Starting phenix.real_space_refine
on Mon Jul 28 05:52:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yjs_39348/07_2025/8yjs_39348.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yjs_39348/07_2025/8yjs_39348.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yjs_39348/07_2025/8yjs_39348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yjs_39348/07_2025/8yjs_39348.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yjs_39348/07_2025/8yjs_39348.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yjs_39348/07_2025/8yjs_39348.cif"
  }
  resolution = 3.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 331 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      61      5.49       5
     S      61      5.16       5
     C    6031      2.51       5
     N    1657      2.21       5
     O    2070      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9880
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "C"
      Number of atoms: 1951
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1951
          Classifications: {'peptide': 254}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 246}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 2769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2769
          Classifications: {'peptide': 351}
          Link IDs: {'PTRANS': 15, 'TRANS': 335}
    Chain: "B"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1947
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 7, 'TRANS': 245}
    Chain: "A"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1947
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 7, 'TRANS': 245}
    Chain: "J"
      Number of atoms: 387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 387
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
    Chain: "E"
      Number of atoms: 590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 590
          Classifications: {'DNA': 29}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 28}
    Chain: "F"
      Number of atoms: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 229
          Classifications: {'DNA': 11}
          Link IDs: {'rna3p': 10}
    Chain: "H"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 60
          Classifications: {'DNA': 3}
          Link IDs: {'rna3p': 2}
  Time building chain proxies: 6.85, per 1000 atoms: 0.69
  Number of scatterers: 9880
  At special positions: 0
  Unit cell: (107.07, 98.77, 106.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      61     16.00
     P      61     15.00
     O    2070      8.00
     N    1657      7.00
     C    6031      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 135 " - pdb=" SG  CYS C 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 135 " - pdb=" SG  CYS B 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 135 " - pdb=" SG  CYS A 162 " 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: 2.92
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2098

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 8 sheets defined
      30.7% alpha, 24.2% beta
      15 base pairs and 52 stacking pairs defined.
    Time for finding SS restraints: 4.06
  Creating SS restraints...
    Processing helix  chain 'C' and resid 9 through 20
      removed outlier: 3.554A  pdb=" N   LYS C  20 " --> pdb=" O   LEU C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 80
    Processing helix  chain 'C' and resid 140 through 155
      removed outlier: 4.066A  pdb=" N   HIS C 153 " --> pdb=" O   ARG C 149 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ILE C 154 " --> pdb=" O   ASP C 150 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLY C 155 " --> pdb=" O   LEU C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 216
    Processing helix  chain 'D' and resid 6 through 14
    Processing helix  chain 'D' and resid 22 through 26
      removed outlier: 3.504A  pdb=" N   SER D  25 " --> pdb=" O   ASP D  22 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   TYR D  26 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 22 through 26'
    Processing helix  chain 'D' and resid 35 through 45
    Processing helix  chain 'D' and resid 61 through 77
    Processing helix  chain 'D' and resid 90 through 92
      No H-bonds generated for 'chain 'D' and resid 90 through 92'
    Processing helix  chain 'D' and resid 93 through 118
      removed outlier: 4.032A  pdb=" N   ALA D 116 " --> pdb=" O   GLN D 112 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA D 117 " --> pdb=" O   GLN D 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 129
    Processing helix  chain 'D' and resid 134 through 149
      removed outlier: 3.524A  pdb=" N   ASN D 138 " --> pdb=" O   THR D 134 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 158 through 169
    Processing helix  chain 'D' and resid 181 through 186
    Processing helix  chain 'D' and resid 209 through 217
    Processing helix  chain 'D' and resid 219 through 231
    Processing helix  chain 'D' and resid 242 through 253
      removed outlier: 3.552A  pdb=" N   ALA D 246 " --> pdb=" O   GLY D 242 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 262
      removed outlier: 4.113A  pdb=" N   ARG D 262 " --> pdb=" O   GLU D 258 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 285
      removed outlier: 3.533A  pdb=" N   ALA D 279 " --> pdb=" O   LEU D 275 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 302 through 313
      removed outlier: 3.669A  pdb=" N   LEU D 306 " --> pdb=" O   ASN D 302 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 317 through 334
      removed outlier: 4.006A  pdb=" N   GLY D 334 " --> pdb=" O   LYS D 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 20
    Processing helix  chain 'B' and resid 72 through 82
    Processing helix  chain 'B' and resid 140 through 152
    Processing helix  chain 'B' and resid 208 through 216
    Processing helix  chain 'B' and resid 217 through 222
      Proline residue:  B 220  - end of helix
      No H-bonds generated for 'chain 'B' and resid 217 through 222'
    Processing helix  chain 'A' and resid 8 through 20
      removed outlier: 4.146A  pdb=" N   LEU A  12 " --> pdb=" O   GLN A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 80
    Processing helix  chain 'A' and resid 141 through 152
    Processing helix  chain 'A' and resid 208 through 216
    Processing helix  chain 'A' and resid 217 through 219
      No H-bonds generated for 'chain 'A' and resid 217 through 219'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 59 through 60
      removed outlier: 3.721A  pdb=" N   PHE C   2 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU B 205 " --> pdb=" O   ILE B 160 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 66 through 71
      removed outlier: 7.163A  pdb=" N   GLU C  25 " --> pdb=" O   MET C  40 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   MET C  40 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   CYS C  27 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   GLN C  38 " --> pdb=" O   CYS C  27 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLY C 245 " --> pdb=" O   ILE C 241 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   TYR C 239 " --> pdb=" O   LEU C 247 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLU C 238 " --> pdb=" O   THR C 226 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 123 through 127
      removed outlier: 6.621A  pdb=" N   VAL C 123 " --> pdb=" O   SER D 349 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   SER D 349 " --> pdb=" O   VAL C 123 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   GLN C 125 " --> pdb=" O   THR D 347 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LYS D 345 " --> pdb=" O   GLY C 127 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 204 through 208
      removed outlier: 5.199A  pdb=" N   ALA C 157 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   SER C 172 " --> pdb=" O   ALA C 157 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 19 through 21
      removed outlier: 3.680A  pdb=" N   GLU D 206 " --> pdb=" O   ARG D  19 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   ALA D 175 " --> pdb=" O   MET D 191 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ASP D  34 " --> pdb=" O   ALA D 176 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 61
    Processing sheet with id=AA7, first strand: chain 'B' and resid 67 through 71
      removed outlier: 3.633A  pdb=" N   MET B  68 " --> pdb=" O   TRP B  28 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 66 through 71
      removed outlier: 5.337A  pdb=" N   SER A 230 " --> pdb=" O   PRO A 234 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   MET A 229 " --> pdb=" O   CYS A 135 " (cutoff:3.500A)

    430 hydrogen bonds defined for protein.
    1209 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      30 hydrogen bonds
      60 hydrogen bond angles
      0 basepair planarities
      15 basepair parallelities
      52 stacking parallelities
  Total time for adding SS restraints: 3.47

  Time building geometry restraints manager: 3.08 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2513
        1.33 -     1.45: 1975
        1.45 -     1.57: 5443
        1.57 -     1.69: 125
        1.69 -     1.81: 98
  Bond restraints: 10154
  Sorted by residual:
  bond pdb=" C   THR C 219 "
       pdb=" N   PRO C 220 "
    ideal  model  delta    sigma   weight residual
    1.337  1.388 -0.052 9.80e-03 1.04e+04 2.79e+01
  bond pdb=" CB  ASN B  24 "
       pdb=" CG  ASN B  24 "
    ideal  model  delta    sigma   weight residual
    1.516  1.570 -0.054 2.50e-02 1.60e+03 4.75e+00
  bond pdb=" CB  GLN D 112 "
       pdb=" CG  GLN D 112 "
    ideal  model  delta    sigma   weight residual
    1.520  1.585 -0.065 3.00e-02 1.11e+03 4.72e+00
  bond pdb=" CA  ALA D 176 "
       pdb=" CB  ALA D 176 "
    ideal  model  delta    sigma   weight residual
    1.531  1.460  0.071 3.28e-02 9.30e+02 4.71e+00
  bond pdb=" CA  VAL D  52 "
       pdb=" CB  VAL D  52 "
    ideal  model  delta    sigma   weight residual
    1.540  1.570 -0.029 1.36e-02 5.41e+03 4.70e+00
  ... (remaining 10149 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.09: 13670
        3.09 -     6.18: 245
        6.18 -     9.26: 40
        9.26 -    12.35: 7
       12.35 -    15.44: 1
  Bond angle restraints: 13963
  Sorted by residual:
  angle pdb=" C   ASP D  51 "
        pdb=" N   VAL D  52 "
        pdb=" CA  VAL D  52 "
      ideal   model   delta    sigma   weight residual
     121.97  131.68   -9.71 1.80e+00 3.09e-01 2.91e+01
  angle pdb=" CA  ARG B  64 "
        pdb=" CB  ARG B  64 "
        pdb=" CG  ARG B  64 "
      ideal   model   delta    sigma   weight residual
     114.10  124.27  -10.17 2.00e+00 2.50e-01 2.59e+01
  angle pdb=" N   VAL B  45 "
        pdb=" CA  VAL B  45 "
        pdb=" C   VAL B  45 "
      ideal   model   delta    sigma   weight residual
     113.71  109.21    4.50 9.50e-01 1.11e+00 2.24e+01
  angle pdb=" CA  VAL D  52 "
        pdb=" CB  VAL D  52 "
        pdb=" CG1 VAL D  52 "
      ideal   model   delta    sigma   weight residual
     110.40  118.35   -7.95 1.70e+00 3.46e-01 2.19e+01
  angle pdb=" CB  GLN D 112 "
        pdb=" CG  GLN D 112 "
        pdb=" CD  GLN D 112 "
      ideal   model   delta    sigma   weight residual
     112.60  120.51   -7.91 1.70e+00 3.46e-01 2.16e+01
  ... (remaining 13958 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 5043
       17.89 -    35.79: 731
       35.79 -    53.68: 287
       53.68 -    71.57: 62
       71.57 -    89.46: 14
  Dihedral angle restraints: 6137
    sinusoidal: 2903
      harmonic: 3234
  Sorted by residual:
  dihedral pdb=" CA  GLU B 198 "
           pdb=" C   GLU B 198 "
           pdb=" N   MET B 199 "
           pdb=" CA  MET B 199 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.81  -27.19     0      5.00e+00 4.00e-02 2.96e+01
  dihedral pdb=" CA  PHE D 126 "
           pdb=" C   PHE D 126 "
           pdb=" N   THR D 127 "
           pdb=" CA  THR D 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.09   24.91     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" CA  ASN C  95 "
           pdb=" C   ASN C  95 "
           pdb=" N   ALA C  96 "
           pdb=" CA  ALA C  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.64  -22.36     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 6134 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 1504
       0.111 -    0.223: 93
       0.223 -    0.334: 9
       0.334 -    0.445: 0
       0.445 -    0.556: 1
  Chirality restraints: 1607
  Sorted by residual:
  chirality pdb=" CB  VAL D  52 "
            pdb=" CA  VAL D  52 "
            pdb=" CG1 VAL D  52 "
            pdb=" CG2 VAL D  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.07   -0.56 2.00e-01 2.50e+01 7.74e+00
  chirality pdb=" CB  ILE C  23 "
            pdb=" CA  ILE C  23 "
            pdb=" CG1 ILE C  23 "
            pdb=" CG2 ILE C  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CB  VAL A 123 "
            pdb=" CA  VAL A 123 "
            pdb=" CG1 VAL A 123 "
            pdb=" CG2 VAL A 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.70e+00
  ... (remaining 1604 not shown)

  Planarity restraints: 1587
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 201 "   -0.080 5.00e-02 4.00e+02   1.19e-01 2.28e+01
        pdb=" N   PRO B 202 "    0.207 5.00e-02 4.00e+02
        pdb=" CA  PRO B 202 "   -0.065 5.00e-02 4.00e+02
        pdb=" CD  PRO B 202 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 274 "    0.028 2.00e-02 2.50e+03   2.74e-02 1.88e+01
        pdb=" CG  TRP D 274 "   -0.073 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 274 "    0.036 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 274 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 274 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 274 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 274 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 274 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 274 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 274 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 136 "    0.018 2.00e-02 2.50e+03   3.59e-02 1.29e+01
        pdb=" C   VAL B 136 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   VAL B 136 "    0.024 2.00e-02 2.50e+03
        pdb=" N   VAL B 137 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1584 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 3071
        2.86 -     3.37: 8455
        3.37 -     3.88: 17488
        3.88 -     4.39: 19562
        4.39 -     4.90: 32794
  Nonbonded interactions: 81370
  Sorted by model distance:
  nonbonded pdb=" O   MET D  67 "
            pdb=" OG1 THR D  71 "
     model   vdw
     2.347 3.040
  nonbonded pdb=" O   THR B 216 "
            pdb=" OG1 THR B 219 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" O   THR A 216 "
            pdb=" OG1 THR A 219 "
     model   vdw
     2.373 3.040
  nonbonded pdb=" OE2 GLU D  76 "
            pdb=" NE  ARG D 327 "
     model   vdw
     2.383 3.120
  nonbonded pdb=" OG  SER B 222 "
            pdb=" O   THR B 224 "
     model   vdw
     2.392 3.040
  ... (remaining 81365 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 2 through 108 or (resid 109 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 110 through 254))
  selection = (chain 'B' and (resid 2 through 108 or (resid 109 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 110 through 254))
  selection = (chain 'C' and resid 2 through 254)
}

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:                  0.010
  Normalize map: mean=0, sd=1:             2.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     29.690
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
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      :  0.006   0.071  10157  Z= 0.269
  Angle     :  1.026  15.440  13969  Z= 0.536
  Chirality :  0.059   0.556   1607
  Planarity :  0.008   0.119   1587
  Dihedral  : 19.677  89.464   4030
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.62 (0.20), residues: 1103
  helix: -2.73 (0.20), residues: 311
  sheet: -2.07 (0.26), residues: 312
  loop : -2.21 (0.23), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.073   0.005   TRP D 274 
 HIS   0.005   0.001   HIS D 253 
 PHE   0.059   0.003   PHE B 214 
 TYR   0.028   0.003   TYR B 249 
 ARG   0.018   0.001   ARG D 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20336 (  460)
  hydrogen bonds       : angle      10.02207 ( 1269)
  SS BOND              : bond        0.00221 (    3)
  SS BOND              : angle       0.55622 (    6)
  covalent geometry    : bond        0.00617 (10154)
  covalent geometry    : angle       1.02662 (13963)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.978 
Fit side-chains
REVERT: D   10 ILE cc_start: 0.8766 (mm) cc_final: 0.8529 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.2045
  time to fit residues: 41.9043
Evaluate side-chains
  108 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 89 optimal weight:    0.3980
   chunk 34 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0670
   chunk 66 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  38 GLN
B  84 ASN
B 108 GLN
A 131 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.136676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.105230 restraints weight = 15170.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.108459 restraints weight = 10679.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.109788 restraints weight = 6673.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10157  Z= 0.151
  Angle     :  0.599   7.216  13969  Z= 0.329
  Chirality :  0.043   0.235   1607
  Planarity :  0.005   0.069   1587
  Dihedral  : 20.837  86.750   1901
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  7.78 %
    Favored  : 91.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.22), residues: 1103
  helix: -1.06 (0.25), residues: 329
  sheet: -1.85 (0.28), residues: 283
  loop : -1.85 (0.24), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP D 274 
 HIS   0.003   0.001   HIS D 253 
 PHE   0.025   0.001   PHE B 214 
 TYR   0.008   0.001   TYR D 152 
 ARG   0.003   0.000   ARG B  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04722 (  460)
  hydrogen bonds       : angle       6.80182 ( 1269)
  SS BOND              : bond        0.00165 (    3)
  SS BOND              : angle       0.41390 (    6)
  covalent geometry    : bond        0.00334 (10154)
  covalent geometry    : angle       0.59897 (13963)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 0.981 
Fit side-chains
REVERT: D   10 ILE cc_start: 0.8820 (mm) cc_final: 0.8572 (mm)
REVERT: B  125 GLN cc_start: 0.5982 (pm20) cc_final: 0.5774 (pm20)
REVERT: B  199 MET cc_start: 0.5518 (tpt) cc_final: 0.5252 (mmm)
REVERT: A   91 ARG cc_start: 0.6683 (tpt90) cc_final: 0.5297 (mtm180)
REVERT: A  229 MET cc_start: 0.8081 (pmm) cc_final: 0.7727 (ptp)
  outliers start: 11
  outliers final: 8
  residues processed: 141
  average time/residue: 0.2035
  time to fit residues: 42.2281
Evaluate side-chains
  118 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  253 HIS
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain A residue   24 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0060
   chunk 84 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 93 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
C  49 GLN
B  38 GLN
B  49 GLN
B 108 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.134596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.102177 restraints weight = 15278.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.104843 restraints weight = 11228.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.106455 restraints weight = 7261.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10157  Z= 0.146
  Angle     :  0.553   6.286  13969  Z= 0.301
  Chirality :  0.042   0.250   1607
  Planarity :  0.004   0.056   1587
  Dihedral  : 20.402  88.815   1901
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 10.89 %
    Favored  : 87.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.23), residues: 1103
  helix: -0.09 (0.27), residues: 333
  sheet: -1.95 (0.27), residues: 296
  loop : -1.62 (0.25), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D 274 
 HIS   0.003   0.001   HIS D 193 
 PHE   0.015   0.001   PHE B 214 
 TYR   0.014   0.001   TYR B 211 
 ARG   0.003   0.000   ARG B 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04042 (  460)
  hydrogen bonds       : angle       6.04703 ( 1269)
  SS BOND              : bond        0.00091 (    3)
  SS BOND              : angle       0.45047 (    6)
  covalent geometry    : bond        0.00331 (10154)
  covalent geometry    : angle       0.55329 (13963)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 1.236 
Fit side-chains
REVERT: C   32 SER cc_start: 0.8854 (t) cc_final: 0.8638 (m)
REVERT: C  199 MET cc_start: 0.7130 (tpp) cc_final: 0.5797 (mtm)
REVERT: D   10 ILE cc_start: 0.8863 (mm) cc_final: 0.8601 (mm)
REVERT: D  126 PHE cc_start: 0.7495 (m-80) cc_final: 0.7241 (m-10)
REVERT: D  259 ILE cc_start: 0.8021 (mm) cc_final: 0.7538 (mt)
REVERT: B  199 MET cc_start: 0.5741 (tpt) cc_final: 0.3636 (mtm)
REVERT: A   91 ARG cc_start: 0.6829 (tpt90) cc_final: 0.5357 (mtm-85)
  outliers start: 15
  outliers final: 11
  residues processed: 135
  average time/residue: 0.1829
  time to fit residues: 37.1083
Evaluate side-chains
  121 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  253 HIS
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0030
   chunk 99 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 1 optimal weight:    0.2980
   chunk 97 optimal weight:    4.9990
   overall best weight:    0.5590

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

Flipped N/Q/H residues before XYZ refinement:
B  49 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.135171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.101944 restraints weight = 14971.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.105202 restraints weight = 11032.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.106802 restraints weight = 6859.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10157  Z= 0.144
  Angle     :  0.539   5.895  13969  Z= 0.295
  Chirality :  0.042   0.281   1607
  Planarity :  0.003   0.051   1587
  Dihedral  : 20.349  88.744   1901
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 12.66 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.24), residues: 1103
  helix:  0.37 (0.28), residues: 334
  sheet: -1.85 (0.27), residues: 304
  loop : -1.40 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 193 
 PHE   0.013   0.001   PHE B 215 
 TYR   0.016   0.001   TYR B 211 
 ARG   0.002   0.000   ARG B  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03707 (  460)
  hydrogen bonds       : angle       5.78211 ( 1269)
  SS BOND              : bond        0.00061 (    3)
  SS BOND              : angle       0.41777 (    6)
  covalent geometry    : bond        0.00328 (10154)
  covalent geometry    : angle       0.53940 (13963)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 1.057 
Fit side-chains
REVERT: C   32 SER cc_start: 0.8834 (t) cc_final: 0.8618 (m)
REVERT: C   88 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8832 (mt)
REVERT: D   10 ILE cc_start: 0.8857 (mm) cc_final: 0.8601 (mm)
REVERT: D  126 PHE cc_start: 0.7566 (m-80) cc_final: 0.7308 (m-10)
REVERT: D  259 ILE cc_start: 0.8222 (mm) cc_final: 0.7627 (mt)
REVERT: D  274 TRP cc_start: 0.7950 (t60) cc_final: 0.7626 (t60)
REVERT: B   64 ARG cc_start: 0.8214 (tpt-90) cc_final: 0.7997 (tmt170)
REVERT: B   86 ASP cc_start: 0.7800 (m-30) cc_final: 0.7585 (m-30)
REVERT: B  199 MET cc_start: 0.5720 (tpt) cc_final: 0.3588 (mtm)
REVERT: A   91 ARG cc_start: 0.6756 (tpt90) cc_final: 0.5323 (mtm-85)
  outliers start: 23
  outliers final: 12
  residues processed: 137
  average time/residue: 0.2065
  time to fit residues: 41.2163
Evaluate side-chains
  122 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  253 HIS
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    0.3980
   chunk 113 optimal weight:    3.9990
   chunk 102 optimal weight:    0.0670
   chunk 16 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 108 optimal weight:    0.8980
   chunk 30 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
D  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.134383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.101029 restraints weight = 15017.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.104257 restraints weight = 11147.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.105622 restraints weight = 6929.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10157  Z= 0.145
  Angle     :  0.539   6.493  13969  Z= 0.291
  Chirality :  0.042   0.279   1607
  Planarity :  0.003   0.049   1587
  Dihedral  : 20.290  89.420   1901
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.11 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.24), residues: 1103
  helix:  0.76 (0.29), residues: 327
  sheet: -1.93 (0.26), residues: 305
  loop : -1.19 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 193 
 PHE   0.013   0.001   PHE B 215 
 TYR   0.018   0.001   TYR B 211 
 ARG   0.003   0.000   ARG A   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03573 (  460)
  hydrogen bonds       : angle       5.63289 ( 1269)
  SS BOND              : bond        0.00106 (    3)
  SS BOND              : angle       0.34969 (    6)
  covalent geometry    : bond        0.00330 (10154)
  covalent geometry    : angle       0.53956 (13963)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 1.102 
Fit side-chains
REVERT: C   32 SER cc_start: 0.8826 (t) cc_final: 0.8588 (m)
REVERT: C   88 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8824 (mt)
REVERT: D   10 ILE cc_start: 0.8885 (mm) cc_final: 0.8628 (mm)
REVERT: D   74 MET cc_start: 0.8900 (ttp) cc_final: 0.8612 (mtp)
REVERT: D  126 PHE cc_start: 0.7563 (m-80) cc_final: 0.7297 (m-10)
REVERT: D  259 ILE cc_start: 0.8246 (mm) cc_final: 0.7628 (mt)
REVERT: D  274 TRP cc_start: 0.8011 (t60) cc_final: 0.7719 (t60)
REVERT: B  199 MET cc_start: 0.5734 (tpt) cc_final: 0.3636 (mtm)
REVERT: A   91 ARG cc_start: 0.6783 (tpt90) cc_final: 0.5319 (mtm180)
  outliers start: 21
  outliers final: 15
  residues processed: 132
  average time/residue: 0.1884
  time to fit residues: 36.9226
Evaluate side-chains
  125 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue  132 GLU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 59 optimal weight:    0.1980
   chunk 95 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 87 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3780 r_free = 0.3780 target = 0.131766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.098655 restraints weight = 14976.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.102025 restraints weight = 10972.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.103052 restraints weight = 6720.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10157  Z= 0.180
  Angle     :  0.576   9.850  13969  Z= 0.306
  Chirality :  0.043   0.313   1607
  Planarity :  0.003   0.049   1587
  Dihedral  : 20.329  89.870   1901
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 15.04 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.24), residues: 1103
  helix:  0.75 (0.29), residues: 328
  sheet: -1.92 (0.25), residues: 329
  loop : -1.15 (0.27), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 193 
 PHE   0.015   0.002   PHE B 215 
 TYR   0.024   0.002   TYR B 211 
 ARG   0.002   0.000   ARG D 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03712 (  460)
  hydrogen bonds       : angle       5.72489 ( 1269)
  SS BOND              : bond        0.00098 (    3)
  SS BOND              : angle       0.46876 (    6)
  covalent geometry    : bond        0.00416 (10154)
  covalent geometry    : angle       0.57555 (13963)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.883 
Fit side-chains
REVERT: D  126 PHE cc_start: 0.7612 (m-80) cc_final: 0.7360 (m-10)
REVERT: D  259 ILE cc_start: 0.8175 (mm) cc_final: 0.7741 (mt)
REVERT: D  274 TRP cc_start: 0.8107 (t60) cc_final: 0.7860 (t60)
REVERT: B  215 PHE cc_start: 0.8459 (m-80) cc_final: 0.8189 (m-80)
REVERT: A   91 ARG cc_start: 0.6796 (tpt90) cc_final: 0.5325 (mtm180)
  outliers start: 23
  outliers final: 17
  residues processed: 127
  average time/residue: 0.1998
  time to fit residues: 37.4864
Evaluate side-chains
  121 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue  132 GLU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 104 optimal weight:    0.6980
   chunk 94 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 93 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3766 r_free = 0.3766 target = 0.130507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.098090 restraints weight = 15500.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.101511 restraints weight = 10536.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.102417 restraints weight = 6394.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10157  Z= 0.164
  Angle     :  0.568   8.769  13969  Z= 0.301
  Chirality :  0.043   0.324   1607
  Planarity :  0.003   0.046   1587
  Dihedral  : 20.317  88.754   1901
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 15.46 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.24), residues: 1103
  helix:  0.83 (0.29), residues: 328
  sheet: -1.87 (0.26), residues: 329
  loop : -1.12 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 193 
 PHE   0.017   0.001   PHE B 215 
 TYR   0.022   0.002   TYR B 211 
 ARG   0.003   0.000   ARG A   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03591 (  460)
  hydrogen bonds       : angle       5.68669 ( 1269)
  SS BOND              : bond        0.00085 (    3)
  SS BOND              : angle       0.47320 (    6)
  covalent geometry    : bond        0.00379 (10154)
  covalent geometry    : angle       0.56843 (13963)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.999 
Fit side-chains
REVERT: D  126 PHE cc_start: 0.7654 (m-80) cc_final: 0.7348 (m-10)
REVERT: D  259 ILE cc_start: 0.8158 (mm) cc_final: 0.7758 (mt)
REVERT: B   75 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8182 (tmm)
REVERT: B  215 PHE cc_start: 0.8537 (m-80) cc_final: 0.8296 (m-80)
REVERT: A   91 ARG cc_start: 0.6758 (tpt90) cc_final: 0.5275 (mtm180)
REVERT: A  156 ASP cc_start: 0.6697 (OUTLIER) cc_final: 0.6318 (t0)
REVERT: A  199 MET cc_start: 0.5661 (tpt) cc_final: 0.5337 (tpt)
  outliers start: 24
  outliers final: 18
  residues processed: 124
  average time/residue: 0.2115
  time to fit residues: 37.7696
Evaluate side-chains
  119 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   32 SER
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  253 HIS
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 33 optimal weight:    0.2980
   chunk 68 optimal weight:    4.9990
   chunk 13 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 18 optimal weight:    0.3980
   chunk 51 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 100 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.131098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.099222 restraints weight = 15386.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.102681 restraints weight = 10730.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.103388 restraints weight = 6493.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.3256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  10157  Z= 0.148
  Angle     :  0.559   7.569  13969  Z= 0.299
  Chirality :  0.043   0.335   1607
  Planarity :  0.003   0.045   1587
  Dihedral  : 20.284  87.891   1901
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.39 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.24), residues: 1103
  helix:  0.90 (0.29), residues: 328
  sheet: -1.83 (0.25), residues: 340
  loop : -1.08 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 274 
 HIS   0.002   0.000   HIS D 193 
 PHE   0.017   0.001   PHE B 215 
 TYR   0.019   0.002   TYR B 211 
 ARG   0.002   0.000   ARG A   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03528 (  460)
  hydrogen bonds       : angle       5.62645 ( 1269)
  SS BOND              : bond        0.00067 (    3)
  SS BOND              : angle       0.42738 (    6)
  covalent geometry    : bond        0.00343 (10154)
  covalent geometry    : angle       0.55898 (13963)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 1.066 
Fit side-chains
REVERT: C  244 MET cc_start: 0.8305 (mpp) cc_final: 0.7257 (mpp)
REVERT: D   10 ILE cc_start: 0.9042 (mm) cc_final: 0.8831 (mm)
REVERT: D  126 PHE cc_start: 0.7641 (m-80) cc_final: 0.7322 (m-10)
REVERT: D  259 ILE cc_start: 0.8147 (mm) cc_final: 0.7733 (mt)
REVERT: B   75 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8172 (tmm)
REVERT: A   75 MET cc_start: 0.9007 (ttt) cc_final: 0.8653 (ttt)
REVERT: A   91 ARG cc_start: 0.6755 (tpt90) cc_final: 0.5267 (mtm180)
REVERT: A  117 LYS cc_start: 0.8094 (mttp) cc_final: 0.7719 (mmmm)
REVERT: A  156 ASP cc_start: 0.6698 (OUTLIER) cc_final: 0.6323 (t0)
  outliers start: 21
  outliers final: 16
  residues processed: 117
  average time/residue: 0.2152
  time to fit residues: 36.7865
Evaluate side-chains
  119 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   32 SER
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 72 optimal weight:    8.9990
   chunk 56 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 79 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 36 optimal weight:    8.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3787 r_free = 0.3787 target = 0.132292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.099247 restraints weight = 15035.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.102393 restraints weight = 11011.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.103996 restraints weight = 6861.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10157  Z= 0.159
  Angle     :  0.569   7.944  13969  Z= 0.302
  Chirality :  0.043   0.337   1607
  Planarity :  0.003   0.044   1587
  Dihedral  : 20.283  88.180   1901
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.60 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.24), residues: 1103
  helix:  0.89 (0.29), residues: 328
  sheet: -1.73 (0.26), residues: 335
  loop : -1.15 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 274 
 HIS   0.003   0.001   HIS C  44 
 PHE   0.019   0.001   PHE B 215 
 TYR   0.022   0.002   TYR B 211 
 ARG   0.002   0.000   ARG D 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03498 (  460)
  hydrogen bonds       : angle       5.61690 ( 1269)
  SS BOND              : bond        0.00086 (    3)
  SS BOND              : angle       0.44947 (    6)
  covalent geometry    : bond        0.00368 (10154)
  covalent geometry    : angle       0.56934 (13963)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.989 
Fit side-chains
REVERT: C  156 ASP cc_start: 0.6844 (p0) cc_final: 0.6530 (p0)
REVERT: C  244 MET cc_start: 0.8542 (mpp) cc_final: 0.8307 (mpp)
REVERT: D  126 PHE cc_start: 0.7676 (m-80) cc_final: 0.7349 (m-10)
REVERT: D  259 ILE cc_start: 0.8159 (mm) cc_final: 0.7742 (mt)
REVERT: B   75 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8173 (tmm)
REVERT: B  215 PHE cc_start: 0.8577 (m-80) cc_final: 0.8238 (m-80)
REVERT: A   75 MET cc_start: 0.9009 (ttt) cc_final: 0.8650 (ttt)
REVERT: A   91 ARG cc_start: 0.6764 (tpt90) cc_final: 0.5290 (mtm180)
REVERT: A  117 LYS cc_start: 0.8053 (mttp) cc_final: 0.7655 (mmmm)
REVERT: A  156 ASP cc_start: 0.6688 (OUTLIER) cc_final: 0.6318 (t0)
  outliers start: 19
  outliers final: 16
  residues processed: 122
  average time/residue: 0.2230
  time to fit residues: 38.9181
Evaluate side-chains
  121 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 108 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 72 optimal weight:    9.9990
   chunk 41 optimal weight:    0.0970
   chunk 22 optimal weight:    0.0980
   chunk 107 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3789 r_free = 0.3789 target = 0.132415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.099365 restraints weight = 14996.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.102562 restraints weight = 10976.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.104078 restraints weight = 6843.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.3426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10157  Z= 0.155
  Angle     :  0.572   7.873  13969  Z= 0.304
  Chirality :  0.043   0.348   1607
  Planarity :  0.003   0.043   1587
  Dihedral  : 20.278  87.559   1901
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.12 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.24), residues: 1103
  helix:  0.85 (0.29), residues: 328
  sheet: -1.79 (0.25), residues: 342
  loop : -1.06 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 276 
 PHE   0.019   0.001   PHE B 215 
 TYR   0.021   0.002   TYR B 211 
 ARG   0.002   0.000   ARG A   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03458 (  460)
  hydrogen bonds       : angle       5.58831 ( 1269)
  SS BOND              : bond        0.00084 (    3)
  SS BOND              : angle       0.43398 (    6)
  covalent geometry    : bond        0.00359 (10154)
  covalent geometry    : angle       0.57184 (13963)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 1.001 
Fit side-chains
REVERT: C  156 ASP cc_start: 0.6829 (p0) cc_final: 0.6506 (p0)
REVERT: C  244 MET cc_start: 0.8598 (mpp) cc_final: 0.8334 (mpp)
REVERT: D  126 PHE cc_start: 0.7665 (m-80) cc_final: 0.7346 (m-10)
REVERT: D  259 ILE cc_start: 0.8149 (mm) cc_final: 0.7744 (mt)
REVERT: B   75 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8170 (tmm)
REVERT: B  146 ARG cc_start: 0.7581 (tpt170) cc_final: 0.7347 (tpt90)
REVERT: B  215 PHE cc_start: 0.8584 (m-80) cc_final: 0.8273 (m-80)
REVERT: A   91 ARG cc_start: 0.6765 (tpt90) cc_final: 0.5288 (mtm180)
REVERT: A  117 LYS cc_start: 0.8075 (mttp) cc_final: 0.7664 (mmmm)
REVERT: A  156 ASP cc_start: 0.6640 (OUTLIER) cc_final: 0.6277 (t0)
REVERT: A  199 MET cc_start: 0.5607 (tpt) cc_final: 0.5123 (tpt)
  outliers start: 17
  outliers final: 15
  residues processed: 116
  average time/residue: 0.2129
  time to fit residues: 35.3837
Evaluate side-chains
  117 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 109 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9990
   chunk 35 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3767 r_free = 0.3767 target = 0.130892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.097639 restraints weight = 15252.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.100966 restraints weight = 10930.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.102157 restraints weight = 6733.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.3519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10157  Z= 0.181
  Angle     :  0.593   7.796  13969  Z= 0.313
  Chirality :  0.044   0.342   1607
  Planarity :  0.003   0.042   1587
  Dihedral  : 20.325  88.263   1901
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.39 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.25), residues: 1103
  helix:  0.82 (0.28), residues: 328
  sheet: -1.85 (0.25), residues: 342
  loop : -1.07 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D 274 
 HIS   0.002   0.001   HIS D 193 
 PHE   0.022   0.002   PHE B 215 
 TYR   0.027   0.002   TYR B 211 
 ARG   0.002   0.000   ARG D 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03562 (  460)
  hydrogen bonds       : angle       5.67246 ( 1269)
  SS BOND              : bond        0.00087 (    3)
  SS BOND              : angle       0.49258 (    6)
  covalent geometry    : bond        0.00422 (10154)
  covalent geometry    : angle       0.59324 (13963)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3036.64 seconds
wall clock time: 53 minutes 39.65 seconds (3219.65 seconds total)