Starting phenix.real_space_refine
on Tue Mar 11 14:30:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d9l_27265/03_2025/8d9l_27265.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d9l_27265/03_2025/8d9l_27265.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d9l_27265/03_2025/8d9l_27265.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d9l_27265/03_2025/8d9l_27265.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d9l_27265/03_2025/8d9l_27265.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d9l_27265/03_2025/8d9l_27265.cif"
  }
  resolution = 4.04
  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=   0.003 sd=   0.023
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      65      5.49       5
     S      23      5.16       5
     C    3418      2.51       5
     N    1000      2.21       5
     O    1251      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5757
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2557
          Classifications: {'peptide': 332}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 321}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "A"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1783
          Classifications: {'peptide': 221}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 204}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 1390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 1390
          Classifications: {'RNA': 65}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 28, 'rna3p_pyr': 27}
          Link IDs: {'rna2p': 10, 'rna3p': 54}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Classifications: {'peptide': 1}
  Residues with excluded nonbonded symmetry interactions: 40
    residue:
      pdb=" N   GLN B  12 " occ=0.85
      ... (7 atoms not shown)
      pdb=" NE2 GLN B  12 " occ=0.85
    residue:
      pdb=" N   ARG B  21 " occ=0.88
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  21 " occ=0.88
    residue:
      pdb=" N   CYS B  40 " occ=0.68
      ... (4 atoms not shown)
      pdb=" SG  CYS B  40 " occ=0.68
    residue:
      pdb=" N   SER B  61 " occ=0.82
      ... (4 atoms not shown)
      pdb=" OG  SER B  61 " occ=0.82
    residue:
      pdb=" N   ASP B  80 " occ=0.85
      ... (6 atoms not shown)
      pdb=" OD2 ASP B  80 " occ=0.85
    residue:
      pdb=" N   ASP B  81 " occ=0.80
      ... (6 atoms not shown)
      pdb=" OD2 ASP B  81 " occ=0.80
    residue:
      pdb=" N   ARG B  84 " occ=0.91
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  84 " occ=0.91
    residue:
      pdb=" N   ARG B  89 " occ=0.99
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  89 " occ=0.99
    residue:
      pdb=" N   CYS B 105 " occ=0.82
      ... (4 atoms not shown)
      pdb=" SG  CYS B 105 " occ=0.82
    residue:
      pdb=" N   LYS B 122 " occ=0.88
      ... (7 atoms not shown)
      pdb=" NZ  LYS B 122 " occ=0.88
    residue:
      pdb=" N   GLU B 133 " occ=0.89
      ... (7 atoms not shown)
      pdb=" OE2 GLU B 133 " occ=0.89
    residue:
      pdb=" N   CYS B 137 " occ=0.86
      ... (4 atoms not shown)
      pdb=" SG  CYS B 137 " occ=0.86
    ... (remaining 28 not shown)
  Time building chain proxies: 4.33, per 1000 atoms: 0.75
  Number of scatterers: 5757
  At special positions: 0
  Unit cell: (65.52, 98.28, 112.14, 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      23     16.00
     P      65     15.00
     O    1251      8.00
     N    1000      7.00
     C    3418      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.60
  Conformation dependent library (CDL) restraints added in 692.5 milliseconds
  

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1032

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 8 sheets defined
      19.0% alpha, 32.2% beta
      27 base pairs and 27 stacking pairs defined.
    Time for finding SS restraints: 2.30
  Creating SS restraints...
    Processing helix  chain 'B' and resid 229 through 233
      removed outlier: 3.516A  pdb=" N   GLN B 233 " --> pdb=" O   LEU B 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 229 through 233'
    Processing helix  chain 'B' and resid 330 through 343
    Processing helix  chain 'B' and resid 353 through 359
      removed outlier: 3.817A  pdb=" N   SER B 359 " --> pdb=" O   ALA B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 362
      No H-bonds generated for 'chain 'B' and resid 360 through 362'
    Processing helix  chain 'A' and resid 88 through 95
    Processing helix  chain 'A' and resid 109 through 126
    Processing helix  chain 'A' and resid 177 through 187
      removed outlier: 3.830A  pdb=" N   GLU A 183 " --> pdb=" O   THR A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 214
      removed outlier: 3.513A  pdb=" N   ASP A 205 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 226
      removed outlier: 3.907A  pdb=" N   SER A 226 " --> pdb=" O   GLU A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 235
      removed outlier: 4.256A  pdb=" N   GLY A 232 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   GLY A 235 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 247
    Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 10
    Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 69
      removed outlier: 7.107A  pdb=" N   THR B  79 " --> pdb=" O   LEU B  65 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   SER B  67 " --> pdb=" O   ALA B  77 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   ALA B  77 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 5.649A  pdb=" N   PHE B  69 " --> pdb=" O   TYR B  75 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   TYR B  75 " --> pdb=" O   PHE B  69 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   ARG B  84 " --> pdb=" O   ASP B  80 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   ARG B  89 " --> pdb=" O   CYS B  95 " (cutoff:3.500A)
      removed outlier: 5.689A  pdb=" N   CYS B  95 " --> pdb=" O   ARG B  89 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 110
      removed outlier: 3.549A  pdb=" N   ALA B 107 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ASP B 125 " --> pdb=" O   ASP B 121 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL B 126 " --> pdb=" O   GLU B 141 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 153
      removed outlier: 3.797A  pdb=" N   ASP B 150 " --> pdb=" O   ALA B 163 " (cutoff:3.500A)
      removed outlier: 5.716A  pdb=" N   ILE B 169 " --> pdb=" O   PHE B 183 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   PHE B 183 " --> pdb=" O   ILE B 169 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL B 171 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 196
      removed outlier: 3.654A  pdb=" N   ARG B 193 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   SER B 208 " --> pdb=" O   THR B 212 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   THR B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   LEU B 213 " --> pdb=" O   CYS B 226 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   CYS B 226 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   LEU B 215 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG B 222 " --> pdb=" O   GLU B 217 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 246 through 252
      removed outlier: 3.995A  pdb=" N   ARG B 248 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LEU B 261 " --> pdb=" O   ARG B 248 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   CYS B 262 " --> pdb=" O   VAL B 267 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   VAL B 267 " --> pdb=" O   CYS B 262 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   GLN B 272 " --> pdb=" O   TYR B 282 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   TYR B 282 " --> pdb=" O   GLN B 272 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ASP B 274 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
      removed outlier: 5.734A  pdb=" N   LEU B 280 " --> pdb=" O   ASP B 274 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 292 through 298
      removed outlier: 3.757A  pdb=" N   ASP B 294 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 134 through 138
      removed outlier: 6.446A  pdb=" N   ILE A 103 " --> pdb=" O   ALA A 135 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   LEU A 137 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   GLY A 105 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   VAL A  78 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   LEU A 104 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   PHE A  80 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   LEU A 106 " --> pdb=" O   PHE A  80 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ASP A  82 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   GLU A  79 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   MET A 157 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ALA A  81 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 5.840A  pdb=" N   PHE A 159 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   ILE A  83 " --> pdb=" O   PHE A 159 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   THR A 155 " --> pdb=" O   LEU A 193 " (cutoff:3.500A)
      removed outlier: 8.599A  pdb=" N   TYR A 195 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   MET A 157 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
      removed outlier: 8.210A  pdb=" N   ILE A 197 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   PHE A 159 " --> pdb=" O   ILE A 197 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   GLY A 192 " --> pdb=" O   ARG A 258 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   ILE A 255 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)

    143 hydrogen bonds defined for protein.
    396 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      69 hydrogen bonds
      114 hydrogen bond angles
      0 basepair planarities
      27 basepair parallelities
      27 stacking parallelities
  Total time for adding SS restraints: 2.06

  Time building geometry restraints manager: 1.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1583
        1.34 -     1.45: 1447
        1.45 -     1.57: 2836
        1.57 -     1.69: 128
        1.69 -     1.81: 32
  Bond restraints: 6026
  Sorted by residual:
  bond pdb=" C2  SAM A 301 "
       pdb=" N3  SAM A 301 "
    ideal  model  delta    sigma   weight residual
    1.322  1.381 -0.059 2.00e-02 2.50e+03 8.71e+00
  bond pdb=" C8  SAM A 301 "
       pdb=" N7  SAM A 301 "
    ideal  model  delta    sigma   weight residual
    1.298  1.351 -0.053 2.00e-02 2.50e+03 7.13e+00
  bond pdb=" C2  SAM A 301 "
       pdb=" N1  SAM A 301 "
    ideal  model  delta    sigma   weight residual
    1.329  1.380 -0.051 2.00e-02 2.50e+03 6.58e+00
  bond pdb=" C6  SAM A 301 "
       pdb=" N1  SAM A 301 "
    ideal  model  delta    sigma   weight residual
    1.337  1.380 -0.043 2.00e-02 2.50e+03 4.57e+00
  bond pdb=" C   SAM A 301 "
       pdb=" OXT SAM A 301 "
    ideal  model  delta    sigma   weight residual
    1.256  1.230  0.026 2.00e-02 2.50e+03 1.64e+00
  ... (remaining 6021 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 8400
        1.75 -     3.49: 71
        3.49 -     5.24: 10
        5.24 -     6.98: 3
        6.98 -     8.73: 3
  Bond angle restraints: 8487
  Sorted by residual:
  angle pdb=" O   SAM A 301 "
        pdb=" C   SAM A 301 "
        pdb=" OXT SAM A 301 "
      ideal   model   delta    sigma   weight residual
     126.77  118.04    8.73 3.00e+00 1.11e-01 8.47e+00
  angle pdb=" N1  SAM A 301 "
        pdb=" C2  SAM A 301 "
        pdb=" N3  SAM A 301 "
      ideal   model   delta    sigma   weight residual
     128.51  120.14    8.37 3.00e+00 1.11e-01 7.79e+00
  angle pdb=" C2  SAM A 301 "
        pdb=" N3  SAM A 301 "
        pdb=" C4  SAM A 301 "
      ideal   model   delta    sigma   weight residual
     112.25  120.28   -8.03 3.00e+00 1.11e-01 7.16e+00
  angle pdb=" C   SER B 113 "
        pdb=" N   GLU B 114 "
        pdb=" CA  GLU B 114 "
      ideal   model   delta    sigma   weight residual
     121.54  125.77   -4.23 1.91e+00 2.74e-01 4.90e+00
  angle pdb=" C2' SAM A 301 "
        pdb=" C3' SAM A 301 "
        pdb=" O3' SAM A 301 "
      ideal   model   delta    sigma   weight residual
     116.14  110.26    5.88 3.00e+00 1.11e-01 3.85e+00
  ... (remaining 8482 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.87: 3304
       15.87 -    31.74: 180
       31.74 -    47.61: 86
       47.61 -    63.47: 75
       63.47 -    79.34: 44
  Dihedral angle restraints: 3689
    sinusoidal: 2094
      harmonic: 1595
  Sorted by residual:
  dihedral pdb=" CA  GLU B 114 "
           pdb=" CB  GLU B 114 "
           pdb=" CG  GLU B 114 "
           pdb=" CD  GLU B 114 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  110.71  -50.71     3      1.50e+01 4.44e-03 8.93e+00
  dihedral pdb=" O5'   U C  47 "
           pdb=" C5'   U C  47 "
           pdb=" C4'   U C  47 "
           pdb=" C3'   U C  47 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.00    9.35   45.65     3      1.50e+01 4.44e-03 8.21e+00
  dihedral pdb=" O5'   U C  20 "
           pdb=" C5'   U C  20 "
           pdb=" C4'   U C  20 "
           pdb=" C3'   U C  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.00  130.27   44.73     3      1.50e+01 4.44e-03 8.05e+00
  ... (remaining 3686 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 794
       0.036 -    0.071: 132
       0.071 -    0.107: 61
       0.107 -    0.142: 14
       0.142 -    0.178: 1
  Chirality restraints: 1002
  Sorted by residual:
  chirality pdb=" C2' SAM A 301 "
            pdb=" C1' SAM A 301 "
            pdb=" C3' SAM A 301 "
            pdb=" O2' SAM A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.76   -2.58   -0.18 2.00e-01 2.50e+01 7.91e-01
  chirality pdb=" C1' SAM A 301 "
            pdb=" C2' SAM A 301 "
            pdb=" N9  SAM A 301 "
            pdb=" O4' SAM A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.30    2.43   -0.13 2.00e-01 2.50e+01 4.42e-01
  chirality pdb=" CA  ILE B  37 "
            pdb=" N   ILE B  37 "
            pdb=" C   ILE B  37 "
            pdb=" CB  ILE B  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.31e-01
  ... (remaining 999 not shown)

  Planarity restraints: 837
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  59 "   -0.019 2.00e-02 2.50e+03   8.07e-03 1.96e+00
        pdb=" N9    G C  59 "    0.019 2.00e-02 2.50e+03
        pdb=" C8    G C  59 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    G C  59 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    G C  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G C  59 "    0.003 2.00e-02 2.50e+03
        pdb=" O6    G C  59 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    G C  59 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G C  59 "   -0.000 2.00e-02 2.50e+03
        pdb=" N2    G C  59 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G C  59 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G C  59 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 318 "   -0.013 5.00e-02 4.00e+02   1.96e-02 6.14e-01
        pdb=" N   PRO B 319 "    0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO B 319 "   -0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO B 319 "   -0.011 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 154 "    0.012 5.00e-02 4.00e+02   1.88e-02 5.67e-01
        pdb=" N   PRO B 155 "   -0.033 5.00e-02 4.00e+02
        pdb=" CA  PRO B 155 "    0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO B 155 "    0.011 5.00e-02 4.00e+02
  ... (remaining 834 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1163
        2.78 -     3.31: 5195
        3.31 -     3.84: 10263
        3.84 -     4.37: 11749
        4.37 -     4.90: 18418
  Nonbonded interactions: 46788
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 154 "
            pdb=" OD1 ASP B 156 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OG1 THR B 188 "
            pdb=" OE1 GLU B 189 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OG  SER B 130 "
            pdb=" OE1 GLU B 133 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O6    G C  10 "
            pdb=" N2    G C  45 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" OD2 ASP B 121 "
            pdb=" OG  SER B 123 "
     model   vdw
     2.307 3.040
  ... (remaining 46783 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=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.150
  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:                    0.070
  Process input model:                     20.440
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.059   6026  Z= 0.131
  Angle     :  0.444   8.728   8487  Z= 0.201
  Chirality :  0.035   0.178   1002
  Planarity :  0.002   0.020    837
  Dihedral  : 16.630  79.343   2657
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  6.21 %
    Favored  : 93.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.09 (0.38), residues: 541
  helix:  1.26 (0.58), residues: 101
  sheet:  1.53 (0.39), residues: 183
  loop : -0.04 (0.39), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 206 
 HIS   0.002   0.000   HIS A 210 
 PHE   0.010   0.001   PHE B  88 
 TYR   0.005   0.001   TYR A  37 
 ARG   0.001   0.000   ARG B  99 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.9286 (pttt) cc_final: 0.8970 (mtmm)
REVERT: B  157 ASP cc_start: 0.9118 (t0) cc_final: 0.8818 (t0)
REVERT: B  166 ASP cc_start: 0.8776 (m-30) cc_final: 0.8425 (m-30)
REVERT: B  195 SER cc_start: 0.9389 (t) cc_final: 0.8737 (m)
REVERT: B  206 SER cc_start: 0.8836 (m) cc_final: 0.8561 (p)
REVERT: A   44 MET cc_start: 0.5282 (tmm) cc_final: 0.3600 (tmm)
REVERT: A  115 TYR cc_start: 0.9514 (t80) cc_final: 0.8865 (t80)
REVERT: A  140 ASN cc_start: 0.9171 (t0) cc_final: 0.8937 (t0)
REVERT: A  157 MET cc_start: 0.9333 (ttm) cc_final: 0.8863 (ttm)
REVERT: A  176 ILE cc_start: 0.9329 (mm) cc_final: 0.9039 (tp)
REVERT: A  180 LEU cc_start: 0.9654 (mt) cc_final: 0.9402 (mm)
REVERT: A  183 GLU cc_start: 0.9262 (pt0) cc_final: 0.8846 (pm20)
  outliers start: 2
  outliers final: 2
  residues processed: 65
  average time/residue: 0.2217
  time to fit residues: 18.2505
Evaluate side-chains
  43 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9990
   chunk 25 optimal weight:    9.9990
   chunk 15 optimal weight:    0.0010
   chunk 31 optimal weight:    9.9990
   chunk 24 optimal weight:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 18 optimal weight:   20.0000
   chunk 29 optimal weight:    4.9990
   chunk 35 optimal weight:   10.0000
   chunk 55 optimal weight:   20.0000
   overall best weight:    3.9994

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

Flipped N/Q/H residues before XYZ refinement:
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.039706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.030285 restraints weight = 46185.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.031425 restraints weight = 23556.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.032250 restraints weight = 15164.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2699
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2699 r_free = 0.2699    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2689 r_free = 0.2689    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2689
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6026  Z= 0.236
  Angle     :  0.525   6.785   8487  Z= 0.268
  Chirality :  0.037   0.155   1002
  Planarity :  0.003   0.022    837
  Dihedral  : 19.242  79.268   1658
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.04 (0.37), residues: 541
  helix:  1.46 (0.59), residues: 97
  sheet:  1.30 (0.38), residues: 186
  loop : -0.02 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  93 
 HIS   0.002   0.001   HIS A 214 
 PHE   0.011   0.002   PHE B 297 
 TYR   0.014   0.002   TYR B 127 
 ARG   0.004   0.000   ARG B  99 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.9374 (pttt) cc_final: 0.9113 (mtmm)
REVERT: B  157 ASP cc_start: 0.9103 (t0) cc_final: 0.8849 (t0)
REVERT: B  166 ASP cc_start: 0.8810 (m-30) cc_final: 0.8574 (m-30)
REVERT: A   27 SER cc_start: 0.9552 (m) cc_final: 0.9174 (t)
REVERT: A   44 MET cc_start: 0.6111 (tmm) cc_final: 0.4822 (tmm)
REVERT: A  115 TYR cc_start: 0.9577 (t80) cc_final: 0.9210 (t80)
REVERT: A  157 MET cc_start: 0.9326 (ttm) cc_final: 0.8787 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.2136
  time to fit residues: 12.5335
Evaluate side-chains
  35 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 17 optimal weight:    0.0670
   chunk 33 optimal weight:    0.8980
   chunk 41 optimal weight:    8.9990
   chunk 25 optimal weight:    0.0670
   chunk 19 optimal weight:    9.9990
   chunk 42 optimal weight:    0.7980
   chunk 59 optimal weight:    9.9990
   chunk 52 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.4856

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

Flipped N/Q/H residues before XYZ refinement:
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.040612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.031012 restraints weight = 44877.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.032180 restraints weight = 22907.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.033058 restraints weight = 14943.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2752
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2752 r_free = 0.2752    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2751
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6026  Z= 0.127
  Angle     :  0.454   5.574   8487  Z= 0.226
  Chirality :  0.037   0.154   1002
  Planarity :  0.003   0.020    837
  Dihedral  : 19.087  80.550   1658
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  1.12 (0.37), residues: 541
  helix:  1.69 (0.59), residues: 91
  sheet:  1.44 (0.38), residues: 186
  loop : -0.07 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 206 
 HIS   0.003   0.001   HIS B 144 
 PHE   0.019   0.001   PHE B  69 
 TYR   0.008   0.001   TYR B 361 
 ARG   0.003   0.000   ARG B 158 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.9381 (pttt) cc_final: 0.9126 (mtmm)
REVERT: B  108 LEU cc_start: 0.9227 (pt) cc_final: 0.8898 (pp)
REVERT: B  157 ASP cc_start: 0.9055 (t0) cc_final: 0.8810 (t0)
REVERT: B  166 ASP cc_start: 0.8909 (m-30) cc_final: 0.8473 (m-30)
REVERT: A   44 MET cc_start: 0.6171 (tmm) cc_final: 0.4581 (tmm)
REVERT: A  115 TYR cc_start: 0.9553 (t80) cc_final: 0.9137 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.1827
  time to fit residues: 10.9134
Evaluate side-chains
  36 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 50 optimal weight:    8.9990
   chunk 35 optimal weight:   10.0000
   chunk 55 optimal weight:   20.0000
   chunk 14 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 33 optimal weight:   20.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 272 GLN
B 325 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.035569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2534 r_free = 0.2534 target = 0.026570 restraints weight = 51136.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2572 r_free = 0.2572 target = 0.027618 restraints weight = 26240.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2596 r_free = 0.2596 target = 0.028320 restraints weight = 17013.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2573
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2573 r_free = 0.2573    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2574 r_free = 0.2574    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2574
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   6026  Z= 0.365
  Angle     :  0.641   6.827   8487  Z= 0.329
  Chirality :  0.041   0.161   1002
  Planarity :  0.004   0.022    837
  Dihedral  : 19.521  79.532   1658
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 17.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.50 (0.35), residues: 541
  helix:  1.03 (0.55), residues: 91
  sheet:  0.96 (0.39), residues: 170
  loop : -0.25 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 252 
 HIS   0.006   0.002   HIS A 214 
 PHE   0.016   0.002   PHE A 211 
 TYR   0.015   0.002   TYR B 127 
 ARG   0.004   0.001   ARG B  99 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.8935 (mtm) cc_final: 0.8443 (mtm)
REVERT: B  148 LEU cc_start: 0.9581 (mt) cc_final: 0.9281 (mt)
REVERT: B  168 LYS cc_start: 0.9047 (mttm) cc_final: 0.8751 (mmmm)
REVERT: A   27 SER cc_start: 0.9686 (m) cc_final: 0.9369 (t)
REVERT: A   44 MET cc_start: 0.6749 (tmm) cc_final: 0.5868 (tmm)
REVERT: A  115 TYR cc_start: 0.9594 (t80) cc_final: 0.9102 (t80)
REVERT: A  157 MET cc_start: 0.9373 (ttm) cc_final: 0.9135 (ttm)
REVERT: A  207 MET cc_start: 0.9655 (mmp) cc_final: 0.9427 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1861
  time to fit residues: 9.5102
Evaluate side-chains
  27 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 20 optimal weight:    0.4980
   chunk 49 optimal weight:    7.9990
   chunk 17 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 52 optimal weight:   10.0000
   chunk 51 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 55 optimal weight:   20.0000
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
B 272 GLN
B 325 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.037549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2601 r_free = 0.2601 target = 0.028206 restraints weight = 47289.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.029311 restraints weight = 24113.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.030054 restraints weight = 15671.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2645 r_free = 0.2645    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2646 r_free = 0.2646    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2646
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6026  Z= 0.133
  Angle     :  0.463   5.578   8487  Z= 0.232
  Chirality :  0.037   0.132   1002
  Planarity :  0.002   0.019    837
  Dihedral  : 19.261  81.570   1658
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.86 (0.37), residues: 541
  helix:  1.75 (0.59), residues: 91
  sheet:  1.10 (0.39), residues: 187
  loop : -0.20 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 206 
 HIS   0.004   0.001   HIS A 144 
 PHE   0.016   0.001   PHE B  88 
 TYR   0.004   0.001   TYR B 361 
 ARG   0.002   0.000   ARG A 219 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.8892 (mtm) cc_final: 0.8623 (mtm)
REVERT: B  166 ASP cc_start: 0.9228 (m-30) cc_final: 0.8984 (m-30)
REVERT: B  168 LYS cc_start: 0.9070 (mttm) cc_final: 0.8686 (mmmm)
REVERT: A   27 SER cc_start: 0.9635 (m) cc_final: 0.9309 (t)
REVERT: A   44 MET cc_start: 0.6591 (tmm) cc_final: 0.5716 (tmm)
REVERT: A  115 TYR cc_start: 0.9590 (t80) cc_final: 0.9071 (t80)
REVERT: A  207 MET cc_start: 0.9684 (mmp) cc_final: 0.9476 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1758
  time to fit residues: 10.0813
Evaluate side-chains
  33 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 15 optimal weight:    0.0670
   chunk 40 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 32 optimal weight:    0.0670
   chunk 41 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   chunk 28 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 47 optimal weight:    0.8980
   chunk 17 optimal weight:    0.1980
   overall best weight:    0.4056

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.039090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.029495 restraints weight = 45461.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.030676 restraints weight = 23238.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.031472 restraints weight = 14929.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2697
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2697 r_free = 0.2697    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2697 r_free = 0.2697    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2697
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.3201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6026  Z= 0.109
  Angle     :  0.462   4.915   8487  Z= 0.225
  Chirality :  0.037   0.138   1002
  Planarity :  0.002   0.020    837
  Dihedral  : 18.994  80.710   1658
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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 (0.37), residues: 541
  helix:  1.60 (0.58), residues: 91
  sheet:  1.23 (0.39), residues: 185
  loop : -0.19 (0.38), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 206 
 HIS   0.003   0.001   HIS A 144 
 PHE   0.014   0.001   PHE B  88 
 TYR   0.011   0.001   TYR A 186 
 ARG   0.002   0.000   ARG B 158 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.9353 (pttt) cc_final: 0.8996 (mtmm)
REVERT: B  147 MET cc_start: 0.8805 (mtm) cc_final: 0.8332 (mtm)
REVERT: B  166 ASP cc_start: 0.9167 (m-30) cc_final: 0.8861 (m-30)
REVERT: B  168 LYS cc_start: 0.9025 (mttm) cc_final: 0.8677 (mmmm)
REVERT: A   44 MET cc_start: 0.6408 (tmm) cc_final: 0.5423 (tmm)
REVERT: A  115 TYR cc_start: 0.9595 (t80) cc_final: 0.9082 (t80)
REVERT: A  140 ASN cc_start: 0.9597 (t0) cc_final: 0.9386 (t0)
REVERT: A  142 MET cc_start: 0.9620 (mmm) cc_final: 0.9247 (mmm)
REVERT: A  175 ILE cc_start: 0.9594 (tp) cc_final: 0.9363 (tp)
REVERT: A  207 MET cc_start: 0.9659 (mmp) cc_final: 0.9444 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.1684
  time to fit residues: 10.3052
Evaluate side-chains
  38 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 42 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   chunk 1 optimal weight:    9.9990
   chunk 33 optimal weight:    0.7980
   chunk 14 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    4.1386

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

Flipped N/Q/H residues before XYZ refinement:
B 272 GLN
B 325 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.036694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2575 r_free = 0.2575 target = 0.027555 restraints weight = 48562.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.028633 restraints weight = 24900.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.029393 restraints weight = 16203.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.2615
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2614
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2614 r_free = 0.2614    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2614 r_free = 0.2614    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2614
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.3608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6026  Z= 0.233
  Angle     :  0.509   5.226   8487  Z= 0.260
  Chirality :  0.037   0.140   1002
  Planarity :  0.003   0.019    837
  Dihedral  : 19.231  80.036   1658
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.80 (0.37), residues: 541
  helix:  1.73 (0.59), residues: 91
  sheet:  1.02 (0.38), residues: 185
  loop : -0.20 (0.38), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 206 
 HIS   0.002   0.001   HIS A 171 
 PHE   0.017   0.002   PHE B 297 
 TYR   0.007   0.001   TYR A  50 
 ARG   0.002   0.000   ARG B  99 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.8934 (mtm) cc_final: 0.8475 (mtm)
REVERT: B  148 LEU cc_start: 0.9578 (mt) cc_final: 0.9341 (mt)
REVERT: B  166 ASP cc_start: 0.9203 (m-30) cc_final: 0.8981 (m-30)
REVERT: B  168 LYS cc_start: 0.9041 (mttm) cc_final: 0.8732 (mmmm)
REVERT: A   44 MET cc_start: 0.6735 (tmm) cc_final: 0.5819 (tmm)
REVERT: A  115 TYR cc_start: 0.9612 (t80) cc_final: 0.9077 (t80)
REVERT: A  142 MET cc_start: 0.9584 (mmm) cc_final: 0.9325 (mmm)
REVERT: A  207 MET cc_start: 0.9670 (mmp) cc_final: 0.9449 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.1590
  time to fit residues: 8.1441
Evaluate side-chains
  28 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0030
   chunk 52 optimal weight:    0.6980
   chunk 16 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   chunk 13 optimal weight:    0.0060
   chunk 56 optimal weight:   20.0000
   chunk 21 optimal weight:    9.9990
   chunk 46 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.7208

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 272 GLN
B 325 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.038704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.029299 restraints weight = 45761.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.030445 restraints weight = 23352.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.031250 restraints weight = 15035.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2686
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2686 r_free = 0.2686    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2686 r_free = 0.2686    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2686
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6026  Z= 0.115
  Angle     :  0.457   5.008   8487  Z= 0.225
  Chirality :  0.036   0.138   1002
  Planarity :  0.002   0.021    837
  Dihedral  : 19.037  80.604   1658
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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 (0.37), residues: 541
  helix:  1.74 (0.58), residues: 91
  sheet:  1.17 (0.39), residues: 185
  loop : -0.19 (0.38), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 206 
 HIS   0.003   0.001   HIS A 144 
 PHE   0.013   0.001   PHE B  88 
 TYR   0.007   0.001   TYR A 186 
 ARG   0.002   0.000   ARG A 119 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.9358 (pttt) cc_final: 0.8998 (mtmm)
REVERT: B  147 MET cc_start: 0.8867 (mtm) cc_final: 0.8635 (mtm)
REVERT: B  166 ASP cc_start: 0.9248 (m-30) cc_final: 0.8941 (m-30)
REVERT: B  168 LYS cc_start: 0.9041 (mttm) cc_final: 0.8725 (mmmm)
REVERT: A   30 MET cc_start: 0.9114 (mmp) cc_final: 0.8774 (mmm)
REVERT: A   44 MET cc_start: 0.6409 (tmm) cc_final: 0.5406 (tmm)
REVERT: A  115 TYR cc_start: 0.9556 (t80) cc_final: 0.9012 (t80)
REVERT: A  140 ASN cc_start: 0.9519 (t0) cc_final: 0.9286 (t0)
REVERT: A  142 MET cc_start: 0.9592 (mmm) cc_final: 0.9285 (mmm)
REVERT: A  207 MET cc_start: 0.9665 (mmp) cc_final: 0.9431 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.1534
  time to fit residues: 10.1140
Evaluate side-chains
  34 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 15 optimal weight:    0.2980
   chunk 24 optimal weight:   10.0000
   chunk 41 optimal weight:    0.0970
   chunk 6 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 25 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 60 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.039373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.029941 restraints weight = 45987.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.031092 restraints weight = 23506.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.031914 restraints weight = 15244.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2709
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2709 r_free = 0.2709    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2709 r_free = 0.2709    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2709
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6026  Z= 0.107
  Angle     :  0.457   6.382   8487  Z= 0.222
  Chirality :  0.036   0.154   1002
  Planarity :  0.002   0.021    837
  Dihedral  : 18.923  79.752   1658
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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 (0.37), residues: 541
  helix:  1.64 (0.58), residues: 91
  sheet:  1.16 (0.39), residues: 185
  loop : -0.14 (0.39), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 206 
 HIS   0.003   0.001   HIS B 144 
 PHE   0.016   0.001   PHE B  88 
 TYR   0.005   0.001   TYR A 184 
 ARG   0.003   0.000   ARG B 283 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.9373 (pttt) cc_final: 0.9028 (mtmm)
REVERT: B  147 MET cc_start: 0.8832 (mtm) cc_final: 0.8353 (mtm)
REVERT: B  166 ASP cc_start: 0.9233 (m-30) cc_final: 0.8899 (m-30)
REVERT: B  168 LYS cc_start: 0.9036 (mttm) cc_final: 0.8698 (mmmm)
REVERT: B  361 TYR cc_start: 0.8671 (m-80) cc_final: 0.8298 (m-10)
REVERT: A   30 MET cc_start: 0.9099 (mmp) cc_final: 0.8788 (mmm)
REVERT: A   44 MET cc_start: 0.6360 (tmm) cc_final: 0.5324 (tmm)
REVERT: A  115 TYR cc_start: 0.9556 (t80) cc_final: 0.9028 (t80)
REVERT: A  140 ASN cc_start: 0.9519 (t0) cc_final: 0.9268 (t0)
REVERT: A  142 MET cc_start: 0.9573 (mmm) cc_final: 0.9257 (mmm)
REVERT: A  176 ILE cc_start: 0.9584 (mm) cc_final: 0.9372 (mm)
REVERT: A  184 TYR cc_start: 0.9187 (m-80) cc_final: 0.8918 (m-80)
REVERT: A  207 MET cc_start: 0.9666 (mmp) cc_final: 0.9423 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.1629
  time to fit residues: 11.1292
Evaluate side-chains
  37 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 43 optimal weight:    0.2980
   chunk 54 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 55 optimal weight:   20.0000
   chunk 6 optimal weight:    7.9990
   overall best weight:    4.2588

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

Flipped N/Q/H residues before XYZ refinement:
B 272 GLN
B 325 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.036497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2570 r_free = 0.2570 target = 0.027467 restraints weight = 49560.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.028547 restraints weight = 25428.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.029278 restraints weight = 16503.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.2608
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2610
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2610 r_free = 0.2610    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2610 r_free = 0.2610    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2610
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.4000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6026  Z= 0.240
  Angle     :  0.523   4.998   8487  Z= 0.266
  Chirality :  0.037   0.148   1002
  Planarity :  0.003   0.018    837
  Dihedral  : 19.306  79.077   1658
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.78 (0.36), residues: 541
  helix:  1.64 (0.58), residues: 91
  sheet:  0.77 (0.38), residues: 180
  loop :  0.03 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 206 
 HIS   0.003   0.001   HIS A 171 
 PHE   0.015   0.002   PHE B  88 
 TYR   0.012   0.001   TYR B 361 
 ARG   0.002   0.000   ARG B  99 

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.8993 (mtm) cc_final: 0.8537 (mtm)
REVERT: B  148 LEU cc_start: 0.9632 (mt) cc_final: 0.9384 (mt)
REVERT: B  166 ASP cc_start: 0.9229 (m-30) cc_final: 0.8892 (m-30)
REVERT: B  168 LYS cc_start: 0.8968 (mttm) cc_final: 0.8705 (mmmm)
REVERT: B  361 TYR cc_start: 0.8627 (m-80) cc_final: 0.8414 (m-80)
REVERT: A   27 SER cc_start: 0.9699 (m) cc_final: 0.9482 (t)
REVERT: A   44 MET cc_start: 0.6811 (tmm) cc_final: 0.5837 (tmm)
REVERT: A  115 TYR cc_start: 0.9557 (t80) cc_final: 0.9022 (t80)
REVERT: A  142 MET cc_start: 0.9590 (mmm) cc_final: 0.9316 (mmm)
REVERT: A  207 MET cc_start: 0.9671 (mmp) cc_final: 0.9461 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1643
  time to fit residues: 9.3977
Evaluate side-chains
  31 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 47 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 40 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.036815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2577 r_free = 0.2577 target = 0.027754 restraints weight = 48701.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.028835 restraints weight = 24862.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.029577 restraints weight = 16059.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.2615
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2616
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2616 r_free = 0.2616    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2616 r_free = 0.2616    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2616
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.4161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6026  Z= 0.198
  Angle     :  0.495   5.541   8487  Z= 0.250
  Chirality :  0.037   0.132   1002
  Planarity :  0.002   0.019    837
  Dihedral  : 19.368  79.791   1658
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.74 (0.37), residues: 541
  helix:  1.65 (0.58), residues: 91
  sheet:  0.82 (0.38), residues: 186
  loop : -0.10 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 206 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.013   0.002   PHE B  88 
 TYR   0.006   0.001   TYR B 361 
 ARG   0.002   0.000   ARG B  99 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1710.72 seconds
wall clock time: 30 minutes 27.45 seconds (1827.45 seconds total)