Starting phenix.real_space_refine
on Tue Mar  3 14:25:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d9l_27265/03_2026/8d9l_27265.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d9l_27265/03_2026/8d9l_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d9l_27265/03_2026/8d9l_27265.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d9l_27265/03_2026/8d9l_27265.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d9l_27265/03_2026/8d9l_27265.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d9l_27265/03_2026/8d9l_27265.map"
  }
  resolution = 4.04
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.27, per 1000 atoms: 0.22
  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: 0.52
  Conformation dependent library (CDL) restraints added in 166.6 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: 0.73
  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: 1.00

  Time building geometry restraints manager: 0.67 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:             0.170
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.120
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.500
-------------------------------------------------------------------------------
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= 0.103
  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 : 7.16
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (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
 ARG   0.001   0.000   ARG B  99 
 TYR   0.005   0.001   TYR A  37 
 PHE   0.010   0.001   PHE B  88 
 TRP   0.012   0.001   TRP A 206 
 HIS   0.002   0.000   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 6026)
  covalent geometry    : angle       0.44416 ( 8487)
  hydrogen bonds       : bond        0.12846 (  212)
  hydrogen bonds       : angle       4.53104 (  510)

*********************** 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  : 0.148 
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  147 MET cc_start: 0.8776 (mtp) cc_final: 0.8398 (mtt)
REVERT: B  157 ASP cc_start: 0.9117 (t0) cc_final: 0.8817 (t0)
REVERT: B  166 ASP cc_start: 0.8776 (m-30) cc_final: 0.8424 (m-30)
REVERT: B  195 SER cc_start: 0.9390 (t) cc_final: 0.8737 (m)
REVERT: B  206 SER cc_start: 0.8836 (m) cc_final: 0.8560 (p)
REVERT: A   44 MET cc_start: 0.5281 (tmm) cc_final: 0.3599 (tmm)
REVERT: A  115 TYR cc_start: 0.9514 (t80) cc_final: 0.8864 (t80)
REVERT: A  140 ASN cc_start: 0.9171 (t0) cc_final: 0.8938 (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: 0.8847 (pm20)
  outliers start: 2
  outliers final: 2
  residues processed: 65
  average time/residue: 0.0985
  time to fit residues: 8.1221
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  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 24 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   chunk 56 optimal weight:   20.0000
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:   20.0000
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:   20.0000
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 58 optimal weight:   10.0000
   overall best weight:    5.7590

-------------------------------------------------------------------------------
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 = 0.2936 r_free = 0.2936 target = 0.038314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.029106 restraints weight = 49163.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.030206 restraints weight = 25539.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.030963 restraints weight = 16611.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.031517 restraints weight = 12284.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.031889 restraints weight = 9862.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2687
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2687 r_free = 0.2687    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 = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2676
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6026  Z= 0.245
  Angle     :  0.613   7.885   8487  Z= 0.314
  Chirality :  0.040   0.160   1002
  Planarity :  0.003   0.023    837
  Dihedral  : 19.381  79.166   1658
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.36), residues: 541
  helix:  1.20 (0.57), residues: 97
  sheet:  1.04 (0.38), residues: 186
  loop : -0.16 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  99 
 TYR   0.017   0.002   TYR B 127 
 PHE   0.026   0.002   PHE B 297 
 TRP   0.016   0.002   TRP B  93 
 HIS   0.004   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 6026)
  covalent geometry    : angle       0.61338 ( 8487)
  hydrogen bonds       : bond        0.06356 (  212)
  hydrogen bonds       : angle       4.37472 (  510)

*********************** 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
  40 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.9392 (pttt) cc_final: 0.8994 (mtmm)
REVERT: B  168 LYS cc_start: 0.8995 (mttp) cc_final: 0.8724 (mmmm)
REVERT: A   27 SER cc_start: 0.9563 (m) cc_final: 0.9263 (t)
REVERT: A   44 MET cc_start: 0.6507 (tmm) cc_final: 0.5249 (tmm)
REVERT: A  115 TYR cc_start: 0.9605 (t80) cc_final: 0.9217 (t80)
REVERT: A  157 MET cc_start: 0.9321 (ttm) cc_final: 0.8711 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0994
  time to fit residues: 5.1304
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  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 49 optimal weight:    7.9990
   chunk 47 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   chunk 16 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   overall best weight:    4.9988

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

Flipped N/Q/H residues before XYZ refinement:
B 279 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 = 0.2879 r_free = 0.2879 target = 0.036240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2557 r_free = 0.2557 target = 0.027193 restraints weight = 48971.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.028266 restraints weight = 24928.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.028922 restraints weight = 16033.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.029497 restraints weight = 12128.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.029866 restraints weight = 9660.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.2635
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2636
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2636 r_free = 0.2636    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 = 0.2637 r_free = 0.2637    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2637
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6026  Z= 0.209
  Angle     :  0.547   5.541   8487  Z= 0.281
  Chirality :  0.038   0.168   1002
  Planarity :  0.004   0.051    837
  Dihedral  : 19.489  80.828   1658
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.36), residues: 541
  helix:  1.55 (0.58), residues: 91
  sheet:  0.65 (0.39), residues: 175
  loop : -0.26 (0.37), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  99 
 TYR   0.008   0.001   TYR A  50 
 PHE   0.021   0.002   PHE B  69 
 TRP   0.015   0.002   TRP B  93 
 HIS   0.004   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 6026)
  covalent geometry    : angle       0.54678 ( 8487)
  hydrogen bonds       : bond        0.04912 (  212)
  hydrogen bonds       : angle       4.19592 (  510)

*********************** 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
  36 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  361 TYR cc_start: 0.8411 (m-80) cc_final: 0.8181 (m-80)
REVERT: A   27 SER cc_start: 0.9640 (m) cc_final: 0.9381 (t)
REVERT: A   44 MET cc_start: 0.6772 (tmm) cc_final: 0.5674 (tmm)
REVERT: A  115 TYR cc_start: 0.9600 (t80) cc_final: 0.9116 (t80)
REVERT: A  157 MET cc_start: 0.9276 (ttm) cc_final: 0.8974 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0878
  time to fit residues: 4.1743
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  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 27 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 21 optimal weight:    0.4980
   chunk 37 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 43 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 57 optimal weight:   20.0000
   chunk 19 optimal weight:    1.9990
   chunk 33 optimal weight:   20.0000
   overall best weight:    4.6988

-------------------------------------------------------------------------------
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 = 0.2863 r_free = 0.2863 target = 0.035654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2535 r_free = 0.2535 target = 0.026573 restraints weight = 49413.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2572 r_free = 0.2572 target = 0.027631 restraints weight = 25292.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2598 r_free = 0.2598 target = 0.028357 restraints weight = 16350.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2617 r_free = 0.2617 target = 0.028894 restraints weight = 12074.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.029271 restraints weight = 9658.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.2608
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2609
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2609 r_free = 0.2609    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 = 0.2609 r_free = 0.2609    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2609
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.3874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6026  Z= 0.199
  Angle     :  0.539   4.797   8487  Z= 0.279
  Chirality :  0.038   0.155   1002
  Planarity :  0.003   0.022    837
  Dihedral  : 19.525  81.275   1658
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.36), residues: 541
  helix:  1.68 (0.57), residues: 91
  sheet:  0.74 (0.39), residues: 176
  loop : -0.51 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  99 
 TYR   0.008   0.001   TYR B 127 
 PHE   0.019   0.002   PHE B  88 
 TRP   0.014   0.002   TRP B  93 
 HIS   0.006   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 6026)
  covalent geometry    : angle       0.53895 ( 8487)
  hydrogen bonds       : bond        0.05032 (  212)
  hydrogen bonds       : angle       4.28420 (  510)

*********************** 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
  36 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.8897 (mtm) cc_final: 0.8512 (mtt)
REVERT: B  148 LEU cc_start: 0.9588 (mt) cc_final: 0.9352 (mt)
REVERT: B  166 ASP cc_start: 0.9447 (m-30) cc_final: 0.9151 (m-30)
REVERT: A   27 SER cc_start: 0.9666 (m) cc_final: 0.9443 (t)
REVERT: A   44 MET cc_start: 0.7059 (tmm) cc_final: 0.6160 (tmm)
REVERT: A  115 TYR cc_start: 0.9593 (t80) cc_final: 0.9053 (t80)
REVERT: A  157 MET cc_start: 0.9214 (ttm) cc_final: 0.8909 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0759
  time to fit residues: 3.7206
Evaluate side-chains
  30 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 11 optimal weight:    0.0270
   chunk 57 optimal weight:   20.0000
   chunk 5 optimal weight:    7.9990
   chunk 40 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 8 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 9 optimal weight:    7.9990
   chunk 18 optimal weight:    9.9990
   chunk 14 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    4.2046

-------------------------------------------------------------------------------
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 = 0.2863 r_free = 0.2863 target = 0.035728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2537 r_free = 0.2537 target = 0.026758 restraints weight = 49543.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2572 r_free = 0.2572 target = 0.027792 restraints weight = 24959.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2599 r_free = 0.2599 target = 0.028542 restraints weight = 16139.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2619 r_free = 0.2619 target = 0.029089 restraints weight = 11725.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.029456 restraints weight = 9280.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2620
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2620 r_free = 0.2620    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 = 0.2620 r_free = 0.2620    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2620
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.4121

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= 0.178
  Angle     :  0.527   5.818   8487  Z= 0.269
  Chirality :  0.038   0.135   1002
  Planarity :  0.003   0.024    837
  Dihedral  : 19.537  81.584   1658
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.36), residues: 541
  helix:  1.71 (0.57), residues: 91
  sheet:  0.71 (0.38), residues: 183
  loop : -0.51 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  99 
 TYR   0.015   0.001   TYR B 361 
 PHE   0.014   0.001   PHE B  88 
 TRP   0.015   0.002   TRP A 206 
 HIS   0.007   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 6026)
  covalent geometry    : angle       0.52677 ( 8487)
  hydrogen bonds       : bond        0.04618 (  212)
  hydrogen bonds       : angle       4.22265 (  510)

*********************** 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
  32 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.9104 (mtm) cc_final: 0.8632 (mtm)
REVERT: B  148 LEU cc_start: 0.9626 (mt) cc_final: 0.9395 (mt)
REVERT: A   27 SER cc_start: 0.9674 (m) cc_final: 0.9448 (t)
REVERT: A   44 MET cc_start: 0.7118 (tmm) cc_final: 0.6209 (tmm)
REVERT: A  115 TYR cc_start: 0.9587 (t80) cc_final: 0.9021 (t80)
REVERT: A  142 MET cc_start: 0.9710 (mmm) cc_final: 0.9411 (mmp)
REVERT: A  157 MET cc_start: 0.9256 (ttm) cc_final: 0.9034 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0755
  time to fit residues: 3.3711
Evaluate side-chains
  29 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 4 optimal weight:    8.9990
   chunk 52 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 28 optimal weight:    7.9990
   overall best weight:    5.3990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.035081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2511 r_free = 0.2511 target = 0.026321 restraints weight = 50708.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2548 r_free = 0.2548 target = 0.027354 restraints weight = 25640.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2572 r_free = 0.2572 target = 0.028049 restraints weight = 16536.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.028562 restraints weight = 12238.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2605 r_free = 0.2605 target = 0.028927 restraints weight = 9749.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2587
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2587 r_free = 0.2587    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 = 0.2587 r_free = 0.2587    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2587
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.4510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6026  Z= 0.227
  Angle     :  0.578   6.268   8487  Z= 0.298
  Chirality :  0.039   0.164   1002
  Planarity :  0.003   0.024    837
  Dihedral  : 19.693  83.407   1658
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.36), residues: 541
  helix:  1.46 (0.55), residues: 91
  sheet:  0.60 (0.39), residues: 174
  loop : -0.61 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  99 
 TYR   0.019   0.002   TYR B 361 
 PHE   0.019   0.002   PHE B 297 
 TRP   0.017   0.002   TRP A 206 
 HIS   0.007   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 6026)
  covalent geometry    : angle       0.57849 ( 8487)
  hydrogen bonds       : bond        0.05550 (  212)
  hydrogen bonds       : angle       4.43465 (  510)

*********************** 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
  29 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.9074 (mtm) cc_final: 0.8697 (mtt)
REVERT: B  148 LEU cc_start: 0.9619 (mt) cc_final: 0.9347 (mt)
REVERT: B  168 LYS cc_start: 0.9067 (mmmm) cc_final: 0.8643 (mmmm)
REVERT: A   27 SER cc_start: 0.9709 (m) cc_final: 0.9509 (t)
REVERT: A   44 MET cc_start: 0.7234 (tmm) cc_final: 0.6348 (tmm)
REVERT: A  115 TYR cc_start: 0.9597 (t80) cc_final: 0.9020 (t80)
REVERT: A  142 MET cc_start: 0.9659 (mmm) cc_final: 0.9414 (mmp)
REVERT: A  157 MET cc_start: 0.9299 (ttm) cc_final: 0.9088 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0637
  time to fit residues: 2.7564
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  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 24 optimal weight:    7.9990
   chunk 48 optimal weight:    8.9990
   chunk 10 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    2.9388

-------------------------------------------------------------------------------
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 = 0.2867 r_free = 0.2867 target = 0.036067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2543 r_free = 0.2543 target = 0.027070 restraints weight = 48719.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2579 r_free = 0.2579 target = 0.028114 restraints weight = 24514.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.028862 restraints weight = 15791.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.029386 restraints weight = 11491.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.029772 restraints weight = 9196.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2622
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2622 r_free = 0.2622    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 = 0.2621 r_free = 0.2621    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2621
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.4459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6026  Z= 0.135
  Angle     :  0.497   5.046   8487  Z= 0.254
  Chirality :  0.038   0.137   1002
  Planarity :  0.003   0.025    837
  Dihedral  : 19.560  82.470   1658
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.37), residues: 541
  helix:  1.61 (0.56), residues: 91
  sheet:  0.77 (0.39), residues: 175
  loop : -0.53 (0.38), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 170 
 TYR   0.011   0.001   TYR A 186 
 PHE   0.013   0.001   PHE B  88 
 TRP   0.018   0.001   TRP A 206 
 HIS   0.013   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6026)
  covalent geometry    : angle       0.49690 ( 8487)
  hydrogen bonds       : bond        0.04095 (  212)
  hydrogen bonds       : angle       4.09528 (  510)

*********************** 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
  35 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.9042 (mtm) cc_final: 0.8676 (mtt)
REVERT: B  148 LEU cc_start: 0.9655 (mt) cc_final: 0.9416 (mt)
REVERT: B  168 LYS cc_start: 0.9070 (mmmm) cc_final: 0.8594 (mmmm)
REVERT: A   27 SER cc_start: 0.9704 (m) cc_final: 0.9495 (t)
REVERT: A   44 MET cc_start: 0.7127 (tmm) cc_final: 0.6416 (tmm)
REVERT: A  115 TYR cc_start: 0.9549 (t80) cc_final: 0.8956 (t80)
REVERT: A  142 MET cc_start: 0.9673 (mmm) cc_final: 0.9413 (mmp)
REVERT: A  157 MET cc_start: 0.9293 (ttm) cc_final: 0.9081 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0661
  time to fit residues: 3.4063
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  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 49 optimal weight:    9.9990
   chunk 52 optimal weight:    0.1980
   chunk 47 optimal weight:    0.9990
   chunk 59 optimal weight:   20.0000
   chunk 39 optimal weight:    8.9990
   chunk 18 optimal weight:    7.9990
   chunk 55 optimal weight:   20.0000
   chunk 16 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    4.2388

-------------------------------------------------------------------------------
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 = 0.2851 r_free = 0.2851 target = 0.035436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2527 r_free = 0.2527 target = 0.026615 restraints weight = 49581.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2564 r_free = 0.2564 target = 0.027644 restraints weight = 25330.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2592 r_free = 0.2592 target = 0.028370 restraints weight = 16430.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2612 r_free = 0.2612 target = 0.028895 restraints weight = 11985.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.029232 restraints weight = 9570.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2603
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2603 r_free = 0.2603    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 = 0.2603 r_free = 0.2603    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2603
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.4693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6026  Z= 0.181
  Angle     :  0.537   5.448   8487  Z= 0.275
  Chirality :  0.038   0.152   1002
  Planarity :  0.003   0.025    837
  Dihedral  : 19.637  83.291   1658
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.37), residues: 541
  helix:  1.53 (0.56), residues: 91
  sheet:  0.60 (0.39), residues: 177
  loop : -0.52 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  99 
 TYR   0.012   0.001   TYR B 361 
 PHE   0.019   0.002   PHE B  88 
 TRP   0.018   0.002   TRP A 206 
 HIS   0.009   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 6026)
  covalent geometry    : angle       0.53742 ( 8487)
  hydrogen bonds       : bond        0.04809 (  212)
  hydrogen bonds       : angle       4.21034 (  510)

*********************** 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
  34 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.9059 (mtm) cc_final: 0.8703 (mtt)
REVERT: B  148 LEU cc_start: 0.9645 (mt) cc_final: 0.9381 (mt)
REVERT: A   44 MET cc_start: 0.7209 (tmm) cc_final: 0.6515 (tmm)
REVERT: A  115 TYR cc_start: 0.9572 (t80) cc_final: 0.8997 (t80)
REVERT: A  142 MET cc_start: 0.9668 (mmm) cc_final: 0.9433 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0670
  time to fit residues: 3.3525
Evaluate side-chains
  29 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    9.9990
   chunk 40 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 3 optimal weight:    0.3980
   chunk 18 optimal weight:    6.9990
   chunk 28 optimal weight:    0.7980
   chunk 8 optimal weight:   10.0000
   chunk 2 optimal weight:    8.9990
   overall best weight:    2.4386

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

Flipped N/Q/H residues before XYZ refinement:
B 325 GLN
A 247 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.036367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2557 r_free = 0.2557 target = 0.027432 restraints weight = 48941.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2594 r_free = 0.2594 target = 0.028497 restraints weight = 24433.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.029263 restraints weight = 15577.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2642 r_free = 0.2642 target = 0.029811 restraints weight = 11302.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.030167 restraints weight = 8944.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2636
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2636 r_free = 0.2636    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 = 0.2635 r_free = 0.2635    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2635
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.4667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6026  Z= 0.120
  Angle     :  0.502   5.936   8487  Z= 0.253
  Chirality :  0.038   0.155   1002
  Planarity :  0.003   0.026    837
  Dihedral  : 19.526  81.737   1658
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.37), residues: 541
  helix:  1.72 (0.57), residues: 91
  sheet:  0.79 (0.39), residues: 177
  loop : -0.42 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 170 
 TYR   0.008   0.001   TYR A 186 
 PHE   0.016   0.001   PHE B  88 
 TRP   0.019   0.002   TRP A 206 
 HIS   0.008   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6026)
  covalent geometry    : angle       0.50228 ( 8487)
  hydrogen bonds       : bond        0.03813 (  212)
  hydrogen bonds       : angle       4.06015 (  510)

*********************** 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
  34 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.9044 (mtm) cc_final: 0.8684 (mtt)
REVERT: B  148 LEU cc_start: 0.9640 (mt) cc_final: 0.9387 (mt)
REVERT: B  168 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8652 (mmmm)
REVERT: A   44 MET cc_start: 0.7094 (tmm) cc_final: 0.6380 (tmm)
REVERT: A  115 TYR cc_start: 0.9542 (t80) cc_final: 0.8937 (t80)
REVERT: A  142 MET cc_start: 0.9661 (mmm) cc_final: 0.9409 (mmp)
REVERT: A  184 TYR cc_start: 0.9180 (m-80) cc_final: 0.8846 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0616
  time to fit residues: 3.0852
Evaluate side-chains
  29 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 54 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 48 optimal weight:    0.5980
   chunk 5 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 53 optimal weight:    6.9990
   chunk 42 optimal weight:   10.0000
   chunk 55 optimal weight:   20.0000
   chunk 1 optimal weight:    3.9990
   chunk 25 optimal weight:    8.9990
   overall best weight:    5.3188

-------------------------------------------------------------------------------
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 = 0.2833 r_free = 0.2833 target = 0.034918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2511 r_free = 0.2511 target = 0.026242 restraints weight = 52530.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2547 r_free = 0.2547 target = 0.027247 restraints weight = 26640.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2574 r_free = 0.2574 target = 0.027955 restraints weight = 17283.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.028473 restraints weight = 12625.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2606 r_free = 0.2606 target = 0.028783 restraints weight = 10073.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2580
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2580 r_free = 0.2580    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 = 0.2580 r_free = 0.2580    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2580
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.4986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6026  Z= 0.221
  Angle     :  0.578   6.136   8487  Z= 0.297
  Chirality :  0.039   0.131   1002
  Planarity :  0.003   0.024    837
  Dihedral  : 19.738  84.748   1658
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 15.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.37), residues: 541
  helix:  1.43 (0.56), residues: 91
  sheet:  0.60 (0.39), residues: 183
  loop : -0.47 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 170 
 TYR   0.012   0.002   TYR B 361 
 PHE   0.020   0.002   PHE B  88 
 TRP   0.019   0.002   TRP A 206 
 HIS   0.009   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 6026)
  covalent geometry    : angle       0.57790 ( 8487)
  hydrogen bonds       : bond        0.05489 (  212)
  hydrogen bonds       : angle       4.38298 (  510)

********************** 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
  33 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.9102 (mtm) cc_final: 0.8748 (mtt)
REVERT: B  148 LEU cc_start: 0.9671 (mt) cc_final: 0.9387 (mt)
REVERT: B  168 LYS cc_start: 0.9108 (mmmm) cc_final: 0.8697 (mmmm)
REVERT: A   44 MET cc_start: 0.7417 (tmm) cc_final: 0.6499 (tmm)
REVERT: A  142 MET cc_start: 0.9652 (mmm) cc_final: 0.9405 (mmp)
REVERT: A  184 TYR cc_start: 0.9159 (m-80) cc_final: 0.8865 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0689
  time to fit residues: 3.3135
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  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 60 optimal weight:   10.0000
   chunk 33 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 36 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    1.8786

-------------------------------------------------------------------------------
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 = 0.2879 r_free = 0.2879 target = 0.036287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2559 r_free = 0.2559 target = 0.027450 restraints weight = 48533.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2596 r_free = 0.2596 target = 0.028505 restraints weight = 24567.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.029248 restraints weight = 15750.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.029803 restraints weight = 11526.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.030146 restraints weight = 9172.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2634
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2634 r_free = 0.2634    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 = 0.2633 r_free = 0.2633    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2633
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.4884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6026  Z= 0.107
  Angle     :  0.496   6.866   8487  Z= 0.249
  Chirality :  0.037   0.136   1002
  Planarity :  0.003   0.027    837
  Dihedral  : 19.483  82.395   1658
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.37), residues: 541
  helix:  1.75 (0.57), residues: 91
  sheet:  0.86 (0.39), residues: 181
  loop : -0.37 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 170 
 TYR   0.008   0.001   TYR A 186 
 PHE   0.016   0.001   PHE B  88 
 TRP   0.019   0.001   TRP A 206 
 HIS   0.008   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 6026)
  covalent geometry    : angle       0.49603 ( 8487)
  hydrogen bonds       : bond        0.03676 (  212)
  hydrogen bonds       : angle       3.97223 (  510)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 854.95 seconds
wall clock time: 15 minutes 30.03 seconds (930.03 seconds total)