Starting phenix.real_space_refine
on Tue Mar  3 16:44:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wvw_32860/03_2026/7wvw_32860.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wvw_32860/03_2026/7wvw_32860.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wvw_32860/03_2026/7wvw_32860.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wvw_32860/03_2026/7wvw_32860.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wvw_32860/03_2026/7wvw_32860.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wvw_32860/03_2026/7wvw_32860.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    4608      2.51       5
     N    1212      2.21       5
     O    1295      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7169
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "L"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 65
          Classifications: {'peptide': 7}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 2344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2344
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 13, 'TRANS': 285}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "A"
      Number of atoms: 1753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1753
          Classifications: {'peptide': 223}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 2, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "B"
      Number of atoms: 2583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2583
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 424
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 1.42, per 1000 atoms: 0.20
  Number of scatterers: 7169
  At special positions: 0
  Unit cell: (114.95, 119.13, 84.645, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1295      8.00
     N    1212      7.00
     C    4608      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  98 " - pdb=" SG  CYS R 176 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 225.9 milliseconds
  

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1734

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 10 sheets defined
      48.3% alpha, 18.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'R' and resid 20 through 55
      Proline residue:  R  29  - end of helix
      removed outlier: 3.737A  pdb=" N   PHE R  53 " --> pdb=" O   TRP R  49 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 58 through 87
      Proline residue:  R  79  - end of helix
    Processing helix  chain 'R' and resid 94 through 129
    Processing helix  chain 'R' and resid 129 through 136
    Processing helix  chain 'R' and resid 138 through 163
      removed outlier: 4.089A  pdb=" N   GLY R 148 " --> pdb=" O   LYS R 144 " (cutoff:3.500A)
      Proline residue:  R 149  - end of helix
      Proline residue:  R 159  - end of helix
    Processing helix  chain 'R' and resid 186 through 209
    Processing helix  chain 'R' and resid 210 through 231
    Processing helix  chain 'R' and resid 237 through 267
      Proline residue:  R 256  - end of helix
    Processing helix  chain 'R' and resid 267 through 274
    Processing helix  chain 'R' and resid 278 through 303
      removed outlier: 4.388A  pdb=" N   ASN R 285 " --> pdb=" O   ASP R 281 " (cutoff:3.500A)
      Proline residue:  R 286  - end of helix
      Proline residue:  R 299  - end of helix
    Processing helix  chain 'R' and resid 306 through 317
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 3.798A  pdb=" N   GLU A  25 " --> pdb=" O   LYS A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.888A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
      removed outlier: 3.700A  pdb=" N   LYS A 211 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   ILE A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 232
      removed outlier: 4.290A  pdb=" N   ASP A 232 " --> pdb=" O   SER A 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 229 through 232'
    Processing helix  chain 'A' and resid 242 through 256
    Processing helix  chain 'A' and resid 257 through 261
      removed outlier: 4.086A  pdb=" N   THR A 261 " --> pdb=" O   LYS A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 4.051A  pdb=" N   GLU A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   THR A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   HIS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 287
      removed outlier: 3.819A  pdb=" N   ILE A 286 " --> pdb=" O   PRO A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 312
      removed outlier: 3.687A  pdb=" N   ASN A 312 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 31 through 35
      removed outlier: 3.614A  pdb=" N   ASN B  35 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 23
      removed outlier: 3.653A  pdb=" N   LEU C  15 " --> pdb=" O   GLN C  11 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.783A  pdb=" N   LEU C  37 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   MET C  38 " --> pdb=" O   ALA C  34 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 164 through 168
      removed outlier: 3.501A  pdb=" N   THR R 177 " --> pdb=" O   THR R 165 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 187
    Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 187
      removed outlier: 6.075A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 198 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   PHE A 200 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.831A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 8.548A  pdb=" N   ALA A 227 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.526A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.661A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.625A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.592A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.687A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 232 through 234
      removed outlier: 3.734A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.559A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    392 hydrogen bonds defined for protein.
    1131 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.92

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2294
        1.35 -     1.47: 1778
        1.47 -     1.59: 3168
        1.59 -     1.71: 0
        1.71 -     1.83: 79
  Bond restraints: 7319
  Sorted by residual:
  bond pdb=" SD  FME L   1 "
       pdb=" CE  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.805  1.752  0.053 2.00e-02 2.50e+03 6.95e+00
  bond pdb=" CG  FME L   1 "
       pdb=" SD  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.817  1.770  0.047 2.00e-02 2.50e+03 5.50e+00
  bond pdb=" N   FME L   1 "
       pdb=" CN  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.335  1.376 -0.041 2.00e-02 2.50e+03 4.24e+00
  bond pdb=" N   FME L   1 "
       pdb=" CA  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.437  0.021 1.90e-02 2.77e+03 1.26e+00
  bond pdb=" CN  FME L   1 "
       pdb=" O1  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.221  1.241 -0.020 2.00e-02 2.50e+03 9.75e-01
  ... (remaining 7314 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 9792
        1.65 -     3.31: 103
        3.31 -     4.96: 25
        4.96 -     6.62: 7
        6.62 -     8.27: 1
  Bond angle restraints: 9928
  Sorted by residual:
  angle pdb=" C   TYR R 175 "
        pdb=" N   CYS R 176 "
        pdb=" CA  CYS R 176 "
      ideal   model   delta    sigma   weight residual
     122.84  118.55    4.29 1.30e+00 5.92e-01 1.09e+01
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     113.71  111.03    2.68 9.50e-01 1.11e+00 7.95e+00
  angle pdb=" CA  CYS R 176 "
        pdb=" CB  CYS R 176 "
        pdb=" SG  CYS R 176 "
      ideal   model   delta    sigma   weight residual
     114.40  120.09   -5.69 2.30e+00 1.89e-01 6.12e+00
  angle pdb=" CA  LEU R 162 "
        pdb=" CB  LEU R 162 "
        pdb=" CG  LEU R 162 "
      ideal   model   delta    sigma   weight residual
     116.30  124.57   -8.27 3.50e+00 8.16e-02 5.58e+00
  angle pdb=" C   ASP A 329 "
        pdb=" N   THR A 330 "
        pdb=" CA  THR A 330 "
      ideal   model   delta    sigma   weight residual
     122.08  125.17   -3.09 1.47e+00 4.63e-01 4.41e+00
  ... (remaining 9923 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.27: 3850
       16.27 -    32.54: 361
       32.54 -    48.81: 88
       48.81 -    65.08: 9
       65.08 -    81.35: 7
  Dihedral angle restraints: 4315
    sinusoidal: 1641
      harmonic: 2674
  Sorted by residual:
  dihedral pdb=" CA  PHE R 161 "
           pdb=" C   PHE R 161 "
           pdb=" N   LEU R 162 "
           pdb=" CA  LEU R 162 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.92  -17.08     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  ASN A 348 "
           pdb=" CB  ASN A 348 "
           pdb=" CG  ASN A 348 "
           pdb=" OD1 ASN A 348 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -177.28  -62.72     2      2.00e+01 2.50e-03 9.48e+00
  dihedral pdb=" CB  MET R 214 "
           pdb=" CG  MET R 214 "
           pdb=" SD  MET R 214 "
           pdb=" CE  MET R 214 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.29  -57.71     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 4312 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 686
       0.027 -    0.053: 280
       0.053 -    0.080: 110
       0.080 -    0.107: 55
       0.107 -    0.133: 28
  Chirality restraints: 1159
  Sorted by residual:
  chirality pdb=" CA  LEU R 162 "
            pdb=" N   LEU R 162 "
            pdb=" C   LEU R 162 "
            pdb=" CB  LEU R 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.45e-01
  chirality pdb=" CA  VAL C  54 "
            pdb=" N   VAL C  54 "
            pdb=" C   VAL C  54 "
            pdb=" CB  VAL C  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.26e-01
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.97e-01
  ... (remaining 1156 not shown)

  Planarity restraints: 1243
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 148 "    0.034 5.00e-02 4.00e+02   5.08e-02 4.14e+00
        pdb=" N   PRO R 149 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO R 149 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO R 149 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.023 5.00e-02 4.00e+02   3.53e-02 2.00e+00
        pdb=" N   PRO B 236 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R  95 "   -0.012 2.00e-02 2.50e+03   8.74e-03 1.91e+00
        pdb=" CG  TRP R  95 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP R  95 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TRP R  95 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP R  95 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP R  95 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP R  95 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R  95 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R  95 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP R  95 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1240 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 448
        2.74 -     3.28: 7244
        3.28 -     3.82: 12448
        3.82 -     4.36: 14507
        4.36 -     4.90: 25386
  Nonbonded interactions: 60033
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASN B 110 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OD1 ASN A 270 "
            pdb=" OG1 THR A 325 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OH  TYR A 231 "
            pdb=" OG  SER A 282 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" NH2 ARG B 256 "
            pdb=" OD2 ASP C  36 "
     model   vdw
     2.309 3.120
  ... (remaining 60028 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.060
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     6.810
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
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      :  0.002   0.053   7320  Z= 0.112
  Angle     :  0.497   8.271   9930  Z= 0.267
  Chirality :  0.040   0.133   1159
  Planarity :  0.003   0.051   1243
  Dihedral  : 13.512  81.345   2578
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.28), residues: 911
  helix:  1.80 (0.26), residues: 413
  sheet:  0.56 (0.45), residues: 152
  loop : -1.09 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  96 
 TYR   0.009   0.001   TYR R 175 
 PHE   0.016   0.001   PHE R 161 
 TRP   0.023   0.001   TRP R  95 
 HIS   0.004   0.000   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 7319)
  covalent geometry    : angle       0.49569 ( 9928)
  SS BOND              : bond        0.00036 (    1)
  SS BOND              : angle       2.85001 (    2)
  hydrogen bonds       : bond        0.21278 (  390)
  hydrogen bonds       : angle       7.14940 ( 1131)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.192 
Fit side-chains
REVERT: R  106 ASP cc_start: 0.7300 (t70) cc_final: 0.7097 (t70)
REVERT: R  204 ILE cc_start: 0.7547 (mt) cc_final: 0.6928 (mt)
REVERT: A  325 THR cc_start: 0.7395 (m) cc_final: 0.7172 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.0782
  time to fit residues: 18.0052
Evaluate side-chains
  125 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
R 294 ASN
B 110 ASN
B 220 GLN
B 311 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.152874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.116922 restraints weight = 8806.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.14
r_work: 0.3279 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.087   7320  Z= 0.197
  Angle     :  0.592   8.059   9930  Z= 0.308
  Chirality :  0.044   0.154   1159
  Planarity :  0.004   0.048   1243
  Dihedral  :  4.143  54.110    984
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 11.85 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.28), residues: 911
  helix:  1.76 (0.25), residues: 424
  sheet:  0.62 (0.41), residues: 171
  loop : -1.09 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R  54 
 TYR   0.015   0.002   TYR R 175 
 PHE   0.018   0.002   PHE B 199 
 TRP   0.016   0.002   TRP B 211 
 HIS   0.004   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 7319)
  covalent geometry    : angle       0.58983 ( 9928)
  SS BOND              : bond        0.00214 (    1)
  SS BOND              : angle       3.43850 (    2)
  hydrogen bonds       : bond        0.04191 (  390)
  hydrogen bonds       : angle       5.19274 ( 1131)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 166
  time to evaluate  : 0.276 
Fit side-chains
REVERT: R  103 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8354 (mp)
REVERT: R  278 LYS cc_start: 0.7883 (mtmt) cc_final: 0.7457 (mttm)
REVERT: A  270 ASN cc_start: 0.8517 (m-40) cc_final: 0.8268 (m-40)
REVERT: B   96 ARG cc_start: 0.8025 (ttm170) cc_final: 0.7659 (mtp-110)
REVERT: B  325 MET cc_start: 0.8289 (tpp) cc_final: 0.8054 (tpp)
  outliers start: 9
  outliers final: 7
  residues processed: 171
  average time/residue: 0.0812
  time to fit residues: 18.6877
Evaluate side-chains
  147 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 139
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue  103 ILE
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  301 LEU
Chi-restraints excluded: chain B residue  173 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 31 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0970
   chunk 48 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
R 102 HIS
A 245 HIS
B 220 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.151899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.117669 restraints weight = 8751.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.06
r_work: 0.3279 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7320  Z= 0.130
  Angle     :  0.508   7.869   9930  Z= 0.265
  Chirality :  0.042   0.139   1159
  Planarity :  0.004   0.049   1243
  Dihedral  :  4.038  53.936    984
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.36 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.28), residues: 911
  helix:  1.93 (0.25), residues: 425
  sheet:  0.49 (0.40), residues: 177
  loop : -0.95 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R  54 
 TYR   0.010   0.001   TYR R 175 
 PHE   0.015   0.001   PHE B 199 
 TRP   0.014   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7319)
  covalent geometry    : angle       0.50705 ( 9928)
  SS BOND              : bond        0.00227 (    1)
  SS BOND              : angle       2.46099 (    2)
  hydrogen bonds       : bond        0.03800 (  390)
  hydrogen bonds       : angle       4.95510 ( 1131)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 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: 13
    poor density    : 148
  time to evaluate  : 0.260 
Fit side-chains
REVERT: R  103 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8342 (mp)
REVERT: R  273 PHE cc_start: 0.8057 (m-10) cc_final: 0.7802 (m-80)
REVERT: R  278 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7394 (mttm)
REVERT: A  242 ASN cc_start: 0.7387 (t0) cc_final: 0.6739 (t0)
REVERT: A  270 ASN cc_start: 0.8488 (m-40) cc_final: 0.8232 (m-40)
REVERT: B   36 ASN cc_start: 0.8243 (p0) cc_final: 0.7849 (p0)
  outliers start: 13
  outliers final: 8
  residues processed: 153
  average time/residue: 0.0773
  time to fit residues: 16.0280
Evaluate side-chains
  146 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 137
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  103 ILE
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  189 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 51 optimal weight:    0.2980
   chunk 40 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 82 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0020
   chunk 41 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.5388

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.151623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.115898 restraints weight = 8846.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 2.12
r_work: 0.3261 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7320  Z= 0.118
  Angle     :  0.497   9.563   9930  Z= 0.258
  Chirality :  0.041   0.127   1159
  Planarity :  0.004   0.049   1243
  Dihedral  :  4.016  54.384    984
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.23 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.29), residues: 911
  helix:  1.96 (0.25), residues: 426
  sheet:  0.31 (0.40), residues: 184
  loop : -0.85 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R  54 
 TYR   0.010   0.001   TYR R 175 
 PHE   0.015   0.001   PHE B 199 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 7319)
  covalent geometry    : angle       0.49643 ( 9928)
  SS BOND              : bond        0.00156 (    1)
  SS BOND              : angle       2.21668 (    2)
  hydrogen bonds       : bond        0.03462 (  390)
  hydrogen bonds       : angle       4.81005 ( 1131)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.182 
Fit side-chains
REVERT: R  143 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.6514 (mpt)
REVERT: R  273 PHE cc_start: 0.8094 (m-10) cc_final: 0.7822 (m-80)
REVERT: R  278 LYS cc_start: 0.7942 (mtmt) cc_final: 0.7446 (mttm)
REVERT: B   13 GLN cc_start: 0.8381 (tm-30) cc_final: 0.8179 (pt0)
  outliers start: 16
  outliers final: 10
  residues processed: 156
  average time/residue: 0.0820
  time to fit residues: 16.9828
Evaluate side-chains
  144 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue  143 MET
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 26 optimal weight:    8.9990
   chunk 72 optimal weight:    3.9990
   chunk 86 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 80 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 57 optimal weight:    0.4980
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.149423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.113780 restraints weight = 8806.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.07
r_work: 0.3229 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.3050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7320  Z= 0.137
  Angle     :  0.500   8.489   9930  Z= 0.261
  Chirality :  0.041   0.130   1159
  Planarity :  0.004   0.049   1243
  Dihedral  :  4.072  54.589    984
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.89 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.28), residues: 911
  helix:  1.91 (0.25), residues: 426
  sheet:  0.22 (0.38), residues: 190
  loop : -0.96 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 238 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7319)
  covalent geometry    : angle       0.49861 ( 9928)
  SS BOND              : bond        0.00247 (    1)
  SS BOND              : angle       2.26327 (    2)
  hydrogen bonds       : bond        0.03492 (  390)
  hydrogen bonds       : angle       4.79922 ( 1131)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 0.253 
Fit side-chains
REVERT: R   27 ILE cc_start: 0.7219 (mm) cc_final: 0.6906 (mt)
REVERT: R   99 LYS cc_start: 0.8140 (tptm) cc_final: 0.7808 (mmtt)
REVERT: R  143 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.6531 (mpt)
REVERT: R  192 LYS cc_start: 0.7855 (tptp) cc_final: 0.7356 (mttp)
REVERT: R  273 PHE cc_start: 0.8101 (m-10) cc_final: 0.7829 (m-80)
REVERT: B   44 GLN cc_start: 0.7361 (tm-30) cc_final: 0.7109 (tm-30)
REVERT: C   31 SER cc_start: 0.8334 (m) cc_final: 0.8029 (p)
  outliers start: 18
  outliers final: 12
  residues processed: 154
  average time/residue: 0.0784
  time to fit residues: 16.3657
Evaluate side-chains
  149 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue  143 MET
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  303 VAL
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 69 optimal weight:    0.2980
   chunk 89 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 77 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.153397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.118320 restraints weight = 8671.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 1.97
r_work: 0.3296 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7320  Z= 0.128
  Angle     :  0.498   8.317   9930  Z= 0.259
  Chirality :  0.041   0.129   1159
  Planarity :  0.004   0.049   1243
  Dihedral  :  4.095  54.733    984
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 17.32 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.28), residues: 911
  helix:  1.89 (0.25), residues: 426
  sheet:  0.05 (0.38), residues: 191
  loop : -0.93 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 238 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7319)
  covalent geometry    : angle       0.49691 ( 9928)
  SS BOND              : bond        0.00301 (    1)
  SS BOND              : angle       2.25812 (    2)
  hydrogen bonds       : bond        0.03417 (  390)
  hydrogen bonds       : angle       4.78681 ( 1131)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 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: 18
    poor density    : 141
  time to evaluate  : 0.264 
Fit side-chains
REVERT: R   27 ILE cc_start: 0.7342 (mm) cc_final: 0.7011 (mt)
REVERT: R   99 LYS cc_start: 0.8353 (tptm) cc_final: 0.8103 (mmtt)
REVERT: R  143 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.6768 (mpt)
REVERT: R  192 LYS cc_start: 0.7871 (tptp) cc_final: 0.7408 (mttp)
REVERT: R  273 PHE cc_start: 0.8099 (m-10) cc_final: 0.7788 (m-80)
REVERT: B   13 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8152 (pt0)
REVERT: B   44 GLN cc_start: 0.7358 (tm-30) cc_final: 0.7095 (tm-30)
REVERT: C   31 SER cc_start: 0.8361 (m) cc_final: 0.8073 (p)
  outliers start: 18
  outliers final: 13
  residues processed: 150
  average time/residue: 0.0768
  time to fit residues: 15.8692
Evaluate side-chains
  148 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 134
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue  143 MET
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  303 VAL
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 83 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 16 optimal weight:    0.2980
   chunk 40 optimal weight:    9.9990
   chunk 59 optimal weight:    0.2980
   chunk 39 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.154108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.118894 restraints weight = 8624.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.97
r_work: 0.3307 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7320  Z= 0.116
  Angle     :  0.496   8.176   9930  Z= 0.258
  Chirality :  0.040   0.128   1159
  Planarity :  0.004   0.049   1243
  Dihedral  :  4.054  54.253    984
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.49 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.29), residues: 911
  helix:  1.92 (0.25), residues: 426
  sheet: -0.05 (0.38), residues: 191
  loop : -0.86 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 238 
 TYR   0.012   0.001   TYR B  59 
 PHE   0.019   0.001   PHE R 161 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.002   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 7319)
  covalent geometry    : angle       0.49501 ( 9928)
  SS BOND              : bond        0.00269 (    1)
  SS BOND              : angle       2.08339 (    2)
  hydrogen bonds       : bond        0.03313 (  390)
  hydrogen bonds       : angle       4.72260 ( 1131)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 0.277 
Fit side-chains
REVERT: R   27 ILE cc_start: 0.7236 (mm) cc_final: 0.6881 (mt)
REVERT: R   33 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6932 (mp)
REVERT: R   99 LYS cc_start: 0.8329 (tptm) cc_final: 0.8128 (mmtt)
REVERT: R  143 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.6751 (mpt)
REVERT: R  192 LYS cc_start: 0.7845 (tptp) cc_final: 0.7406 (mttp)
REVERT: R  273 PHE cc_start: 0.8101 (m-10) cc_final: 0.7782 (m-80)
REVERT: B   13 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8146 (pt0)
REVERT: C   31 SER cc_start: 0.8336 (m) cc_final: 0.8056 (p)
  outliers start: 15
  outliers final: 13
  residues processed: 148
  average time/residue: 0.0745
  time to fit residues: 15.1761
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  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue  104 VAL
Chi-restraints excluded: chain R residue  143 MET
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  312 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 57 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B 259 GLN
B 311 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.142166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.107546 restraints weight = 8859.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 2.05
r_work: 0.3111 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.3775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7320  Z= 0.212
  Angle     :  0.576   9.104   9930  Z= 0.303
  Chirality :  0.043   0.135   1159
  Planarity :  0.004   0.046   1243
  Dihedral  :  4.466  56.765    984
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.49 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.28), residues: 911
  helix:  1.81 (0.25), residues: 425
  sheet: -0.28 (0.40), residues: 177
  loop : -0.98 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R 238 
 TYR   0.020   0.002   TYR B  59 
 PHE   0.022   0.002   PHE R 161 
 TRP   0.011   0.002   TRP B  63 
 HIS   0.006   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 7319)
  covalent geometry    : angle       0.57442 ( 9928)
  SS BOND              : bond        0.00321 (    1)
  SS BOND              : angle       2.84046 (    2)
  hydrogen bonds       : bond        0.04007 (  390)
  hydrogen bonds       : angle       5.06782 ( 1131)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 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: 22
    poor density    : 139
  time to evaluate  : 0.296 
Fit side-chains
REVERT: R   33 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7119 (mp)
REVERT: R   99 LYS cc_start: 0.8273 (tptm) cc_final: 0.8006 (mmtt)
REVERT: R  143 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.6953 (mpp)
REVERT: R  192 LYS cc_start: 0.7938 (tptp) cc_final: 0.7461 (mttp)
REVERT: R  273 PHE cc_start: 0.8162 (m-10) cc_final: 0.7845 (m-80)
REVERT: A   25 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7178 (mp0)
REVERT: A  242 ASN cc_start: 0.7510 (t0) cc_final: 0.7175 (t0)
REVERT: B   13 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8168 (pt0)
  outliers start: 22
  outliers final: 16
  residues processed: 149
  average time/residue: 0.0784
  time to fit residues: 15.8956
Evaluate side-chains
  147 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue  104 VAL
Chi-restraints excluded: chain R residue  143 MET
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  321 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 74 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 82 optimal weight:    7.9990
   chunk 81 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 85 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.144757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.109549 restraints weight = 8685.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.00
r_work: 0.3163 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.3771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7320  Z= 0.150
  Angle     :  0.547  10.221   9930  Z= 0.283
  Chirality :  0.042   0.130   1159
  Planarity :  0.004   0.047   1243
  Dihedral  :  4.343  55.143    984
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.92 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.28), residues: 911
  helix:  1.71 (0.25), residues: 426
  sheet: -0.42 (0.39), residues: 175
  loop : -0.95 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 238 
 TYR   0.019   0.001   TYR A 231 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 7319)
  covalent geometry    : angle       0.54570 ( 9928)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       2.37250 (    2)
  hydrogen bonds       : bond        0.03581 (  390)
  hydrogen bonds       : angle       4.94985 ( 1131)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.324 
Fit side-chains
REVERT: R   33 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7035 (mp)
REVERT: R   54 ARG cc_start: 0.7820 (mtp-110) cc_final: 0.7612 (mtp85)
REVERT: R  143 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.6648 (mpt)
REVERT: R  273 PHE cc_start: 0.8151 (m-10) cc_final: 0.7816 (m-80)
REVERT: A   25 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6632 (mp0)
REVERT: B   13 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8174 (pt0)
  outliers start: 22
  outliers final: 16
  residues processed: 142
  average time/residue: 0.0674
  time to fit residues: 13.5576
Evaluate side-chains
  145 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue  104 VAL
Chi-restraints excluded: chain R residue  143 MET
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  303 VAL
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 37 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.144374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.109001 restraints weight = 8760.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 2.01
r_work: 0.3161 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3014 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.3832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7320  Z= 0.157
  Angle     :  0.554   9.871   9930  Z= 0.285
  Chirality :  0.042   0.130   1159
  Planarity :  0.004   0.047   1243
  Dihedral  :  4.338  55.493    984
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 19.79 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.28), residues: 911
  helix:  1.68 (0.25), residues: 427
  sheet: -0.42 (0.40), residues: 174
  loop : -0.94 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 238 
 TYR   0.017   0.001   TYR A 231 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.011   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 7319)
  covalent geometry    : angle       0.55262 ( 9928)
  SS BOND              : bond        0.00209 (    1)
  SS BOND              : angle       2.33655 (    2)
  hydrogen bonds       : bond        0.03602 (  390)
  hydrogen bonds       : angle       4.93684 ( 1131)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.356 
Fit side-chains
REVERT: R   33 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6975 (mp)
REVERT: R   54 ARG cc_start: 0.7806 (mtp-110) cc_final: 0.7261 (mtp85)
REVERT: R  143 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.6673 (mpt)
REVERT: R  192 LYS cc_start: 0.8243 (tmtt) cc_final: 0.7571 (mttp)
REVERT: R  273 PHE cc_start: 0.8147 (m-10) cc_final: 0.7804 (m-80)
REVERT: R  312 ARG cc_start: 0.7460 (tpp-160) cc_final: 0.7027 (mtp85)
REVERT: A   25 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6621 (mp0)
REVERT: B   13 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8179 (pt0)
  outliers start: 21
  outliers final: 16
  residues processed: 141
  average time/residue: 0.0750
  time to fit residues: 14.5576
Evaluate side-chains
  143 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue  143 MET
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  173 ASP
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  303 VAL
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 78 optimal weight:    0.0670
   chunk 75 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0970
   chunk 49 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 61 optimal weight:    0.4980
   chunk 1 optimal weight:    4.9990
   overall best weight:    0.4316

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

Flipped N/Q/H residues before XYZ refinement:
B 311 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.147665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.112560 restraints weight = 8662.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 2.03
r_work: 0.3210 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.3753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7320  Z= 0.117
  Angle     :  0.534  11.244   9930  Z= 0.274
  Chirality :  0.041   0.133   1159
  Planarity :  0.004   0.048   1243
  Dihedral  :  4.219  54.441    984
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 20.57 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.28), residues: 911
  helix:  1.73 (0.25), residues: 427
  sheet: -0.24 (0.38), residues: 188
  loop : -0.85 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 238 
 TYR   0.017   0.001   TYR A 231 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.015   0.001   TRP B 211 
 HIS   0.003   0.000   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7319)
  covalent geometry    : angle       0.53302 ( 9928)
  SS BOND              : bond        0.00091 (    1)
  SS BOND              : angle       2.04781 (    2)
  hydrogen bonds       : bond        0.03349 (  390)
  hydrogen bonds       : angle       4.83190 ( 1131)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2092.86 seconds
wall clock time: 36 minutes 28.72 seconds (2188.72 seconds total)