Starting phenix.real_space_refine
on Fri Jul 25 00:20:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j0f_61054/07_2025/9j0f_61054.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j0f_61054/07_2025/9j0f_61054.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j0f_61054/07_2025/9j0f_61054.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j0f_61054/07_2025/9j0f_61054.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j0f_61054/07_2025/9j0f_61054.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j0f_61054/07_2025/9j0f_61054.cif"
  }
  resolution = 2.76
  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=  -0.001 sd=   0.069
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      47      5.16       5
     C    4434      2.51       5
     N    1153      2.21       5
     O    1219      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6855
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1615
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 135
          Unresolved non-hydrogen angles: 165
          Unresolved non-hydrogen dihedrals: 105
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'ARG:plan': 2, 'ASP:plan': 9}
          Unresolved non-hydrogen planarities: 89
    Chain: "B"
      Number of atoms: 2475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2475
          Classifications: {'peptide': 337}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 116
          Unresolved non-hydrogen angles: 141
          Unresolved non-hydrogen dihedrals: 91
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 91
    Chain: "G"
      Number of atoms: 377
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 377
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "R"
      Number of atoms: 2344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2344
          Classifications: {'peptide': 295}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 10, 'TRANS': 284}
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 95
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 46
    Chain: "R"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'NAI': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.59, per 1000 atoms: 0.67
  Number of scatterers: 6855
  At special positions: 0
  Unit cell: (70.72, 98.176, 128.96, 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      47     16.00
     P       2     15.00
     O    1219      8.00
     N    1153      7.00
     C    4434      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  94 " - pdb=" SG  CYS R 172 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.71
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1720

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 8 sheets defined
      46.6% alpha, 18.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.747A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 52
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.555A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 3.676A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.784A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.548A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 5 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'R' and resid 24 through 48
      removed outlier: 4.324A  pdb=" N   LEU R  39 " --> pdb=" O   ALA R  35 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 54 through 83
      Proline residue:  R  75  - end of helix
    Processing helix  chain 'R' and resid 87 through 96
    Processing helix  chain 'R' and resid 96 through 125
    Processing helix  chain 'R' and resid 137 through 154
      removed outlier: 3.568A  pdb=" N   LEU R 141 " --> pdb=" O   TYR R 137 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 154 through 159
    Processing helix  chain 'R' and resid 177 through 215
    Processing helix  chain 'R' and resid 221 through 251
      Proline residue:  R 248  - end of helix
    Processing helix  chain 'R' and resid 252 through 261
    Processing helix  chain 'R' and resid 268 through 286
      removed outlier: 3.726A  pdb=" N   ARG R 274 " --> pdb=" O   LYS R 270 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 286 through 291
    Processing helix  chain 'R' and resid 299 through 310
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.742A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.595A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.697A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.417A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 152
      removed outlier: 3.724A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.899A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.481A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.637A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    407 hydrogen bonds defined for protein.
    1170 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: 2.01

  Time building geometry restraints manager: 1.98 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: 1606
        1.33 -     1.45: 1483
        1.45 -     1.57: 3850
        1.57 -     1.69: 4
        1.69 -     1.81: 66
  Bond restraints: 7009
  Sorted by residual:
  bond pdb=" C4A NAI R 401 "
       pdb=" C5A NAI R 401 "
    ideal  model  delta    sigma   weight residual
    1.386  1.472 -0.086 2.00e-02 2.50e+03 1.85e+01
  bond pdb=" CA  LYS R  77 "
       pdb=" C   LYS R  77 "
    ideal  model  delta    sigma   weight residual
    1.524  1.473  0.051 1.24e-02 6.50e+03 1.71e+01
  bond pdb=" CA  ASN R 188 "
       pdb=" CB  ASN R 188 "
    ideal  model  delta    sigma   weight residual
    1.530  1.470  0.060 1.57e-02 4.06e+03 1.44e+01
  bond pdb=" C5A NAI R 401 "
       pdb=" C6A NAI R 401 "
    ideal  model  delta    sigma   weight residual
    1.404  1.480 -0.076 2.00e-02 2.50e+03 1.44e+01
  bond pdb=" C6N NAI R 401 "
       pdb=" N1N NAI R 401 "
    ideal  model  delta    sigma   weight residual
    1.394  1.334  0.060 2.00e-02 2.50e+03 8.86e+00
  ... (remaining 7004 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 9379
        1.85 -     3.71: 133
        3.71 -     5.56: 20
        5.56 -     7.42: 5
        7.42 -     9.27: 3
  Bond angle restraints: 9540
  Sorted by residual:
  angle pdb=" C2A NAI R 401 "
        pdb=" N3A NAI R 401 "
        pdb=" C4A NAI R 401 "
      ideal   model   delta    sigma   weight residual
     111.83  121.10   -9.27 3.00e+00 1.11e-01 9.55e+00
  angle pdb=" N   LYS R  77 "
        pdb=" CA  LYS R  77 "
        pdb=" C   LYS R  77 "
      ideal   model   delta    sigma   weight residual
     110.97  107.68    3.29 1.09e+00 8.42e-01 9.10e+00
  angle pdb=" N   ARG R 274 "
        pdb=" CA  ARG R 274 "
        pdb=" C   ARG R 274 "
      ideal   model   delta    sigma   weight residual
     112.23  108.68    3.55 1.26e+00 6.30e-01 7.93e+00
  angle pdb=" C5A NAI R 401 "
        pdb=" C4A NAI R 401 "
        pdb=" N3A NAI R 401 "
      ideal   model   delta    sigma   weight residual
     126.33  118.21    8.12 3.00e+00 1.11e-01 7.33e+00
  angle pdb=" PA  NAI R 401 "
        pdb=" O3  NAI R 401 "
        pdb=" PN  NAI R 401 "
      ideal   model   delta    sigma   weight residual
     129.27  121.23    8.04 3.00e+00 1.11e-01 7.19e+00
  ... (remaining 9535 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 3755
       17.47 -    34.93: 323
       34.93 -    52.40: 39
       52.40 -    69.86: 12
       69.86 -    87.33: 7
  Dihedral angle restraints: 4136
    sinusoidal: 1487
      harmonic: 2649
  Sorted by residual:
  dihedral pdb=" CA  GLY R  85 "
           pdb=" C   GLY R  85 "
           pdb=" N   PRO R  86 "
           pdb=" CA  PRO R  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.55   32.45     0      5.00e+00 4.00e-02 4.21e+01
  dihedral pdb=" CA  GLU R 262 "
           pdb=" C   GLU R 262 "
           pdb=" N   ALA R 263 "
           pdb=" CA  ALA R 263 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.69   23.31     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  THR B 249 "
           pdb=" C   THR B 249 "
           pdb=" N   CYS B 250 "
           pdb=" CA  CYS B 250 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.06   18.94     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 4133 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 905
       0.051 -    0.102: 192
       0.102 -    0.153: 28
       0.153 -    0.205: 1
       0.205 -    0.256: 1
  Chirality restraints: 1127
  Sorted by residual:
  chirality pdb=" C1B NAI R 401 "
            pdb=" C2B NAI R 401 "
            pdb=" N9A NAI R 401 "
            pdb=" O4B NAI R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.31    2.57   -0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CB  ILE R  20 "
            pdb=" CA  ILE R  20 "
            pdb=" CG1 ILE R  20 "
            pdb=" CG2 ILE R  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.80e-01
  chirality pdb=" CA  ILE B 123 "
            pdb=" N   ILE B 123 "
            pdb=" C   ILE B 123 "
            pdb=" CB  ILE B 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.84e-01
  ... (remaining 1124 not shown)

  Planarity restraints: 1178
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG R 274 "    0.303 9.50e-02 1.11e+02   1.36e-01 1.13e+01
        pdb=" NE  ARG R 274 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG R 274 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG R 274 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG R 274 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 273 "    0.008 2.00e-02 2.50e+03   1.57e-02 2.45e+00
        pdb=" C   LEU R 273 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   LEU R 273 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ARG R 274 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.021 5.00e-02 4.00e+02   3.11e-02 1.54e+00
        pdb=" N   PRO B 236 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1175 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 78
        2.64 -     3.20: 6335
        3.20 -     3.77: 11366
        3.77 -     4.33: 15957
        4.33 -     4.90: 26036
  Nonbonded interactions: 59772
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.069 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OD1 ASP R 118 "
            pdb=" OG  SER R 134 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD2 ASP B 163 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" N   ASN R  17 "
            pdb=" OH  TYR R 275 "
     model   vdw
     2.261 3.120
  ... (remaining 59767 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.380
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.470
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
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   0.086   7010  Z= 0.219
  Angle     :  0.591   9.272   9542  Z= 0.304
  Chirality :  0.042   0.256   1127
  Planarity :  0.005   0.136   1178
  Dihedral  : 13.670  87.327   2413
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.29 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.28), residues: 893
  helix:  1.84 (0.26), residues: 394
  sheet:  0.26 (0.38), residues: 167
  loop : -0.63 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.006   0.001   HIS B 142 
 PHE   0.018   0.001   PHE R 195 
 TYR   0.015   0.001   TYR R 106 
 ARG   0.003   0.000   ARG B 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11998 (  407)
  hydrogen bonds       : angle       5.45645 ( 1170)
  SS BOND              : bond        0.00312 (    1)
  SS BOND              : angle       1.78915 (    2)
  covalent geometry    : bond        0.00430 ( 7009)
  covalent geometry    : angle       0.59007 ( 9540)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7419 (mtt90)
  outliers start: 1
  outliers final: 0
  residues processed: 143
  average time/residue: 0.9411
  time to fit residues: 143.8075
Evaluate side-chains
  102 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 66 optimal weight:   20.0000
   chunk 37 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 322 HIS
B 142 HIS
B 156 GLN
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  18 GLN
** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 217 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.214117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.168494 restraints weight = 7387.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 1.90
r_work: 0.3784 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3668 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7010  Z= 0.194
  Angle     :  0.582   6.887   9542  Z= 0.309
  Chirality :  0.043   0.155   1127
  Planarity :  0.004   0.039   1178
  Dihedral  :  7.444  82.705   1020
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 11.03 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.29), residues: 893
  helix:  1.69 (0.26), residues: 404
  sheet:  0.27 (0.38), residues: 178
  loop : -0.57 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.006   0.001   HIS R 184 
 PHE   0.021   0.002   PHE R 195 
 TYR   0.016   0.002   TYR R 256 
 ARG   0.004   0.001   ARG R 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04528 (  407)
  hydrogen bonds       : angle       4.81720 ( 1170)
  SS BOND              : bond        0.00079 (    1)
  SS BOND              : angle       0.88629 (    2)
  covalent geometry    : bond        0.00447 ( 7009)
  covalent geometry    : angle       0.58198 ( 9540)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.773 
Fit side-chains
REVERT: A  240 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5011 (ttm)
REVERT: A  337 ASP cc_start: 0.8116 (m-30) cc_final: 0.7884 (m-30)
REVERT: B   96 ARG cc_start: 0.8238 (mtt180) cc_final: 0.7935 (mtt90)
REVERT: B  263 THR cc_start: 0.8674 (t) cc_final: 0.8206 (m)
REVERT: R  229 LYS cc_start: 0.7143 (tppt) cc_final: 0.6832 (mptt)
  outliers start: 18
  outliers final: 8
  residues processed: 109
  average time/residue: 0.9178
  time to fit residues: 107.3116
Evaluate side-chains
  102 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 78 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
B 156 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 188 ASN ** 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 = 0.4588 r_free = 0.4588 target = 0.222857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.180486 restraints weight = 7410.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.4141 rms_B_bonded: 2.06
r_work: 0.3910 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3791 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7010  Z= 0.176
  Angle     :  0.559   7.611   9542  Z= 0.296
  Chirality :  0.042   0.146   1127
  Planarity :  0.003   0.034   1178
  Dihedral  :  7.030  65.831   1020
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 13.93 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.29), residues: 893
  helix:  1.69 (0.26), residues: 404
  sheet:  0.24 (0.37), residues: 178
  loop : -0.61 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R 184 
 PHE   0.020   0.002   PHE R 195 
 TYR   0.012   0.001   TYR A 320 
 ARG   0.003   0.000   ARG R 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04217 (  407)
  hydrogen bonds       : angle       4.67245 ( 1170)
  SS BOND              : bond        0.00058 (    1)
  SS BOND              : angle       0.87570 (    2)
  covalent geometry    : bond        0.00401 ( 7009)
  covalent geometry    : angle       0.55850 ( 9540)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.793 
Fit side-chains
REVERT: A  240 MET cc_start: 0.6293 (OUTLIER) cc_final: 0.5213 (ttm)
REVERT: A  337 ASP cc_start: 0.8227 (m-30) cc_final: 0.8024 (m-30)
REVERT: B   96 ARG cc_start: 0.8390 (mtt180) cc_final: 0.8152 (mtt90)
REVERT: B  263 THR cc_start: 0.8665 (t) cc_final: 0.8213 (m)
REVERT: R  121 TYR cc_start: 0.7611 (t80) cc_final: 0.7045 (t80)
REVERT: R  229 LYS cc_start: 0.7378 (tppt) cc_final: 0.7077 (mptt)
  outliers start: 21
  outliers final: 12
  residues processed: 115
  average time/residue: 0.9125
  time to fit residues: 112.5672
Evaluate side-chains
  109 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   24 ILE
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  272 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 43 optimal weight:    0.3980
   chunk 52 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 37 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
** B 340 ASN ** 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 = 0.4571 r_free = 0.4571 target = 0.220934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.177788 restraints weight = 7484.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.4119 rms_B_bonded: 1.96
r_work: 0.3895 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3781 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7010  Z= 0.204
  Angle     :  0.588   7.850   9542  Z= 0.308
  Chirality :  0.043   0.146   1127
  Planarity :  0.004   0.035   1178
  Dihedral  :  7.029  61.130   1020
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 15.97 %
    Favored  : 80.55 %
  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:  0.75 (0.28), residues: 893
  helix:  1.60 (0.26), residues: 404
  sheet:  0.18 (0.38), residues: 178
  loop : -0.73 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.005   0.001   HIS R 184 
 PHE   0.021   0.002   PHE R 195 
 TYR   0.012   0.002   TYR A 320 
 ARG   0.003   0.001   ARG R 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04254 (  407)
  hydrogen bonds       : angle       4.72968 ( 1170)
  SS BOND              : bond        0.00056 (    1)
  SS BOND              : angle       0.68903 (    2)
  covalent geometry    : bond        0.00472 ( 7009)
  covalent geometry    : angle       0.58832 ( 9540)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.841 
Fit side-chains
REVERT: A  240 MET cc_start: 0.6304 (OUTLIER) cc_final: 0.5211 (ttm)
REVERT: B   96 ARG cc_start: 0.8320 (mtt180) cc_final: 0.8036 (mtt90)
REVERT: R   61 LYS cc_start: 0.7846 (mmmt) cc_final: 0.7628 (mmmt)
REVERT: R  121 TYR cc_start: 0.7632 (t80) cc_final: 0.7045 (t80)
REVERT: R  122 LYS cc_start: 0.7857 (mtpp) cc_final: 0.7272 (mtmm)
REVERT: R  229 LYS cc_start: 0.7429 (tppt) cc_final: 0.7126 (mptt)
  outliers start: 24
  outliers final: 12
  residues processed: 113
  average time/residue: 1.2211
  time to fit residues: 147.3423
Evaluate side-chains
  113 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   24 ILE
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  187 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 65 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 80 optimal weight:    9.9990
   chunk 23 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
B 142 HIS
** B 340 ASN ** 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 = 0.4581 r_free = 0.4581 target = 0.221957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.178625 restraints weight = 7346.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.4133 rms_B_bonded: 1.85
r_work: 0.3916 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3801 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7010  Z= 0.173
  Angle     :  0.555   7.844   9542  Z= 0.292
  Chirality :  0.042   0.143   1127
  Planarity :  0.003   0.035   1178
  Dihedral  :  6.944  58.107   1020
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 16.98 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.28), residues: 893
  helix:  1.69 (0.26), residues: 405
  sheet:  0.12 (0.37), residues: 178
  loop : -0.74 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  82 
 HIS   0.006   0.001   HIS B 142 
 PHE   0.020   0.002   PHE R 195 
 TYR   0.017   0.001   TYR R 256 
 ARG   0.003   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04019 (  407)
  hydrogen bonds       : angle       4.62352 ( 1170)
  SS BOND              : bond        0.00007 (    1)
  SS BOND              : angle       0.71511 (    2)
  covalent geometry    : bond        0.00395 ( 7009)
  covalent geometry    : angle       0.55527 ( 9540)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 1.108 
Fit side-chains
REVERT: A  240 MET cc_start: 0.6154 (OUTLIER) cc_final: 0.5087 (ttm)
REVERT: A  343 ILE cc_start: 0.8485 (mt) cc_final: 0.8189 (mp)
REVERT: B   96 ARG cc_start: 0.8359 (mtt180) cc_final: 0.8052 (mtt180)
REVERT: B  263 THR cc_start: 0.8701 (t) cc_final: 0.8236 (m)
REVERT: R   61 LYS cc_start: 0.7795 (mmmt) cc_final: 0.7578 (mmmt)
REVERT: R  121 TYR cc_start: 0.7641 (t80) cc_final: 0.7077 (t80)
REVERT: R  122 LYS cc_start: 0.7872 (mtpp) cc_final: 0.7250 (mtmm)
REVERT: R  229 LYS cc_start: 0.7365 (tppt) cc_final: 0.7066 (mptt)
  outliers start: 21
  outliers final: 12
  residues processed: 111
  average time/residue: 1.5121
  time to fit residues: 178.9629
Evaluate side-chains
  113 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  187 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 74 optimal weight:    5.9990
   chunk 86 optimal weight:    0.0670
   chunk 1 optimal weight:    0.9980
   chunk 67 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
B  35 ASN
B 142 HIS
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** 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 = 0.4592 r_free = 0.4592 target = 0.223391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.180513 restraints weight = 7409.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.4148 rms_B_bonded: 1.84
r_work: 0.3936 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3823 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7010  Z= 0.139
  Angle     :  0.529   7.674   9542  Z= 0.282
  Chirality :  0.041   0.208   1127
  Planarity :  0.003   0.035   1178
  Dihedral  :  6.779  55.451   1020
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 17.27 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.28), residues: 893
  helix:  1.71 (0.26), residues: 409
  sheet:  0.23 (0.37), residues: 177
  loop : -0.70 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 142 
 PHE   0.023   0.001   PHE R 236 
 TYR   0.010   0.001   TYR A 320 
 ARG   0.007   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03761 (  407)
  hydrogen bonds       : angle       4.53740 ( 1170)
  SS BOND              : bond        0.00069 (    1)
  SS BOND              : angle       0.76491 (    2)
  covalent geometry    : bond        0.00310 ( 7009)
  covalent geometry    : angle       0.52926 ( 9540)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
REVERT: A  240 MET cc_start: 0.6130 (OUTLIER) cc_final: 0.5067 (ttm)
REVERT: A  343 ILE cc_start: 0.8464 (mt) cc_final: 0.8186 (mp)
REVERT: B   96 ARG cc_start: 0.8334 (mtt180) cc_final: 0.8058 (mtt180)
REVERT: B  263 THR cc_start: 0.8608 (t) cc_final: 0.8153 (m)
REVERT: R   78 ILE cc_start: 0.6930 (pp) cc_final: 0.6629 (tt)
REVERT: R  121 TYR cc_start: 0.7609 (t80) cc_final: 0.7058 (t80)
REVERT: R  229 LYS cc_start: 0.7386 (tppt) cc_final: 0.7092 (mptt)
  outliers start: 23
  outliers final: 11
  residues processed: 117
  average time/residue: 0.8620
  time to fit residues: 108.4058
Evaluate side-chains
  108 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  172 CYS
Chi-restraints excluded: chain R residue  272 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 60 optimal weight:    7.9990
   chunk 75 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0020
   chunk 21 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 71 optimal weight:    7.9990
   chunk 64 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9990
   overall best weight:    1.3394

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 256 ASN
** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
B 142 HIS
B 156 GLN
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** 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 = 0.4560 r_free = 0.4560 target = 0.219708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.176374 restraints weight = 7341.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.4109 rms_B_bonded: 1.81
r_work: 0.3883 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3768 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   7010  Z= 0.230
  Angle     :  0.618   7.673   9542  Z= 0.322
  Chirality :  0.044   0.147   1127
  Planarity :  0.004   0.036   1178
  Dihedral  :  7.045  54.728   1020
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 17.85 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.28), residues: 893
  helix:  1.52 (0.26), residues: 408
  sheet:  0.09 (0.37), residues: 183
  loop : -0.75 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.007   0.001   HIS B 142 
 PHE   0.019   0.002   PHE R 195 
 TYR   0.011   0.002   TYR A 320 
 ARG   0.003   0.001   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04212 (  407)
  hydrogen bonds       : angle       4.77627 ( 1170)
  SS BOND              : bond        0.00143 (    1)
  SS BOND              : angle       0.35716 (    2)
  covalent geometry    : bond        0.00537 ( 7009)
  covalent geometry    : angle       0.61778 ( 9540)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7133 (mtmm) cc_final: 0.6701 (pttp)
REVERT: A  197 LYS cc_start: 0.8914 (mttt) cc_final: 0.8661 (mtmt)
REVERT: A  240 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.5117 (ttm)
REVERT: B   96 ARG cc_start: 0.8367 (mtt180) cc_final: 0.8092 (mtt90)
REVERT: R   78 ILE cc_start: 0.6912 (pp) cc_final: 0.6627 (tt)
REVERT: R  121 TYR cc_start: 0.7675 (t80) cc_final: 0.7111 (t80)
REVERT: R  122 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7547 (mtpt)
REVERT: R  229 LYS cc_start: 0.7400 (tppt) cc_final: 0.7111 (mptt)
  outliers start: 27
  outliers final: 17
  residues processed: 112
  average time/residue: 1.1897
  time to fit residues: 141.3410
Evaluate side-chains
  117 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  172 CYS
Chi-restraints excluded: chain R residue  187 SER
Chi-restraints excluded: chain R residue  190 ILE
Chi-restraints excluded: chain R residue  272 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0980
   chunk 55 optimal weight:    4.9990
   chunk 30 optimal weight:    0.5980
   chunk 87 optimal weight:    7.9990
   chunk 13 optimal weight:    0.8980
   chunk 86 optimal weight:    0.3980
   chunk 85 optimal weight:    0.0970
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
B  35 ASN
B 142 HIS
** B 340 ASN ** 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 = 0.4599 r_free = 0.4599 target = 0.223779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.180772 restraints weight = 7368.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.4158 rms_B_bonded: 1.83
r_work: 0.3962 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3850 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7010  Z= 0.124
  Angle     :  0.529   7.674   9542  Z= 0.282
  Chirality :  0.041   0.136   1127
  Planarity :  0.003   0.035   1178
  Dihedral  :  6.735  52.358   1020
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 18.43 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.29), residues: 893
  helix:  1.75 (0.26), residues: 408
  sheet:  0.24 (0.37), residues: 177
  loop : -0.70 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 142 
 PHE   0.024   0.001   PHE R 236 
 TYR   0.017   0.001   TYR R 256 
 ARG   0.008   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03671 (  407)
  hydrogen bonds       : angle       4.53386 ( 1170)
  SS BOND              : bond        0.00106 (    1)
  SS BOND              : angle       0.72923 (    2)
  covalent geometry    : bond        0.00268 ( 7009)
  covalent geometry    : angle       0.52944 ( 9540)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.771 
Fit side-chains
REVERT: A  240 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.4880 (ttm)
REVERT: A  343 ILE cc_start: 0.8430 (mt) cc_final: 0.8146 (mp)
REVERT: B   96 ARG cc_start: 0.8333 (mtt180) cc_final: 0.8034 (mtt180)
REVERT: B  263 THR cc_start: 0.8558 (t) cc_final: 0.8074 (m)
REVERT: B  304 ARG cc_start: 0.7556 (ttp80) cc_final: 0.7351 (ttt-90)
REVERT: R   78 ILE cc_start: 0.6937 (pp) cc_final: 0.6663 (tt)
REVERT: R  121 TYR cc_start: 0.7609 (t80) cc_final: 0.7054 (t80)
REVERT: R  122 LYS cc_start: 0.7845 (mtpp) cc_final: 0.7223 (mtmm)
REVERT: R  229 LYS cc_start: 0.7405 (tppt) cc_final: 0.7121 (mptt)
  outliers start: 20
  outliers final: 12
  residues processed: 111
  average time/residue: 1.0156
  time to fit residues: 120.5892
Evaluate side-chains
  111 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  172 CYS
Chi-restraints excluded: chain R residue  272 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
B 142 HIS
B 156 GLN
** B 340 ASN ** 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 = 0.4587 r_free = 0.4587 target = 0.222397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.179305 restraints weight = 7391.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.4144 rms_B_bonded: 1.81
r_work: 0.3922 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3808 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7010  Z= 0.168
  Angle     :  0.582   8.003   9542  Z= 0.302
  Chirality :  0.042   0.141   1127
  Planarity :  0.003   0.035   1178
  Dihedral  :  6.753  52.056   1020
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 19.01 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.28), residues: 893
  helix:  1.75 (0.26), residues: 408
  sheet:  0.22 (0.37), residues: 177
  loop : -0.71 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.008   0.001   HIS B 142 
 PHE   0.020   0.002   PHE R 195 
 TYR   0.012   0.001   TYR R 256 
 ARG   0.004   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03880 (  407)
  hydrogen bonds       : angle       4.64027 ( 1170)
  SS BOND              : bond        0.00021 (    1)
  SS BOND              : angle       0.59542 (    2)
  covalent geometry    : bond        0.00384 ( 7009)
  covalent geometry    : angle       0.58189 ( 9540)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.812 
Fit side-chains
REVERT: A  197 LYS cc_start: 0.8856 (mttt) cc_final: 0.8639 (mtmt)
REVERT: A  240 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.4909 (ttm)
REVERT: A  343 ILE cc_start: 0.8497 (mt) cc_final: 0.8195 (mp)
REVERT: B   96 ARG cc_start: 0.8381 (mtt180) cc_final: 0.8155 (mtt90)
REVERT: B  263 THR cc_start: 0.8632 (t) cc_final: 0.8141 (m)
REVERT: B  304 ARG cc_start: 0.7602 (ttp80) cc_final: 0.7395 (ttt-90)
REVERT: R   78 ILE cc_start: 0.6927 (pp) cc_final: 0.6665 (tt)
REVERT: R  121 TYR cc_start: 0.7657 (t80) cc_final: 0.7109 (t80)
REVERT: R  122 LYS cc_start: 0.7842 (mtpp) cc_final: 0.7459 (mtpt)
REVERT: R  229 LYS cc_start: 0.7441 (tppt) cc_final: 0.7158 (mptt)
  outliers start: 17
  outliers final: 13
  residues processed: 108
  average time/residue: 0.9244
  time to fit residues: 106.8992
Evaluate side-chains
  108 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  172 CYS
Chi-restraints excluded: chain R residue  272 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 21 optimal weight:    9.9990
   chunk 3 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 12 optimal weight:    0.4980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
B 142 HIS
B 156 GLN
** B 340 ASN ** 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 = 0.4591 r_free = 0.4591 target = 0.222980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.179805 restraints weight = 7517.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.4140 rms_B_bonded: 1.95
r_work: 0.3934 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3820 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7010  Z= 0.146
  Angle     :  0.563   9.450   9542  Z= 0.295
  Chirality :  0.042   0.190   1127
  Planarity :  0.003   0.036   1178
  Dihedral  :  6.658  53.148   1020
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 19.01 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.29), residues: 893
  helix:  1.82 (0.26), residues: 403
  sheet:  0.21 (0.37), residues: 177
  loop : -0.72 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.007   0.001   HIS B 142 
 PHE   0.025   0.002   PHE R 236 
 TYR   0.011   0.001   TYR R  49 
 ARG   0.009   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03763 (  407)
  hydrogen bonds       : angle       4.60033 ( 1170)
  SS BOND              : bond        0.00049 (    1)
  SS BOND              : angle       0.65189 (    2)
  covalent geometry    : bond        0.00330 ( 7009)
  covalent geometry    : angle       0.56323 ( 9540)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 1.281 
Fit side-chains
REVERT: A  197 LYS cc_start: 0.8810 (mttt) cc_final: 0.8608 (mtmt)
REVERT: A  240 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.4879 (ttm)
REVERT: A  343 ILE cc_start: 0.8456 (mt) cc_final: 0.8171 (mp)
REVERT: B   96 ARG cc_start: 0.8348 (mtt180) cc_final: 0.8076 (mtt180)
REVERT: B  263 THR cc_start: 0.8574 (t) cc_final: 0.8103 (m)
REVERT: B  304 ARG cc_start: 0.7617 (ttp80) cc_final: 0.7387 (ttt-90)
REVERT: R   78 ILE cc_start: 0.6918 (pp) cc_final: 0.6652 (tt)
REVERT: R  121 TYR cc_start: 0.7620 (t80) cc_final: 0.7075 (t80)
REVERT: R  122 LYS cc_start: 0.7827 (mtpp) cc_final: 0.7438 (mtpt)
REVERT: R  256 TYR cc_start: 0.6787 (t80) cc_final: 0.5840 (t80)
  outliers start: 17
  outliers final: 15
  residues processed: 105
  average time/residue: 1.1308
  time to fit residues: 127.0315
Evaluate side-chains
  108 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  111 PHE
Chi-restraints excluded: chain R residue  172 CYS
Chi-restraints excluded: chain R residue  187 SER
Chi-restraints excluded: chain R residue  272 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 14 optimal weight:    0.0060
   chunk 22 optimal weight:    0.6980
   chunk 62 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 79 optimal weight:    8.9990
   chunk 50 optimal weight:    0.7980
   chunk 85 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
** B 340 ASN ** 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 = 0.4592 r_free = 0.4592 target = 0.223027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.179851 restraints weight = 7440.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.4148 rms_B_bonded: 1.81
r_work: 0.3935 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3822 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7010  Z= 0.148
  Angle     :  0.568   9.587   9542  Z= 0.296
  Chirality :  0.042   0.183   1127
  Planarity :  0.003   0.036   1178
  Dihedral  :  6.625  53.782   1020
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 18.87 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.29), residues: 893
  helix:  1.86 (0.26), residues: 403
  sheet:  0.20 (0.37), residues: 177
  loop : -0.72 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.007   0.001   HIS B 142 
 PHE   0.021   0.001   PHE R 195 
 TYR   0.009   0.001   TYR R  49 
 ARG   0.007   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03754 (  407)
  hydrogen bonds       : angle       4.60014 ( 1170)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       0.64474 (    2)
  covalent geometry    : bond        0.00333 ( 7009)
  covalent geometry    : angle       0.56785 ( 9540)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6129.61 seconds
wall clock time: 109 minutes 52.98 seconds (6592.98 seconds total)