.054   1172
  Dihedral  :  4.283  22.169    908
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  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:  0.38 (0.29), residues: 833
  helix:  1.09 (0.22), residues: 537
  sheet: -1.59 (0.56), residues: 96
  loop : -0.88 (0.45), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.079   0.004   TRP D1158 
 HIS   0.005   0.001   HIS D1008 
 PHE   0.019   0.001   PHE D 279 
 TYR   0.026   0.002   TYR D 224 
 ARG   0.006   0.001   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
  146 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.781 
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   61 LEU cc_start: 0.6970 (tp) cc_final: 0.6391 (tp)
REVERT: A   70 ILE cc_start: 0.8968 (tt) cc_final: 0.8663 (mt)
REVERT: A  156 LYS cc_start: 0.8132 (ptmm) cc_final: 0.7874 (tttp)
REVERT: A  174 LEU cc_start: 0.7077 (tp) cc_final: 0.6623 (tp)
REVERT: A  230 ARG cc_start: 0.8706 (ptm160) cc_final: 0.8486 (ptm-80)
REVERT: A  240 GLU cc_start: 0.5992 (pp20) cc_final: 0.5617 (tm-30)
REVERT: A  279 GLN cc_start: 0.8171 (mp10) cc_final: 0.7954 (mp10)
REVERT: A  304 ASP cc_start: 0.7985 (m-30) cc_final: 0.7722 (m-30)
REVERT: A  332 ASN cc_start: 0.7072 (m-40) cc_final: 0.6820 (p0)
REVERT: B   37 LEU cc_start: 0.8199 (mm) cc_final: 0.7955 (mm)
REVERT: C 1065 MET cc_start: 0.8164 (mmp) cc_final: 0.7553 (mmt)
REVERT: D  261 MET cc_start: 0.5145 (ptt) cc_final: 0.3951 (tmm)
REVERT: D  267 MET cc_start: 0.2948 (mmm) cc_final: 0.2221 (mpp)
REVERT: D 1022 ASN cc_start: 0.8908 (m110) cc_final: 0.8676 (m110)
REVERT: D 1082 MET cc_start: 0.7886 (mmm) cc_final: 0.7281 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1743
  time to fit residues: 34.2087
Evaluate side-chains
  117 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
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:    0.0270
   chunk 43 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0060
   chunk 32 optimal weight:    0.0020
   chunk 81 optimal weight:    3.9990
   chunk 68 optimal weight:    8.9990
   chunk 30 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 8 optimal weight:    6.9990
   overall best weight:    0.2662

-------------------------------------------------------------------------------
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**
B 235 GLN
D1022 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.206481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.173623 restraints weight = 9475.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.167287 restraints weight = 11879.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.165955 restraints weight = 10354.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.4135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6510
moved from start:          1.2864

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= 0.184
  Angle     :  0.727   8.601   9413  Z= 0.376
  Chirality :  0.045   0.192   1081
  Planarity :  0.004   0.053   1172
  Dihedral  :  4.153  22.617    908
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  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:  0.52 (0.30), residues: 833
  helix:  1.17 (0.22), residues: 539
  sheet: -1.45 (0.55), residues: 96
  loop : -0.80 (0.45), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.070   0.003   TRP D1158 
 HIS   0.004   0.001   HIS D1008 
 PHE   0.015   0.001   PHE D 279 
 TYR   0.021   0.001   TYR B 148 
 ARG   0.007   0.001   ARG D1074 

*********************** 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
  140 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.7062 (tp) cc_final: 0.6528 (tp)
REVERT: A   70 ILE cc_start: 0.8996 (tt) cc_final: 0.8688 (mt)
REVERT: A  156 LYS cc_start: 0.8038 (ptmm) cc_final: 0.7701 (tttp)
REVERT: A  174 LEU cc_start: 0.6882 (tp) cc_final: 0.6464 (tp)
REVERT: A  240 GLU cc_start: 0.5894 (pp20) cc_final: 0.5328 (tm-30)
REVERT: B   37 LEU cc_start: 0.8228 (mm) cc_final: 0.7988 (mm)
REVERT: B  306 MET cc_start: 0.8005 (mtp) cc_final: 0.7584 (ttp)
REVERT: B  332 ASN cc_start: 0.7991 (m110) cc_final: 0.7707 (m110)
REVERT: C 1065 MET cc_start: 0.8305 (mmp) cc_final: 0.7947 (mmp)
REVERT: D  261 MET cc_start: 0.4783 (ptt) cc_final: 0.3532 (tmm)
REVERT: D  265 SER cc_start: 0.6182 (p) cc_final: 0.4940 (p)
REVERT: D  267 MET cc_start: 0.3370 (mmm) cc_final: 0.2651 (mpp)
REVERT: D 1065 MET cc_start: 0.8517 (tpp) cc_final: 0.8148 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1851
  time to fit residues: 34.7340
Evaluate side-chains
  120 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 19 optimal weight:    0.0870
   chunk 38 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 62 optimal weight:   20.0000
   chunk 3 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.6558

-------------------------------------------------------------------------------
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 273 HIS
** A 305 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 = 0.4499 r_free = 0.4499 target = 0.203226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.179109 restraints weight = 9602.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.169176 restraints weight = 11385.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.168900 restraints weight = 11508.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.4178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6529
moved from start:          1.3274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6975  Z= 0.211
  Angle     :  0.758   8.687   9413  Z= 0.397
  Chirality :  0.046   0.230   1081
  Planarity :  0.006   0.113   1172
  Dihedral  :  4.233  22.133    908
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  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:  0.57 (0.30), residues: 833
  helix:  1.15 (0.22), residues: 545
  sheet: -1.45 (0.56), residues: 96
  loop : -0.62 (0.47), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.069   0.003   TRP D1158 
 HIS   0.003   0.001   HIS B 323 
 PHE   0.014   0.001   PHE D 279 
 TYR   0.022   0.002   TYR D 230 
 ARG   0.005   0.001   ARG D1074 

********************** 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
  139 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.7163 (tp) cc_final: 0.6673 (tp)
REVERT: A   70 ILE cc_start: 0.8879 (tt) cc_final: 0.8620 (mt)
REVERT: A  156 LYS cc_start: 0.8087 (ptmm) cc_final: 0.7704 (tttp)
REVERT: B   37 LEU cc_start: 0.8231 (mm) cc_final: 0.7976 (mm)
REVERT: B  306 MET cc_start: 0.7901 (mtp) cc_final: 0.7589 (mtm)
REVERT: B  332 ASN cc_start: 0.7902 (m110) cc_final: 0.7610 (m110)
REVERT: D  261 MET cc_start: 0.4680 (ptt) cc_final: 0.3559 (tmm)
REVERT: D  265 SER cc_start: 0.5165 (p) cc_final: 0.4817 (p)
REVERT: D  267 MET cc_start: 0.3100 (mmm) cc_final: 0.2446 (mpp)
REVERT: D 1065 MET cc_start: 0.8490 (tpp) cc_final: 0.8258 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1757
  time to fit residues: 33.1322
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  : 0.758 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 64 optimal weight:    8.9990
   chunk 75 optimal weight:    0.1980
   chunk 12 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.0388

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.199367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.171722 restraints weight = 9524.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.169074 restraints weight = 12532.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.165564 restraints weight = 11325.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6645
moved from start:          1.3984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   6975  Z= 0.268
  Angle     :  0.795   9.908   9413  Z= 0.422
  Chirality :  0.048   0.200   1081
  Planarity :  0.005   0.085   1172
  Dihedral  :  4.568  22.539    908
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.13 %
    Favored  : 99.74 %
  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:  0.40 (0.30), residues: 833
  helix:  1.04 (0.22), residues: 545
  sheet: -1.69 (0.56), residues: 96
  loop : -0.66 (0.47), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.068   0.003   TRP D1158 
 HIS   0.004   0.001   HIS A 314 
 PHE   0.013   0.002   PHE D 279 
 TYR   0.018   0.001   TYR D 210 
 ARG   0.005   0.001   ARG A 153 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2464.98 seconds
wall clock time: 43 minutes 31.34 seconds (2611.34 seconds total)