Starting phenix.real_space_refine
on Fri Jun 13 20:02:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8irv_35687/06_2025/8irv_35687_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8irv_35687/06_2025/8irv_35687.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8irv_35687/06_2025/8irv_35687.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8irv_35687/06_2025/8irv_35687.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8irv_35687/06_2025/8irv_35687_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8irv_35687/06_2025/8irv_35687_trim.cif"
  }
  resolution = 3.1
  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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    4887      2.51       5
     N    1266      2.21       5
     O    1340      1.98       5
     H    7182      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 63 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14729
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 3924
          Classifications: {'peptide': 238}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 231}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 5107
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 885
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "R"
      Number of atoms: 4493
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 4493
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 9, 'TRANS': 269}
          Chain breaks: 3
    Chain: "R"
      Number of atoms: 320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 320
          Unusual residues: {'CLR': 10, 'PLM': 1, 'R5F': 1}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
  Time building chain proxies: 7.48, per 1000 atoms: 0.51
  Number of scatterers: 14729
  At special positions: 0
  Unit cell: (91.035, 101.745, 115.668, 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)
     S      54     16.00
     O    1340      8.00
     N    1266      7.00
     C    4887      6.00
     H    7182      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 113 " - pdb=" SG  CYS R 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 322 " - pdb=" SG  CYS R 335 " 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: 4.18
  Conformation dependent library (CDL) restraints added in 3.4 seconds
  

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1738

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 8 sheets defined
      51.0% alpha, 18.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.958A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
      removed outlier: 3.646A  pdb=" N   ARG A  61 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 64
      No H-bonds generated for 'chain 'A' and resid 62 through 64'
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.508A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 268
      removed outlier: 4.456A  pdb=" N   GLN A 257 " --> pdb=" O   TYR A 253 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   GLU A 258 " --> pdb=" O   ASN A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 273
      removed outlier: 3.987A  pdb=" N   ARG A 273 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 293
    Processing helix  chain 'A' and resid 297 through 302
      removed outlier: 3.964A  pdb=" N   TYR A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 307
    Processing helix  chain 'A' and resid 321 through 340
      removed outlier: 3.670A  pdb=" N   PHE A 335 " --> pdb=" O   ILE A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 381
      removed outlier: 3.528A  pdb=" N   TYR A 381 " --> pdb=" O   HIS A 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.858A  pdb=" N   ARG B   8 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 25
      removed outlier: 3.644A  pdb=" N   ILE G  25 " --> pdb=" O   MET G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.507A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'R' and resid 38 through 68
      removed outlier: 3.622A  pdb=" N   VAL R  66 " --> pdb=" O   CYS R  62 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ARG R  67 " --> pdb=" O   ALA R  63 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   SER R  68 " --> pdb=" O   ALA R  64 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 74
    Processing helix  chain 'R' and resid 75 through 94
      removed outlier: 4.155A  pdb=" N   PHE R  79 " --> pdb=" O   MET R  75 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 94 through 105
      removed outlier: 3.562A  pdb=" N   LYS R  98 " --> pdb=" O   VAL R  94 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 109 through 144
      removed outlier: 4.184A  pdb=" N   ASP R 114 " --> pdb=" O   GLY R 110 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   VAL R 115 " --> pdb=" O   ALA R 111 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 144 through 152
    Processing helix  chain 'R' and resid 153 through 178
      Proline residue:  R 175  - end of helix
    Processing helix  chain 'R' and resid 222 through 234
    Processing helix  chain 'R' and resid 234 through 271
    Processing helix  chain 'R' and resid 290 through 323
      removed outlier: 3.554A  pdb=" N   VAL R 294 " --> pdb=" O   LYS R 290 " (cutoff:3.500A)
      Proline residue:  R 311  - end of helix
      Proline residue:  R 320  - end of helix
    Processing helix  chain 'R' and resid 337 through 361
      removed outlier: 3.753A  pdb=" N   SER R 352 " --> pdb=" O   GLY R 348 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   SER R 353 " --> pdb=" O   TRP R 349 " (cutoff:3.500A)
      Proline residue:  R 356  - end of helix
      removed outlier: 3.722A  pdb=" N   PHE R 361 " --> pdb=" O   VAL R 357 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 362 through 374
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.167A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.599A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   PHE A 280 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   ASN A 282 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.641A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.945A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.904A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.582A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.670A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.769A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.805A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    407 hydrogen bonds defined for protein.
    1185 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: 8.44

  Time building geometry restraints manager: 4.81 seconds

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

  Histogram of bond lengths:
        0.94 -     1.12: 7155
        1.12 -     1.29: 1198
        1.29 -     1.47: 2781
        1.47 -     1.64: 3695
        1.64 -     1.82: 77
  Bond restraints: 14906
  Sorted by residual:
  bond pdb=" N   LYS R 296 "
       pdb=" H   LYS R 296 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" N   THR R 125 "
       pdb=" H   THR R 125 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" CE2 PHE B 234 "
       pdb=" HE2 PHE B 234 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" CD1 TYR R 235 "
       pdb=" HD1 TYR R 235 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   GLY R 374 "
       pdb=" H   GLY R 374 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  ... (remaining 14901 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.73: 22984
        2.73 -     5.46: 2917
        5.46 -     8.19: 779
        8.19 -    10.92: 16
       10.92 -    13.65: 27
  Bond angle restraints: 26723
  Sorted by residual:
  angle pdb=" CB  HIS B  54 "
        pdb=" CG  HIS B  54 "
        pdb=" CD2 HIS B  54 "
      ideal   model   delta    sigma   weight residual
     131.20  123.59    7.61 1.30e+00 5.92e-01 3.43e+01
  angle pdb=" N   ASP B 186 "
        pdb=" CA  ASP B 186 "
        pdb=" CB  ASP B 186 "
      ideal   model   delta    sigma   weight residual
     109.71  101.18    8.53 1.54e+00 4.22e-01 3.07e+01
  angle pdb=" N   ASP B 228 "
        pdb=" CA  ASP B 228 "
        pdb=" CB  ASP B 228 "
      ideal   model   delta    sigma   weight residual
     109.69  101.40    8.29 1.53e+00 4.27e-01 2.94e+01
  angle pdb=" C   SER B 227 "
        pdb=" N   ASP B 228 "
        pdb=" CA  ASP B 228 "
      ideal   model   delta    sigma   weight residual
     120.82  128.28   -7.46 1.41e+00 5.03e-01 2.80e+01
  angle pdb=" CB  HIS A 220 "
        pdb=" CG  HIS A 220 "
        pdb=" CD2 HIS A 220 "
      ideal   model   delta    sigma   weight residual
     131.20  124.38    6.82 1.30e+00 5.92e-01 2.75e+01
  ... (remaining 26718 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 6960
       17.39 -    34.79: 387
       34.79 -    52.18: 93
       52.18 -    69.57: 84
       69.57 -    86.96: 4
  Dihedral angle restraints: 7528
    sinusoidal: 4355
      harmonic: 3173
  Sorted by residual:
  dihedral pdb=" CA  THR B 165 "
           pdb=" C   THR B 165 "
           pdb=" N   CYS B 166 "
           pdb=" CA  CYS B 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.93   28.07     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  LEU B   4 "
           pdb=" C   LEU B   4 "
           pdb=" N   ASP B   5 "
           pdb=" CA  ASP B   5 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.00  -28.00     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CA  LEU B  70 "
           pdb=" C   LEU B  70 "
           pdb=" N   VAL B  71 "
           pdb=" CA  VAL B  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.05   26.95     0      5.00e+00 4.00e-02 2.91e+01
  ... (remaining 7525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 866
       0.096 -    0.192: 288
       0.192 -    0.289: 44
       0.289 -    0.385: 14
       0.385 -    0.481: 4
  Chirality restraints: 1216
  Sorted by residual:
  chirality pdb=" CA  SER B 334 "
            pdb=" N   SER B 334 "
            pdb=" C   SER B 334 "
            pdb=" CB  SER B 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.78e+00
  chirality pdb=" CA  THR B  87 "
            pdb=" N   THR B  87 "
            pdb=" C   THR B  87 "
            pdb=" CB  THR B  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.05    0.47 2.00e-01 2.50e+01 5.56e+00
  chirality pdb=" CA  TYR R 359 "
            pdb=" N   TYR R 359 "
            pdb=" C   TYR R 359 "
            pdb=" CB  TYR R 359 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.42 2.00e-01 2.50e+01 4.31e+00
  ... (remaining 1213 not shown)

  Planarity restraints: 2150
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 105 "    0.211 2.00e-02 2.50e+03   8.32e-02 2.08e+02
        pdb=" CG  TYR B 105 "   -0.135 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 105 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 105 "   -0.085 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 105 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 105 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 105 "    0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR B 105 "    0.085 2.00e-02 2.50e+03
        pdb=" HD1 TYR B 105 "   -0.009 2.00e-02 2.50e+03
        pdb=" HD2 TYR B 105 "   -0.026 2.00e-02 2.50e+03
        pdb=" HE1 TYR B 105 "    0.007 2.00e-02 2.50e+03
        pdb=" HE2 TYR B 105 "    0.037 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 271 "    0.162 2.00e-02 2.50e+03   7.19e-02 2.07e+02
        pdb=" CG  TRP A 271 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 271 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 271 "   -0.071 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 271 "   -0.061 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 271 "   -0.038 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 271 "   -0.074 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 271 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 271 "   -0.016 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 271 "    0.044 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 271 "    0.082 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 271 "   -0.100 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 271 "   -0.086 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 271 "    0.048 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 271 "   -0.000 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 271 "    0.107 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B  54 "    0.141 2.00e-02 2.50e+03   8.21e-02 1.52e+02
        pdb=" CG  HIS B  54 "   -0.075 2.00e-02 2.50e+03
        pdb=" ND1 HIS B  54 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD2 HIS B  54 "   -0.101 2.00e-02 2.50e+03
        pdb=" CE1 HIS B  54 "   -0.035 2.00e-02 2.50e+03
        pdb=" NE2 HIS B  54 "   -0.053 2.00e-02 2.50e+03
        pdb=" HD2 HIS B  54 "   -0.016 2.00e-02 2.50e+03
        pdb=" HE1 HIS B  54 "    0.044 2.00e-02 2.50e+03
        pdb=" HE2 HIS B  54 "    0.132 2.00e-02 2.50e+03
  ... (remaining 2147 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 857
        2.18 -     2.79: 25538
        2.79 -     3.39: 41104
        3.39 -     4.00: 55614
        4.00 -     4.60: 80491
  Nonbonded interactions: 203604
  Sorted by model distance:
  nonbonded pdb=" HG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     1.576 2.450
  nonbonded pdb=" HH  TYR B 145 "
            pdb=" OD2 ASP B 186 "
     model   vdw
     1.581 2.450
  nonbonded pdb=" HG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     1.585 2.450
  nonbonded pdb=" OD1 ASP R 218 "
            pdb=" HG  SER R 220 "
     model   vdw
     1.600 2.450
  nonbonded pdb=" HG  SER A  13 "
            pdb=" OD2 ASP A  16 "
     model   vdw
     1.602 2.450
  ... (remaining 203599 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             18.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.220
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.140
  Set scattering table:                    0.160
  Process input model:                     44.090
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.050
  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:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   67.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
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      :  0.013   0.049   7726  Z= 0.756
  Angle     :  1.757   8.799  10522  Z= 1.183
  Chirality :  0.098   0.481   1216
  Planarity :  0.016   0.127   1270
  Dihedral  : 11.469  86.963   3347
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 0.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.46 %
  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 (0.26), residues: 896
  helix:  0.10 (0.22), residues: 412
  sheet:  1.02 (0.43), residues: 142
  loop :  0.17 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.118   0.023   TRP A 271 
 HIS   0.014   0.004   HIS B  62 
 PHE   0.110   0.014   PHE R 312 
 TYR   0.199   0.020   TYR B 105 
 ARG   0.012   0.001   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17082 (  407)
  hydrogen bonds       : angle       6.77671 ( 1185)
  SS BOND              : bond        0.00388 (    2)
  SS BOND              : angle       1.66361 (    4)
  covalent geometry    : bond        0.01257 ( 7724)
  covalent geometry    : angle       1.75739 (10518)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 1.205 
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  256 LEU cc_start: 0.8657 (tp) cc_final: 0.8438 (mt)
REVERT: A  329 TYR cc_start: 0.8706 (m-80) cc_final: 0.8437 (m-80)
REVERT: B   16 ASN cc_start: 0.8251 (m-40) cc_final: 0.7856 (m110)
REVERT: R   58 ASN cc_start: 0.8239 (m-40) cc_final: 0.7980 (m-40)
REVERT: R  156 MET cc_start: 0.8286 (tpp) cc_final: 0.8064 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.6236
  time to fit residues: 179.2854
Evaluate side-chains
  144 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 26 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A 380 GLN
B 132 ASN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.138354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.099870 restraints weight = 28043.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.63
r_work: 0.2996 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2836 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7726  Z= 0.153
  Angle     :  0.602   5.070  10522  Z= 0.335
  Chirality :  0.041   0.159   1216
  Planarity :  0.005   0.047   1270
  Dihedral  :  6.311  49.746   1677
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  6.47 %
    Favored  : 91.75 %
  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:  1.16 (0.27), residues: 896
  helix:  1.30 (0.24), residues: 412
  sheet:  0.40 (0.38), residues: 172
  loop :  0.49 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.025   0.002   PHE R 312 
 TYR   0.033   0.002   TYR B 105 
 ARG   0.004   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06342 (  407)
  hydrogen bonds       : angle       5.01574 ( 1185)
  SS BOND              : bond        0.00614 (    2)
  SS BOND              : angle       1.59507 (    4)
  covalent geometry    : bond        0.00317 ( 7724)
  covalent geometry    : angle       0.60165 (10518)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 153
  time to evaluate  : 1.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.8931 (tp) cc_final: 0.8617 (mt)
REVERT: A  329 TYR cc_start: 0.8667 (m-80) cc_final: 0.8076 (m-80)
REVERT: B   12 GLU cc_start: 0.8428 (tp30) cc_final: 0.8226 (tp30)
REVERT: B   16 ASN cc_start: 0.8550 (m-40) cc_final: 0.8199 (m110)
REVERT: G   31 SER cc_start: 0.8576 (p) cc_final: 0.8371 (p)
REVERT: R   77 ASN cc_start: 0.8104 (m-40) cc_final: 0.7880 (m-40)
REVERT: R  180 TRP cc_start: 0.8939 (m-10) cc_final: 0.8519 (m-10)
  outliers start: 14
  outliers final: 7
  residues processed: 159
  average time/residue: 0.5041
  time to fit residues: 103.8451
Evaluate side-chains
  140 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 133
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue  113 CYS
Chi-restraints excluded: chain R residue  137 ASP
Chi-restraints excluded: chain R residue  166 THR
Chi-restraints excluded: chain R residue  318 MET
Chi-restraints excluded: chain R residue  336 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.134270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.096418 restraints weight = 28257.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 2.58
r_work: 0.2960 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.4029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7726  Z= 0.186
  Angle     :  0.565   7.137  10522  Z= 0.312
  Chirality :  0.040   0.156   1216
  Planarity :  0.004   0.040   1270
  Dihedral  :  5.876  45.175   1677
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  :  9.77 %
    Favored  : 88.32 %
  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:  1.35 (0.27), residues: 896
  helix:  1.68 (0.24), residues: 410
  sheet:  0.10 (0.36), residues: 175
  loop :  0.50 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 234 
 HIS   0.005   0.001   HIS A 347 
 PHE   0.020   0.002   PHE R 312 
 TYR   0.023   0.001   TYR B 105 
 ARG   0.003   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05727 (  407)
  hydrogen bonds       : angle       4.77912 ( 1185)
  SS BOND              : bond        0.00239 (    2)
  SS BOND              : angle       4.46430 (    4)
  covalent geometry    : bond        0.00410 ( 7724)
  covalent geometry    : angle       0.55861 (10518)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.8966 (tp) cc_final: 0.8680 (mt)
REVERT: A  329 TYR cc_start: 0.8693 (m-80) cc_final: 0.8230 (m-80)
REVERT: B   16 ASN cc_start: 0.8539 (m-40) cc_final: 0.8181 (m110)
REVERT: B  134 ARG cc_start: 0.8192 (ptt180) cc_final: 0.7703 (ptm-80)
REVERT: R  180 TRP cc_start: 0.8881 (m-10) cc_final: 0.8458 (m-10)
REVERT: R  218 ASP cc_start: 0.7994 (t0) cc_final: 0.7727 (t70)
  outliers start: 15
  outliers final: 11
  residues processed: 153
  average time/residue: 0.4723
  time to fit residues: 95.1020
Evaluate side-chains
  141 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 1.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  113 CYS
Chi-restraints excluded: chain R residue  137 ASP
Chi-restraints excluded: chain R residue  166 THR
Chi-restraints excluded: chain R residue  171 ILE
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain R residue  336 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 87 optimal weight:    0.6980
   chunk 78 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R 351 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.135261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.097454 restraints weight = 28046.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 2.57
r_work: 0.2963 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2805 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.4338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7726  Z= 0.151
  Angle     :  0.514   6.319  10522  Z= 0.281
  Chirality :  0.039   0.170   1216
  Planarity :  0.004   0.042   1270
  Dihedral  :  5.511  51.393   1677
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 10.03 %
    Favored  : 87.44 %
  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:  1.37 (0.27), residues: 896
  helix:  1.92 (0.25), residues: 411
  sheet: -0.13 (0.36), residues: 172
  loop :  0.31 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.017   0.001   PHE R 312 
 TYR   0.016   0.001   TYR B 105 
 ARG   0.007   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05108 (  407)
  hydrogen bonds       : angle       4.55894 ( 1185)
  SS BOND              : bond        0.00164 (    2)
  SS BOND              : angle       3.68891 (    4)
  covalent geometry    : bond        0.00330 ( 7724)
  covalent geometry    : angle       0.50936 (10518)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.8976 (tp) cc_final: 0.8700 (mt)
REVERT: A  329 TYR cc_start: 0.8630 (m-80) cc_final: 0.8157 (m-80)
REVERT: B  132 ASN cc_start: 0.7867 (t0) cc_final: 0.7603 (t0)
REVERT: B  134 ARG cc_start: 0.8250 (ptt180) cc_final: 0.7729 (ptm-80)
REVERT: B  234 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.7771 (m-80)
REVERT: R  180 TRP cc_start: 0.8836 (m-10) cc_final: 0.8427 (m-10)
  outliers start: 20
  outliers final: 11
  residues processed: 149
  average time/residue: 0.4993
  time to fit residues: 96.6963
Evaluate side-chains
  141 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue   60 LEU
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  135 SER
Chi-restraints excluded: chain R residue  137 ASP
Chi-restraints excluded: chain R residue  166 THR
Chi-restraints excluded: chain R residue  228 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0040
   chunk 23 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    1.3796

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
R 177 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.135930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.096804 restraints weight = 28631.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 2.67
r_work: 0.2962 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.4501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7726  Z= 0.143
  Angle     :  0.503   5.114  10522  Z= 0.274
  Chirality :  0.039   0.176   1216
  Planarity :  0.003   0.039   1270
  Dihedral  :  5.456  57.346   1677
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.06 %
    Favored  : 86.04 %
  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:  1.41 (0.28), residues: 896
  helix:  2.00 (0.25), residues: 411
  sheet: -0.27 (0.36), residues: 172
  loop :  0.36 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.016   0.001   PHE R 312 
 TYR   0.011   0.001   TYR B 105 
 ARG   0.002   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04973 (  407)
  hydrogen bonds       : angle       4.48521 ( 1185)
  SS BOND              : bond        0.00377 (    2)
  SS BOND              : angle       2.55662 (    4)
  covalent geometry    : bond        0.00313 ( 7724)
  covalent geometry    : angle       0.50074 (10518)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.8983 (tp) cc_final: 0.8685 (mt)
REVERT: A  329 TYR cc_start: 0.8565 (m-80) cc_final: 0.8175 (m-80)
REVERT: B  132 ASN cc_start: 0.7999 (t0) cc_final: 0.7758 (t0)
REVERT: B  134 ARG cc_start: 0.8312 (ptt180) cc_final: 0.7835 (ptm-80)
REVERT: B  234 PHE cc_start: 0.9375 (OUTLIER) cc_final: 0.7714 (m-80)
REVERT: R  180 TRP cc_start: 0.8855 (m-10) cc_final: 0.8451 (m-10)
REVERT: R  367 LYS cc_start: 0.8806 (tttp) cc_final: 0.8239 (pttt)
  outliers start: 15
  outliers final: 9
  residues processed: 142
  average time/residue: 0.5366
  time to fit residues: 97.0706
Evaluate side-chains
  137 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  135 SER
Chi-restraints excluded: chain R residue  137 ASP
Chi-restraints excluded: chain R residue  166 THR
Chi-restraints excluded: chain R residue  228 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 57 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.134052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.096469 restraints weight = 28435.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 2.57
r_work: 0.2960 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.4706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7726  Z= 0.153
  Angle     :  0.496   4.680  10522  Z= 0.271
  Chirality :  0.039   0.195   1216
  Planarity :  0.004   0.055   1270
  Dihedral  :  5.372  50.125   1677
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 11.80 %
    Favored  : 86.80 %
  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:  1.46 (0.28), residues: 896
  helix:  2.02 (0.25), residues: 413
  sheet: -0.25 (0.37), residues: 164
  loop :  0.38 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.017   0.001   PHE R 312 
 TYR   0.011   0.001   TYR B 105 
 ARG   0.008   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04872 (  407)
  hydrogen bonds       : angle       4.45100 ( 1185)
  SS BOND              : bond        0.00088 (    2)
  SS BOND              : angle       1.30326 (    4)
  covalent geometry    : bond        0.00339 ( 7724)
  covalent geometry    : angle       0.49495 (10518)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 1.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.8914 (tp) cc_final: 0.8566 (mt)
REVERT: B  132 ASN cc_start: 0.7921 (t0) cc_final: 0.7716 (t0)
REVERT: B  197 ARG cc_start: 0.8182 (mtp85) cc_final: 0.7619 (mmt90)
REVERT: B  234 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.7746 (m-80)
REVERT: R  180 TRP cc_start: 0.8829 (m-10) cc_final: 0.8421 (m-10)
REVERT: R  250 ARG cc_start: 0.8262 (mtm110) cc_final: 0.7962 (mtp180)
  outliers start: 11
  outliers final: 8
  residues processed: 134
  average time/residue: 0.5057
  time to fit residues: 87.7088
Evaluate side-chains
  130 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   60 LEU
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  135 SER
Chi-restraints excluded: chain R residue  137 ASP
Chi-restraints excluded: chain R residue  166 THR
Chi-restraints excluded: chain R residue  228 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9980
   chunk 25 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.136353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.097587 restraints weight = 28583.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 2.66
r_work: 0.2983 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2823 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.4837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7726  Z= 0.122
  Angle     :  0.469   4.702  10522  Z= 0.256
  Chirality :  0.038   0.139   1216
  Planarity :  0.003   0.048   1270
  Dihedral  :  5.062  46.954   1677
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 12.44 %
    Favored  : 86.29 %
  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:  1.58 (0.28), residues: 896
  helix:  2.17 (0.25), residues: 413
  sheet: -0.12 (0.38), residues: 164
  loop :  0.33 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.014   0.001   PHE R 312 
 TYR   0.009   0.001   TYR B 105 
 ARG   0.009   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04538 (  407)
  hydrogen bonds       : angle       4.31628 ( 1185)
  SS BOND              : bond        0.00246 (    2)
  SS BOND              : angle       1.51310 (    4)
  covalent geometry    : bond        0.00263 ( 7724)
  covalent geometry    : angle       0.46802 (10518)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 1.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.8960 (tp) cc_final: 0.8638 (mt)
REVERT: B  197 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7641 (mmt90)
REVERT: B  234 PHE cc_start: 0.9333 (OUTLIER) cc_final: 0.7702 (m-80)
REVERT: R   75 MET cc_start: 0.7771 (tpp) cc_final: 0.7409 (tpp)
REVERT: R  180 TRP cc_start: 0.8821 (m-10) cc_final: 0.8432 (m-10)
REVERT: R  250 ARG cc_start: 0.8256 (mtm110) cc_final: 0.7969 (mtp180)
  outliers start: 10
  outliers final: 5
  residues processed: 129
  average time/residue: 0.6540
  time to fit residues: 113.7875
Evaluate side-chains
  125 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 119
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  113 CYS
Chi-restraints excluded: chain R residue  135 SER
Chi-restraints excluded: chain R residue  166 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 83 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0010
   chunk 81 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.9190

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.136702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.098295 restraints weight = 28254.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 2.64
r_work: 0.2990 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.4944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7726  Z= 0.115
  Angle     :  0.466   4.703  10522  Z= 0.253
  Chirality :  0.038   0.135   1216
  Planarity :  0.003   0.060   1270
  Dihedral  :  4.960  47.733   1677
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.82 %
    Favored  : 86.04 %
  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:  1.72 (0.28), residues: 896
  helix:  2.25 (0.25), residues: 413
  sheet: -0.01 (0.39), residues: 162
  loop :  0.42 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.014   0.001   PHE R 312 
 TYR   0.008   0.001   TYR B 105 
 ARG   0.011   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04427 (  407)
  hydrogen bonds       : angle       4.26685 ( 1185)
  SS BOND              : bond        0.00099 (    2)
  SS BOND              : angle       0.96082 (    4)
  covalent geometry    : bond        0.00246 ( 7724)
  covalent geometry    : angle       0.46593 (10518)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.9005 (tp) cc_final: 0.8622 (mt)
REVERT: B  197 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7684 (mmt90)
REVERT: B  234 PHE cc_start: 0.9320 (OUTLIER) cc_final: 0.7736 (m-80)
REVERT: R  180 TRP cc_start: 0.8794 (m-10) cc_final: 0.8396 (m-10)
REVERT: R  250 ARG cc_start: 0.8247 (mtm110) cc_final: 0.7965 (mtp180)
  outliers start: 9
  outliers final: 7
  residues processed: 126
  average time/residue: 0.5255
  time to fit residues: 84.9871
Evaluate side-chains
  128 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  113 CYS
Chi-restraints excluded: chain R residue  137 ASP
Chi-restraints excluded: chain R residue  166 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0970
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.7978

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.138449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.101155 restraints weight = 28191.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.58
r_work: 0.3000 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.5043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7726  Z= 0.108
  Angle     :  0.458   4.716  10522  Z= 0.248
  Chirality :  0.037   0.134   1216
  Planarity :  0.003   0.063   1270
  Dihedral  :  4.850  47.736   1677
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.94 %
    Favored  : 85.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.77 (0.28), residues: 896
  helix:  2.29 (0.25), residues: 413
  sheet:  0.05 (0.39), residues: 162
  loop :  0.42 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.013   0.001   PHE R 312 
 TYR   0.007   0.001   TYR A 329 
 ARG   0.011   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04333 (  407)
  hydrogen bonds       : angle       4.24560 ( 1185)
  SS BOND              : bond        0.00107 (    2)
  SS BOND              : angle       0.90447 (    4)
  covalent geometry    : bond        0.00229 ( 7724)
  covalent geometry    : angle       0.45789 (10518)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 1.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.8948 (tp) cc_final: 0.8606 (mt)
REVERT: B  197 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7699 (mmt90)
REVERT: B  234 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.7717 (m-80)
REVERT: G   46 LYS cc_start: 0.8913 (ttpp) cc_final: 0.7790 (ptmm)
REVERT: R   75 MET cc_start: 0.7783 (tpp) cc_final: 0.7475 (tpp)
REVERT: R  180 TRP cc_start: 0.8782 (m-10) cc_final: 0.8405 (m-10)
REVERT: R  250 ARG cc_start: 0.8227 (mtm110) cc_final: 0.7951 (mtp180)
  outliers start: 9
  outliers final: 7
  residues processed: 132
  average time/residue: 0.4983
  time to fit residues: 85.0420
Evaluate side-chains
  129 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 121
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  113 CYS
Chi-restraints excluded: chain R residue  137 ASP
Chi-restraints excluded: chain R residue  166 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
** R 154 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 = 0.3625 r_free = 0.3625 target = 0.133004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.094189 restraints weight = 28631.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 2.65
r_work: 0.2928 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.5022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7726  Z= 0.239
  Angle     :  0.540   4.894  10522  Z= 0.294
  Chirality :  0.040   0.152   1216
  Planarity :  0.004   0.070   1270
  Dihedral  :  5.708  54.946   1677
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 13.07 %
    Favored  : 85.79 %
  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:  1.46 (0.28), residues: 896
  helix:  1.97 (0.25), residues: 419
  sheet: -0.06 (0.38), residues: 165
  loop :  0.31 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 234 
 HIS   0.010   0.001   HIS A 220 
 PHE   0.021   0.002   PHE R 312 
 TYR   0.016   0.001   TYR B 105 
 ARG   0.012   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05133 (  407)
  hydrogen bonds       : angle       4.49926 ( 1185)
  SS BOND              : bond        0.00182 (    2)
  SS BOND              : angle       1.36123 (    4)
  covalent geometry    : bond        0.00542 ( 7724)
  covalent geometry    : angle       0.53972 (10518)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 1.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.9017 (tp) cc_final: 0.8694 (mt)
REVERT: A  286 LEU cc_start: 0.8786 (mp) cc_final: 0.8559 (mp)
REVERT: B  197 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7715 (mmt90)
REVERT: B  234 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.7942 (m-80)
REVERT: R   75 MET cc_start: 0.7882 (tpp) cc_final: 0.7591 (tpp)
REVERT: R  180 TRP cc_start: 0.8822 (m-10) cc_final: 0.8410 (m-10)
REVERT: R  250 ARG cc_start: 0.8304 (mtm110) cc_final: 0.8013 (mtp180)
REVERT: R  291 GLU cc_start: 0.7289 (mp0) cc_final: 0.6914 (pm20)
  outliers start: 9
  outliers final: 8
  residues processed: 127
  average time/residue: 0.5329
  time to fit residues: 87.5055
Evaluate side-chains
  130 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  113 CYS
Chi-restraints excluded: chain R residue  137 ASP
Chi-restraints excluded: chain R residue  166 THR
Chi-restraints excluded: chain R residue  361 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0010
   chunk 23 optimal weight:    3.9990
   chunk 61 optimal weight:    0.4980
   chunk 36 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
B 340 ASN
R 270 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.136644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.098030 restraints weight = 28221.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.67
r_work: 0.2985 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2828 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.5114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7726  Z= 0.102
  Angle     :  0.473   5.110  10522  Z= 0.255
  Chirality :  0.038   0.135   1216
  Planarity :  0.004   0.067   1270
  Dihedral  :  5.017  51.546   1677
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 13.20 %
    Favored  : 85.66 %
  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:  1.68 (0.28), residues: 896
  helix:  2.20 (0.25), residues: 419
  sheet:  0.02 (0.39), residues: 162
  loop :  0.36 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.014   0.001   PHE R 312 
 TYR   0.006   0.001   TYR B 105 
 ARG   0.012   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04407 (  407)
  hydrogen bonds       : angle       4.26616 ( 1185)
  SS BOND              : bond        0.00113 (    2)
  SS BOND              : angle       0.72832 (    4)
  covalent geometry    : bond        0.00211 ( 7724)
  covalent geometry    : angle       0.47317 (10518)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9234.43 seconds
wall clock time: 160 minutes 28.28 seconds (9628.28 seconds total)