Starting phenix.real_space_refine
on Tue Mar  3 20:35:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9xpg_67097/03_2026/9xpg_67097.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9xpg_67097/03_2026/9xpg_67097.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9xpg_67097/03_2026/9xpg_67097.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9xpg_67097/03_2026/9xpg_67097.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9xpg_67097/03_2026/9xpg_67097.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9xpg_67097/03_2026/9xpg_67097.cif"
  }
  resolution = 4.14
  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=   0.004 sd=   0.053
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      23      5.16       5
     C    5226      2.51       5
     N    1440      2.21       5
     O    1578      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  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: 8267
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1973
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 14, 'TRANS': 239}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1986
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 1986
          Classifications: {'peptide': 258}
          Link IDs: {'PTRANS': 15, 'TRANS': 242}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2249
          Classifications: {'peptide': 291}
          Link IDs: {'PTRANS': 16, 'TRANS': 274}
    Chain: "D"
      Number of atoms: 2059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 2059
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 14, 'TRANS': 250}
          Chain breaks: 3
  Time building chain proxies: 1.92, per 1000 atoms: 0.23
  Number of scatterers: 8267
  At special positions: 0
  Unit cell: (126.48, 96.56, 150.96, 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      23     16.00
     O    1578      8.00
     N    1440      7.00
     C    5226      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 227 " - pdb=" SG  CYS B 252 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 227 " - pdb=" SG  CYS C 252 " 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: 0.69
  Conformation dependent library (CDL) restraints added in 357.4 milliseconds
  

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1976

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 16 sheets defined
      17.1% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 27
    Processing helix  chain 'A' and resid 37 through 42
      removed outlier: 3.695A  pdb=" N   LYS A  41 " --> pdb=" O   THR A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 115
      removed outlier: 3.610A  pdb=" N   MET A 114 " --> pdb=" O   ARG A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 126
      removed outlier: 3.796A  pdb=" N   GLY A 125 " --> pdb=" O   GLU A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 168
    Processing helix  chain 'A' and resid 198 through 214
    Processing helix  chain 'B' and resid 16 through 27
      removed outlier: 3.519A  pdb=" N   LEU B  26 " --> pdb=" O   THR B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 43
      removed outlier: 3.556A  pdb=" N   LYS B  41 " --> pdb=" O   THR B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 113
    Processing helix  chain 'B' and resid 151 through 154
      removed outlier: 3.576A  pdb=" N   GLU B 154 " --> pdb=" O   VAL B 151 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 151 through 154'
    Processing helix  chain 'B' and resid 163 through 168
    Processing helix  chain 'B' and resid 198 through 214
    Processing helix  chain 'C' and resid 14 through 27
    Processing helix  chain 'C' and resid 108 through 112
    Processing helix  chain 'C' and resid 198 through 212
      removed outlier: 3.847A  pdb=" N   ILE C 205 " --> pdb=" O   GLU C 201 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG C 212 " --> pdb=" O   ALA C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 263 through 267
      removed outlier: 4.366A  pdb=" N   TYR C 266 " --> pdb=" O   ALA C 263 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 14 through 27
    Processing helix  chain 'D' and resid 108 through 114
    Processing helix  chain 'D' and resid 163 through 167
      removed outlier: 3.519A  pdb=" N   ASP D 166 " --> pdb=" O   ASN D 163 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 199 through 212
      removed outlier: 3.667A  pdb=" N   GLU D 204 " --> pdb=" O   GLU D 200 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ARG D 210 " --> pdb=" O   THR D 206 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13
      removed outlier: 3.586A  pdb=" N   ASN A  10 " --> pdb=" O   ALA A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 62
      removed outlier: 5.623A  pdb=" N   VAL A  58 " --> pdb=" O   GLY A 229 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   GLY A 229 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   VAL A  62 " --> pdb=" O   GLY A 225 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLY A 225 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   VAL A 230 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
      removed outlier: 5.561A  pdb=" N   ALA A 251 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   LYS A 232 " --> pdb=" O   VAL A 249 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   VAL A 249 " --> pdb=" O   LYS A 232 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   VAL A 234 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   THR A 247 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   GLY A 236 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   ILE A 245 " --> pdb=" O   GLY A 236 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   SER A 238 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
      removed outlier: 5.256A  pdb=" N   ASN A 243 " --> pdb=" O   SER A 238 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 102
      removed outlier: 3.999A  pdb=" N   VAL A  99 " --> pdb=" O   TYR A 131 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ARG A 119 " --> pdb=" O   ALA A 130 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 159
    Processing sheet with id=AA5, first strand: chain 'A' and resid 193 through 196
    Processing sheet with id=AA6, first strand: chain 'B' and resid 115 through 116
      removed outlier: 3.667A  pdb=" N   ARG B 116 " --> pdb=" O   ALA B 133 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ALA B 133 " --> pdb=" O   ARG B 116 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   VAL B  58 " --> pdb=" O   GLY B 229 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   GLY B 229 " --> pdb=" O   VAL B  58 " (cutoff:3.500A)
      removed outlier: 4.926A  pdb=" N   ILE B 220 " --> pdb=" O   HIS B 262 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   HIS B 262 " --> pdb=" O   ILE B 220 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   SER B 222 " --> pdb=" O   THR B 260 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   VAL B 256 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   SER B 228 " --> pdb=" O   ILE B 254 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   ILE B 254 " --> pdb=" O   SER B 228 " (cutoff:3.500A)
      removed outlier: 8.182A  pdb=" N   VAL B 230 " --> pdb=" O   CYS B 252 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   CYS B 252 " --> pdb=" O   VAL B 230 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   LYS B 232 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ILE B 250 " --> pdb=" O   LYS B 232 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   VAL B 234 " --> pdb=" O   GLU B 248 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   GLU B 248 " --> pdb=" O   VAL B 234 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   GLY B 236 " --> pdb=" O   TYR B 246 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   TYR B 246 " --> pdb=" O   GLY B 236 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 102
      removed outlier: 3.691A  pdb=" N   TYR B 128 " --> pdb=" O   GLU B 121 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 156 through 159
    Processing sheet with id=AA9, first strand: chain 'C' and resid 11 through 13
      removed outlier: 3.608A  pdb=" N   VAL C 230 " --> pdb=" O   ILE C 250 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   CYS C 252 " --> pdb=" O   SER C 228 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   SER C 228 " --> pdb=" O   CYS C 252 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   ILE C 254 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   LEU C 226 " --> pdb=" O   ILE C 254 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   VAL C 256 " --> pdb=" O   ILE C 224 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ILE C 224 " --> pdb=" O   VAL C 256 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   GLY C 229 " --> pdb=" O   VAL C  58 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   VAL C  58 " --> pdb=" O   GLY C 229 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ARG C 134 " --> pdb=" O   MET C  61 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   ILE C  63 " --> pdb=" O   TYR C 132 " (cutoff:3.500A)
      removed outlier: 9.443A  pdb=" N   TYR C 132 " --> pdb=" O   ILE C  63 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   TYR C 131 " --> pdb=" O   ARG C 118 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   ARG C 118 " --> pdb=" O   TYR C 131 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 122 through 123
    Processing sheet with id=AB2, first strand: chain 'C' and resid 156 through 159
    Processing sheet with id=AB3, first strand: chain 'C' and resid 193 through 197
      removed outlier: 3.814A  pdb=" N   LEU C 197 " --> pdb=" O   LEU C 271 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LEU C 271 " --> pdb=" O   LEU C 197 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 11 through 13
      removed outlier: 3.812A  pdb=" N   CYS D 252 " --> pdb=" O   SER D 228 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   SER D 228 " --> pdb=" O   CYS D 252 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   ILE D 254 " --> pdb=" O   LEU D 226 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   LEU D 226 " --> pdb=" O   ILE D 254 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   VAL D 256 " --> pdb=" O   ILE D 224 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   ILE D 224 " --> pdb=" O   VAL D 256 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ILE D 258 " --> pdb=" O   SER D 222 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   SER D 222 " --> pdb=" O   ILE D 258 " (cutoff:3.500A)
      removed outlier: 8.781A  pdb=" N   THR D 260 " --> pdb=" O   ILE D 220 " (cutoff:3.500A)
      removed outlier: 9.185A  pdb=" N   ILE D 220 " --> pdb=" O   THR D 260 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   VAL D  62 " --> pdb=" O   GLY D 225 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   CYS D 227 " --> pdb=" O   TYR D  60 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   TYR D  60 " --> pdb=" O   CYS D 227 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   GLY D 229 " --> pdb=" O   VAL D  58 " (cutoff:3.500A)
      removed outlier: 6.042A  pdb=" N   VAL D  58 " --> pdb=" O   GLY D 229 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ARG D 134 " --> pdb=" O   MET D  61 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 99 through 102
      removed outlier: 3.969A  pdb=" N   VAL D  99 " --> pdb=" O   TYR D 131 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 144 through 146
    Processing sheet with id=AB7, first strand: chain 'D' and resid 196 through 198

    216 hydrogen bonds defined for protein.
    570 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.09

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2742
        1.34 -     1.46: 1182
        1.46 -     1.57: 4465
        1.57 -     1.69: 0
        1.69 -     1.81: 34
  Bond restraints: 8423
  Sorted by residual:
  bond pdb=" CG1 ILE B 205 "
       pdb=" CD1 ILE B 205 "
    ideal  model  delta    sigma   weight residual
    1.513  1.438  0.075 3.90e-02 6.57e+02 3.66e+00
  bond pdb=" CG  LEU A  38 "
       pdb=" CD2 LEU A  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.468  0.053 3.30e-02 9.18e+02 2.56e+00
  bond pdb=" CA  GLU B 281 "
       pdb=" C   GLU B 281 "
    ideal  model  delta    sigma   weight residual
    1.524  1.540 -0.016 1.26e-02 6.30e+03 1.58e+00
  bond pdb=" CB  LEU A  38 "
       pdb=" CG  LEU A  38 "
    ideal  model  delta    sigma   weight residual
    1.530  1.507  0.023 2.00e-02 2.50e+03 1.36e+00
  bond pdb=" CA  GLU D 223 "
       pdb=" CB  GLU D 223 "
    ideal  model  delta    sigma   weight residual
    1.527  1.547 -0.020 1.75e-02 3.27e+03 1.33e+00
  ... (remaining 8418 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 10860
        1.53 -     3.06: 504
        3.06 -     4.59: 82
        4.59 -     6.11: 16
        6.11 -     7.64: 3
  Bond angle restraints: 11465
  Sorted by residual:
  angle pdb=" N   ALA C 292 "
        pdb=" CA  ALA C 292 "
        pdb=" C   ALA C 292 "
      ideal   model   delta    sigma   weight residual
     110.91  116.33   -5.42 1.17e+00 7.31e-01 2.15e+01
  angle pdb=" N   VAL B 216 "
        pdb=" CA  VAL B 216 "
        pdb=" C   VAL B 216 "
      ideal   model   delta    sigma   weight residual
     113.47  108.97    4.50 1.01e+00 9.80e-01 1.98e+01
  angle pdb=" N   GLU D  40 "
        pdb=" CA  GLU D  40 "
        pdb=" C   GLU D  40 "
      ideal   model   delta    sigma   weight residual
     113.18  108.14    5.04 1.33e+00 5.65e-01 1.44e+01
  angle pdb=" N   THR C 213 "
        pdb=" CA  THR C 213 "
        pdb=" C   THR C 213 "
      ideal   model   delta    sigma   weight residual
     114.56  110.12    4.44 1.27e+00 6.20e-01 1.22e+01
  angle pdb=" CA  TYR A   8 "
        pdb=" CB  TYR A   8 "
        pdb=" CG  TYR A   8 "
      ideal   model   delta    sigma   weight residual
     113.90  120.01   -6.11 1.80e+00 3.09e-01 1.15e+01
  ... (remaining 11460 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.60: 4683
       17.60 -    35.20: 335
       35.20 -    52.80: 36
       52.80 -    70.40: 23
       70.40 -    88.00: 7
  Dihedral angle restraints: 5084
    sinusoidal: 1996
      harmonic: 3088
  Sorted by residual:
  dihedral pdb=" CB  CYS C 227 "
           pdb=" SG  CYS C 227 "
           pdb=" SG  CYS C 252 "
           pdb=" CB  CYS C 252 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.34  -80.34     1      1.00e+01 1.00e-02 7.99e+01
  dihedral pdb=" CA  TYR D 115 "
           pdb=" C   TYR D 115 "
           pdb=" N   ARG D 116 "
           pdb=" CA  ARG D 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.28  -22.72     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" CA  PHE D  42 "
           pdb=" C   PHE D  42 "
           pdb=" N   SER D  43 "
           pdb=" CA  SER D  43 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.29  -22.71     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 5081 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 949
       0.046 -    0.092: 277
       0.092 -    0.138: 100
       0.138 -    0.184: 5
       0.184 -    0.229: 2
  Chirality restraints: 1333
  Sorted by residual:
  chirality pdb=" CB  ILE A 221 "
            pdb=" CA  ILE A 221 "
            pdb=" CG1 ILE A 221 "
            pdb=" CG2 ILE A 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CB  VAL C 264 "
            pdb=" CA  VAL C 264 "
            pdb=" CG1 VAL C 264 "
            pdb=" CG2 VAL C 264 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 8.87e-01
  chirality pdb=" CB  ILE D 277 "
            pdb=" CA  ILE D 277 "
            pdb=" CG1 ILE D 277 "
            pdb=" CG2 ILE D 277 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.31e-01
  ... (remaining 1330 not shown)

  Planarity restraints: 1500
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  44 "   -0.010 2.00e-02 2.50e+03   2.00e-02 3.99e+00
        pdb=" C   ILE B  44 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ILE B  44 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLN B  45 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C 122 "    0.010 2.00e-02 2.50e+03   1.96e-02 3.83e+00
        pdb=" CD  GLU C 122 "   -0.034 2.00e-02 2.50e+03
        pdb=" OE1 GLU C 122 "    0.012 2.00e-02 2.50e+03
        pdb=" OE2 GLU C 122 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C 261 "   -0.009 2.00e-02 2.50e+03   1.72e-02 2.96e+00
        pdb=" C   ASN C 261 "    0.030 2.00e-02 2.50e+03
        pdb=" O   ASN C 261 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   HIS C 262 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1497 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 3304
        2.89 -     3.40: 8361
        3.40 -     3.90: 13153
        3.90 -     4.40: 13876
        4.40 -     4.90: 23184
  Nonbonded interactions: 61878
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B  39 "
            pdb=" O   ILE B  44 "
     model   vdw
     2.393 3.040
  nonbonded pdb=" O   ASN C 261 "
            pdb=" OD1 ASN C 261 "
     model   vdw
     2.441 3.040
  nonbonded pdb=" O   GLU C 122 "
            pdb=" OE1 GLU C 122 "
     model   vdw
     2.452 3.040
  nonbonded pdb=" O   HIS D 123 "
            pdb=" OD1 ASN D 124 "
     model   vdw
     2.491 3.040
  nonbonded pdb=" O   THR C  36 "
            pdb=" OG1 THR C  37 "
     model   vdw
     2.503 3.040
  ... (remaining 61873 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 9 through 151 or resid 158 through 175 or resid 182 throug \ 
h 277))
  selection = (chain 'B' and (resid 9 through 151 or resid 158 through 175 or resid 182 throug \ 
h 277))
  selection = (chain 'C' and (resid 9 through 64 or resid 84 through 151 or resid 158 through  \ 
175 or resid 182 through 277))
  selection = (chain 'D' and (resid 9 through 64 or resid 84 through 277))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.000
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.670
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   8425  Z= 0.213
  Angle     :  0.752   7.642  11469  Z= 0.427
  Chirality :  0.048   0.229   1333
  Planarity :  0.005   0.045   1500
  Dihedral  : 12.981  88.002   3102
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 11.05 %
    Favored  : 88.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  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: -2.06 (0.25), residues: 1050
  helix:  0.24 (0.44), residues: 152
  sheet: -1.01 (0.36), residues: 228
  loop : -1.98 (0.23), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D  13 
 TYR   0.025   0.002   TYR A   8 
 PHE   0.019   0.002   PHE A  30 
 HIS   0.008   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 8423)
  covalent geometry    : angle       0.75098 (11465)
  SS BOND              : bond        0.00341 (    2)
  SS BOND              : angle       2.32228 (    4)
  hydrogen bonds       : bond        0.22892 (  216)
  hydrogen bonds       : angle       9.91121 (  570)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.307 
Fit side-chains
REVERT: B   47 ASN cc_start: 0.9018 (t0) cc_final: 0.8716 (t0)
REVERT: D   21 GLN cc_start: 0.7717 (mt0) cc_final: 0.7473 (mt0)
REVERT: D   23 CYS cc_start: 0.9048 (m) cc_final: 0.8698 (t)
REVERT: D  105 ASP cc_start: 0.9082 (t0) cc_final: 0.8850 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0642
  time to fit residues: 5.6719
Evaluate side-chains
  42 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:   20.0000
   chunk 100 optimal weight:   30.0000
   chunk 38 optimal weight:   30.0000
   chunk 61 optimal weight:    6.9990
   overall best weight:    5.1988

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

Flipped N/Q/H residues before XYZ refinement:
C  21 GLN
C  45 GLN
C 127 GLN
D  68 HIS
** D 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.056883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.048471 restraints weight = 60973.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.049640 restraints weight = 35189.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.050433 restraints weight = 23594.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.050977 restraints weight = 17535.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.051347 restraints weight = 14053.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.1034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8425  Z= 0.164
  Angle     :  0.627   7.551  11469  Z= 0.336
  Chirality :  0.048   0.151   1333
  Planarity :  0.004   0.036   1500
  Dihedral  :  4.972  23.514   1166
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 10.95 %
    Favored  : 88.57 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  5.91 %
    Favored  : 93.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.03 (0.25), residues: 1050
  helix:  0.29 (0.43), residues: 154
  sheet: -1.19 (0.36), residues: 211
  loop : -1.89 (0.23), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  13 
 TYR   0.020   0.002   TYR A   8 
 PHE   0.012   0.001   PHE B 257 
 HIS   0.006   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 8423)
  covalent geometry    : angle       0.62663 (11465)
  SS BOND              : bond        0.00206 (    2)
  SS BOND              : angle       1.48460 (    4)
  hydrogen bonds       : bond        0.03792 (  216)
  hydrogen bonds       : angle       7.06867 (  570)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8482 (ppp) cc_final: 0.8265 (ppp)
REVERT: A  272 LYS cc_start: 0.9668 (ptpt) cc_final: 0.9407 (ptpp)
REVERT: B  283 MET cc_start: 0.6409 (tmm) cc_final: 0.5606 (tmm)
REVERT: C   61 MET cc_start: 0.8885 (ppp) cc_final: 0.8573 (ppp)
REVERT: D   23 CYS cc_start: 0.9119 (m) cc_final: 0.8869 (t)
REVERT: D  105 ASP cc_start: 0.9136 (t0) cc_final: 0.8875 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0645
  time to fit residues: 6.4083
Evaluate side-chains
  45 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 32 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 8 optimal weight:    4.9990
   chunk 104 optimal weight:   30.0000
   chunk 4 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 2 optimal weight:    9.9990
   chunk 90 optimal weight:    8.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 GLN
** C  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 196 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 = 0.3341 r_free = 0.3341 target = 0.056270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.047864 restraints weight = 60118.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.049066 restraints weight = 34018.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.049872 restraints weight = 22475.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.050427 restraints weight = 16588.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.050813 restraints weight = 13193.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8425  Z= 0.167
  Angle     :  0.624   6.803  11469  Z= 0.335
  Chirality :  0.048   0.251   1333
  Planarity :  0.004   0.037   1500
  Dihedral  :  4.973  22.284   1166
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 11.14 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  5.91 %
    Favored  : 93.98 %
  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: -1.96 (0.25), residues: 1050
  helix:  0.28 (0.44), residues: 152
  sheet: -0.80 (0.37), residues: 198
  loop : -1.94 (0.22), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 116 
 TYR   0.021   0.002   TYR D  19 
 PHE   0.017   0.002   PHE B 257 
 HIS   0.006   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 8423)
  covalent geometry    : angle       0.62240 (11465)
  SS BOND              : bond        0.00168 (    2)
  SS BOND              : angle       2.28990 (    4)
  hydrogen bonds       : bond        0.03879 (  216)
  hydrogen bonds       : angle       6.66753 (  570)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 LYS cc_start: 0.9675 (ptpt) cc_final: 0.9393 (ptpp)
REVERT: B  283 MET cc_start: 0.6101 (tmm) cc_final: 0.5483 (tmm)
REVERT: C   61 MET cc_start: 0.8987 (ppp) cc_final: 0.8687 (ppp)
REVERT: D   23 CYS cc_start: 0.9208 (m) cc_final: 0.8952 (t)
REVERT: D  105 ASP cc_start: 0.9127 (t0) cc_final: 0.8857 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0752
  time to fit residues: 7.1043
Evaluate side-chains
  41 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 67 optimal weight:    0.0970
   chunk 82 optimal weight:   10.0000
   chunk 58 optimal weight:   30.0000
   chunk 98 optimal weight:   30.0000
   chunk 89 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   chunk 30 optimal weight:    0.8980
   chunk 91 optimal weight:   20.0000
   chunk 11 optimal weight:   20.0000
   chunk 101 optimal weight:    5.9990
   chunk 93 optimal weight:   20.0000
   overall best weight:    4.5984

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

Flipped N/Q/H residues before XYZ refinement:
** A  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 GLN
** C  45 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 = 0.3343 r_free = 0.3343 target = 0.056425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.048160 restraints weight = 61490.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.049319 restraints weight = 35437.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.050102 restraints weight = 23609.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.050624 restraints weight = 17491.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.051014 restraints weight = 14077.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8425  Z= 0.151
  Angle     :  0.616   7.459  11469  Z= 0.325
  Chirality :  0.048   0.211   1333
  Planarity :  0.004   0.037   1500
  Dihedral  :  4.899  21.233   1166
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 11.24 %
    Favored  : 88.29 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.07 %
    Favored  : 96.82 %
  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: -1.76 (0.26), residues: 1050
  helix:  0.45 (0.44), residues: 154
  sheet: -0.72 (0.38), residues: 200
  loop : -1.79 (0.23), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 116 
 TYR   0.024   0.002   TYR A  93 
 PHE   0.014   0.001   PHE B 257 
 HIS   0.006   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 8423)
  covalent geometry    : angle       0.61583 (11465)
  SS BOND              : bond        0.00295 (    2)
  SS BOND              : angle       1.51719 (    4)
  hydrogen bonds       : bond        0.03396 (  216)
  hydrogen bonds       : angle       6.35175 (  570)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 LYS cc_start: 0.9651 (ptpt) cc_final: 0.9397 (ptpp)
REVERT: B  283 MET cc_start: 0.6030 (tmm) cc_final: 0.5457 (tmm)
REVERT: C   61 MET cc_start: 0.8912 (ppp) cc_final: 0.8457 (ppp)
REVERT: D  105 ASP cc_start: 0.9150 (t0) cc_final: 0.8886 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0670
  time to fit residues: 6.1579
Evaluate side-chains
  44 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 93 optimal weight:    5.9990
   chunk 98 optimal weight:    0.9990
   chunk 67 optimal weight:    6.9990
   chunk 92 optimal weight:   20.0000
   chunk 22 optimal weight:   30.0000
   chunk 4 optimal weight:    8.9990
   chunk 71 optimal weight:   10.0000
   chunk 73 optimal weight:    0.0050
   chunk 43 optimal weight:    7.9990
   chunk 46 optimal weight:    9.9990
   overall best weight:    4.2002

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

Flipped N/Q/H residues before XYZ refinement:
** A  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 GLN
C  45 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.056295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.047967 restraints weight = 60439.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.049149 restraints weight = 34115.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.049945 restraints weight = 22456.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.050504 restraints weight = 16537.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.050896 restraints weight = 13124.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8425  Z= 0.141
  Angle     :  0.601   6.678  11469  Z= 0.320
  Chirality :  0.048   0.188   1333
  Planarity :  0.004   0.039   1500
  Dihedral  :  4.815  19.753   1166
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  : 10.76 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.07 %
    Favored  : 96.82 %
  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: -1.66 (0.26), residues: 1050
  helix:  0.41 (0.44), residues: 154
  sheet: -0.54 (0.38), residues: 207
  loop : -1.74 (0.23), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 116 
 TYR   0.018   0.002   TYR B 131 
 PHE   0.014   0.001   PHE B 257 
 HIS   0.006   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8423)
  covalent geometry    : angle       0.59930 (11465)
  SS BOND              : bond        0.00528 (    2)
  SS BOND              : angle       2.74789 (    4)
  hydrogen bonds       : bond        0.03336 (  216)
  hydrogen bonds       : angle       6.14723 (  570)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 LYS cc_start: 0.9632 (ptpt) cc_final: 0.9366 (ptpp)
REVERT: B  271 LEU cc_start: 0.9447 (tp) cc_final: 0.9142 (tt)
REVERT: B  283 MET cc_start: 0.5706 (tmm) cc_final: 0.5349 (tmm)
REVERT: C   61 MET cc_start: 0.8919 (ppp) cc_final: 0.8402 (ppp)
REVERT: D   70 PHE cc_start: 0.7602 (m-80) cc_final: 0.7394 (p90)
REVERT: D  105 ASP cc_start: 0.9151 (t0) cc_final: 0.8891 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0824
  time to fit residues: 7.1951
Evaluate side-chains
  44 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 80 optimal weight:    9.9990
   chunk 95 optimal weight:   20.0000
   chunk 89 optimal weight:   20.0000
   chunk 12 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 91 optimal weight:    9.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 GLN
** C  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 127 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.055765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.047590 restraints weight = 60558.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.048750 restraints weight = 34760.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.049522 restraints weight = 23114.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.050066 restraints weight = 17102.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.050418 restraints weight = 13615.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8425  Z= 0.168
  Angle     :  0.632   6.038  11469  Z= 0.336
  Chirality :  0.048   0.172   1333
  Planarity :  0.004   0.039   1500
  Dihedral  :  4.958  20.029   1166
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 12.38 %
    Favored  : 87.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  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: -1.65 (0.26), residues: 1050
  helix:  0.58 (0.45), residues: 154
  sheet: -0.56 (0.37), residues: 209
  loop : -1.77 (0.23), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 119 
 TYR   0.021   0.002   TYR A   8 
 PHE   0.015   0.002   PHE B 257 
 HIS   0.006   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 8423)
  covalent geometry    : angle       0.62898 (11465)
  SS BOND              : bond        0.00305 (    2)
  SS BOND              : angle       3.08807 (    4)
  hydrogen bonds       : bond        0.03501 (  216)
  hydrogen bonds       : angle       6.06974 (  570)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 LYS cc_start: 0.9607 (ptpt) cc_final: 0.9313 (ptpp)
REVERT: B  271 LEU cc_start: 0.9448 (tp) cc_final: 0.9204 (tt)
REVERT: B  283 MET cc_start: 0.5642 (tmm) cc_final: 0.5242 (tmm)
REVERT: C  127 GLN cc_start: 0.7589 (tt0) cc_final: 0.7357 (tt0)
REVERT: D   70 PHE cc_start: 0.7719 (m-80) cc_final: 0.7387 (p90)
REVERT: D  105 ASP cc_start: 0.9130 (t0) cc_final: 0.8870 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.1040
  time to fit residues: 8.9926
Evaluate side-chains
  46 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 44 optimal weight:   20.0000
   chunk 66 optimal weight:   40.0000
   chunk 56 optimal weight:   20.0000
   chunk 34 optimal weight:   20.0000
   chunk 80 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 78 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0770
   chunk 15 optimal weight:   20.0000
   chunk 62 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   overall best weight:    3.0144

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

Flipped N/Q/H residues before XYZ refinement:
** A  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 GLN
B 237 GLN
** C  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.056599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.048431 restraints weight = 60774.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.049602 restraints weight = 34862.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.050383 restraints weight = 23138.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.050895 restraints weight = 17124.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.051286 restraints weight = 13792.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8425  Z= 0.121
  Angle     :  0.599   5.872  11469  Z= 0.318
  Chirality :  0.048   0.312   1333
  Planarity :  0.004   0.040   1500
  Dihedral  :  4.813  19.251   1166
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 10.29 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  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: -1.49 (0.26), residues: 1050
  helix:  0.61 (0.45), residues: 152
  sheet: -0.09 (0.38), residues: 202
  loop : -1.75 (0.23), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 112 
 TYR   0.015   0.001   TYR C 128 
 PHE   0.012   0.001   PHE C 257 
 HIS   0.006   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8423)
  covalent geometry    : angle       0.59846 (11465)
  SS BOND              : bond        0.00266 (    2)
  SS BOND              : angle       1.95048 (    4)
  hydrogen bonds       : bond        0.03271 (  216)
  hydrogen bonds       : angle       5.84038 (  570)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 LYS cc_start: 0.9636 (ptpt) cc_final: 0.9336 (ptpp)
REVERT: B  271 LEU cc_start: 0.9482 (tp) cc_final: 0.9232 (tt)
REVERT: B  283 MET cc_start: 0.5486 (tmm) cc_final: 0.5129 (tmm)
REVERT: D   70 PHE cc_start: 0.7635 (m-80) cc_final: 0.7417 (p90)
REVERT: D  105 ASP cc_start: 0.9110 (t0) cc_final: 0.8872 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0853
  time to fit residues: 7.0763
Evaluate side-chains
  43 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   chunk 11 optimal weight:    8.9990
   chunk 77 optimal weight:    9.9990
   chunk 92 optimal weight:   20.0000
   chunk 14 optimal weight:    2.9990
   chunk 87 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9980
   chunk 68 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 66 optimal weight:   20.0000
   overall best weight:    3.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 GLN
B 237 GLN
B 255 ASN
** C  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.056370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.048038 restraints weight = 59881.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.049220 restraints weight = 33960.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.050026 restraints weight = 22461.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.050598 restraints weight = 16471.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.050974 restraints weight = 13059.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8425  Z= 0.133
  Angle     :  0.609   6.009  11469  Z= 0.322
  Chirality :  0.048   0.269   1333
  Planarity :  0.004   0.040   1500
  Dihedral  :  4.838  19.628   1166
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 11.52 %
    Favored  : 88.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  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: -1.51 (0.26), residues: 1050
  helix:  0.57 (0.45), residues: 152
  sheet: -0.11 (0.38), residues: 199
  loop : -1.75 (0.23), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 116 
 TYR   0.017   0.001   TYR A   8 
 PHE   0.020   0.002   PHE C 257 
 HIS   0.006   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8423)
  covalent geometry    : angle       0.60607 (11465)
  SS BOND              : bond        0.00216 (    2)
  SS BOND              : angle       3.29287 (    4)
  hydrogen bonds       : bond        0.03329 (  216)
  hydrogen bonds       : angle       5.76631 (  570)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 GLU cc_start: 0.7481 (pt0) cc_final: 0.7278 (pt0)
REVERT: A  272 LYS cc_start: 0.9632 (ptpt) cc_final: 0.9393 (ptpp)
REVERT: B  271 LEU cc_start: 0.9487 (tp) cc_final: 0.9251 (tt)
REVERT: B  283 MET cc_start: 0.5508 (tmm) cc_final: 0.5151 (tmm)
REVERT: D   70 PHE cc_start: 0.7634 (m-80) cc_final: 0.7431 (p90)
REVERT: D  105 ASP cc_start: 0.9127 (t0) cc_final: 0.8892 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0782
  time to fit residues: 6.4103
Evaluate side-chains
  40 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.4980
   chunk 20 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 4 optimal weight:    7.9990
   chunk 79 optimal weight:    6.9990
   chunk 31 optimal weight:    9.9990
   chunk 24 optimal weight:   20.0000
   chunk 94 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 65 optimal weight:   20.0000
   overall best weight:    3.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 GLN
B 237 GLN
** C  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.056504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.048369 restraints weight = 59941.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.049508 restraints weight = 34652.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.050275 restraints weight = 23228.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.050829 restraints weight = 17245.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.051216 restraints weight = 13757.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.2941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8425  Z= 0.127
  Angle     :  0.604   6.480  11469  Z= 0.319
  Chirality :  0.048   0.264   1333
  Planarity :  0.004   0.040   1500
  Dihedral  :  4.754  19.931   1166
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 11.14 %
    Favored  : 88.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.49 (0.26), residues: 1050
  helix:  0.58 (0.45), residues: 152
  sheet: -0.09 (0.38), residues: 199
  loop : -1.74 (0.23), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 116 
 TYR   0.016   0.001   TYR C  19 
 PHE   0.020   0.001   PHE C 257 
 HIS   0.006   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8423)
  covalent geometry    : angle       0.60128 (11465)
  SS BOND              : bond        0.00155 (    2)
  SS BOND              : angle       3.01795 (    4)
  hydrogen bonds       : bond        0.03306 (  216)
  hydrogen bonds       : angle       5.71880 (  570)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 LYS cc_start: 0.9598 (ptpt) cc_final: 0.9365 (ptpp)
REVERT: B  271 LEU cc_start: 0.9408 (tp) cc_final: 0.9195 (tt)
REVERT: B  283 MET cc_start: 0.5683 (tmm) cc_final: 0.5398 (tmm)
REVERT: C   61 MET cc_start: 0.8942 (ptm) cc_final: 0.8193 (ppp)
REVERT: D  105 ASP cc_start: 0.9158 (t0) cc_final: 0.8927 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.0796
  time to fit residues: 6.1921
Evaluate side-chains
  39 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 102 optimal weight:   20.0000
   chunk 19 optimal weight:   30.0000
   chunk 13 optimal weight:    0.8980
   chunk 62 optimal weight:   10.0000
   chunk 78 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   chunk 60 optimal weight:    0.7980
   chunk 7 optimal weight:    8.9990
   chunk 59 optimal weight:   10.0000
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 GLN
** C  45 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 = 0.3350 r_free = 0.3350 target = 0.056868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.048558 restraints weight = 59861.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.049755 restraints weight = 33753.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.050558 restraints weight = 22213.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.051140 restraints weight = 16288.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.051518 restraints weight = 12858.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8425  Z= 0.116
  Angle     :  0.600   6.580  11469  Z= 0.318
  Chirality :  0.048   0.262   1333
  Planarity :  0.004   0.041   1500
  Dihedral  :  4.696  19.701   1166
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 10.76 %
    Favored  : 88.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  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: -1.47 (0.26), residues: 1050
  helix:  0.54 (0.45), residues: 152
  sheet: -0.07 (0.39), residues: 191
  loop : -1.69 (0.23), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 116 
 TYR   0.016   0.001   TYR D  19 
 PHE   0.010   0.001   PHE D  70 
 HIS   0.006   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8423)
  covalent geometry    : angle       0.59729 (11465)
  SS BOND              : bond        0.00238 (    2)
  SS BOND              : angle       3.26533 (    4)
  hydrogen bonds       : bond        0.03234 (  216)
  hydrogen bonds       : angle       5.62465 (  570)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 LYS cc_start: 0.9636 (ptpt) cc_final: 0.9390 (ptpp)
REVERT: B   42 PHE cc_start: 0.8960 (m-80) cc_final: 0.8643 (m-80)
REVERT: B  271 LEU cc_start: 0.9446 (tp) cc_final: 0.9235 (tt)
REVERT: B  283 MET cc_start: 0.5629 (tmm) cc_final: 0.5351 (tmm)
REVERT: C   61 MET cc_start: 0.9087 (ptm) cc_final: 0.8335 (ppp)
REVERT: D  105 ASP cc_start: 0.9135 (t0) cc_final: 0.8906 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0780
  time to fit residues: 6.2149
Evaluate side-chains
  39 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   chunk 87 optimal weight:    9.9990
   chunk 51 optimal weight:   20.0000
   chunk 40 optimal weight:    8.9990
   chunk 77 optimal weight:    7.9990
   chunk 66 optimal weight:   20.0000
   chunk 41 optimal weight:    9.9990
   chunk 24 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 70 optimal weight:   10.0000
   overall best weight:    5.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 GLN
** C  45 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 = 0.3313 r_free = 0.3313 target = 0.055569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.047413 restraints weight = 60977.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.048553 restraints weight = 34845.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.049309 restraints weight = 23181.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.049867 restraints weight = 17173.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.050217 restraints weight = 13662.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.3201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8425  Z= 0.171
  Angle     :  0.649   7.367  11469  Z= 0.345
  Chirality :  0.049   0.251   1333
  Planarity :  0.004   0.040   1500
  Dihedral  :  4.944  21.571   1166
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 11.90 %
    Favored  : 87.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  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: -1.58 (0.26), residues: 1050
  helix:  0.40 (0.44), residues: 152
  sheet: -0.12 (0.40), residues: 184
  loop : -1.75 (0.22), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 116 
 TYR   0.022   0.002   TYR A   8 
 PHE   0.015   0.002   PHE B 257 
 HIS   0.006   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 8423)
  covalent geometry    : angle       0.64522 (11465)
  SS BOND              : bond        0.00331 (    2)
  SS BOND              : angle       3.67680 (    4)
  hydrogen bonds       : bond        0.03530 (  216)
  hydrogen bonds       : angle       5.72354 (  570)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1290.28 seconds
wall clock time: 22 minutes 59.53 seconds (1379.53 seconds total)