Starting phenix.real_space_refine
on Thu Jul  2 02:48:04 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8d9l_27265/07_2026/8d9l_27265.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d9l_27265/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d9l_27265/07_2026/8d9l_27265.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d9l_27265/07_2026/8d9l_27265.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d9l_27265/07_2026/8d9l_27265.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d9l_27265/07_2026/8d9l_27265.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8d9l_27265/07_2026/8d9l_27265.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8d9l_27265/07_2026/8d9l_27265.cif"
  }
  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-6108/lib/python3.11/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: 1.48, per 1000 atoms: 0.26
  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: 0.54
  Conformation dependent library (CDL) restraints added in 330.3 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: 0.86
  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: 1.20

  Time building geometry restraints manager: 0.70 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: 3206
       15.87 -    31.74: 153
       31.74 -    47.61: 29
       47.61 -    63.47: 9
       63.47 -    79.34: 4
  Dihedral angle restraints: 3401
    sinusoidal: 1806
      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 3398 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:             0.180
  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:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     8.370
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
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  :  9.712  79.343   2369
  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/Z
  covalent geometry    : bond        0.00205 /  0.10 ( 6026)
  covalent geometry    : angle       0.44416 /  0.20 ( 8487)
  hydrogen bonds       : bond        0.12846 /  8.26 (  212)
  hydrogen bonds       : angle       4.53104 /  3.04 (  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  : 0.223 
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: 0.0866
  time to fit residues: 7.2912
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  : 0.179 
-------------------------------------------------------------------------------
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...
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 = 0.2931 r_free = 0.2931 target = 0.038046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.028756 restraints weight = 48868.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.029862 restraints weight = 25376.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.030636 restraints weight = 16504.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.031171 restraints weight = 12183.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.031551 restraints weight = 9789.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2691
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2691 r_free = 0.2691    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 = 0.2679 r_free = 0.2679    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (17 function evaluations)
r_final: 0.2679
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6026  Z= 0.243
  Angle     :  0.602   7.603   8487  Z= 0.307
  Chirality :  0.039   0.161   1002
  Planarity :  0.003   0.022    837
  Dihedral  : 10.249  79.697   1370
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  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:  0.77 (0.36), residues: 541
  helix:  1.26 (0.58), residues: 97
  sheet:  1.07 (0.38), residues: 186
  loop : -0.14 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  99 
 TYR   0.015   0.002   TYR B 127 
 PHE   0.024   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/Z
  covalent geometry    : bond        0.00487 /  0.24 ( 6026)
  covalent geometry    : angle       0.60203 /  0.31 ( 8487)
  hydrogen bonds       : bond        0.06233 /  4.26 (  212)
  hydrogen bonds       : angle       4.32127 /  2.89 (  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
  41 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.9415 (pttt) cc_final: 0.9041 (mtmm)
REVERT: B  168 LYS cc_start: 0.9015 (mttp) cc_final: 0.8724 (mmmm)
REVERT: A   27 SER cc_start: 0.9565 (m) cc_final: 0.9272 (t)
REVERT: A   44 MET cc_start: 0.6455 (tmm) cc_final: 0.5178 (tmm)
REVERT: A  115 TYR cc_start: 0.9591 (t80) cc_final: 0.9193 (t80)
REVERT: A  157 MET cc_start: 0.9356 (ttm) cc_final: 0.8798 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0798
  time to fit residues: 4.2062
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  : 0.212 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 49 optimal weight:   10.0000
   chunk 47 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 3 optimal weight:    9.9990
   chunk 16 optimal weight:    8.9990
   chunk 6 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   overall best weight:    3.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 272 GLN
B 279 GLN
B 325 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.036959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2582 r_free = 0.2582 target = 0.027795 restraints weight = 48209.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.028901 restraints weight = 24380.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.029639 restraints weight = 15626.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.030208 restraints weight = 11541.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.030587 restraints weight = 9175.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2665
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2665 r_free = 0.2665    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (12 function evaluations)
r_final: 0.2666
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.2985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6026  Z= 0.174
  Angle     :  0.507   5.884   8487  Z= 0.261
  Chirality :  0.037   0.167   1002
  Planarity :  0.003   0.019    837
  Dihedral  : 10.425  81.547   1370
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  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:  1.68 (0.59), residues: 91
  sheet:  0.93 (0.39), residues: 172
  loop : -0.18 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  99 
 TYR   0.007   0.001   TYR A  50 
 PHE   0.019   0.002   PHE B  69 
 TRP   0.014   0.002   TRP B  93 
 HIS   0.003   0.001   HIS A 214 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.17 ( 6026)
  covalent geometry    : angle       0.50741 /  0.26 ( 8487)
  hydrogen bonds       : bond        0.04341 /  2.88 (  212)
  hydrogen bonds       : angle       4.04392 /  2.68 (  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
  41 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 LYS cc_start: 0.9387 (pttt) cc_final: 0.8956 (mtmm)
REVERT: B  157 ASP cc_start: 0.9152 (t70) cc_final: 0.8799 (t0)
REVERT: B  168 LYS cc_start: 0.9020 (mttp) cc_final: 0.8773 (mmmm)
REVERT: A   27 SER cc_start: 0.9591 (m) cc_final: 0.9314 (t)
REVERT: A   44 MET cc_start: 0.6580 (tmm) cc_final: 0.5705 (tmm)
REVERT: A  115 TYR cc_start: 0.9593 (t80) cc_final: 0.9129 (t80)
REVERT: A  157 MET cc_start: 0.9253 (ttm) cc_final: 0.8948 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0891
  time to fit residues: 4.8527
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  : 0.180 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 7 optimal weight:   20.0000
   chunk 21 optimal weight:    0.7980
   chunk 37 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 43 optimal weight:    8.9990
   chunk 10 optimal weight:   10.0000
   chunk 57 optimal weight:   20.0000
   chunk 19 optimal weight:    0.5980
   chunk 33 optimal weight:   20.0000
   overall best weight:    3.6786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.2896 r_free = 0.2896 target = 0.036693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2571 r_free = 0.2571 target = 0.027481 restraints weight = 48437.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2608 r_free = 0.2608 target = 0.028572 restraints weight = 24832.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.029313 restraints weight = 16117.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.029870 restraints weight = 11906.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2669 r_free = 0.2669 target = 0.030262 restraints weight = 9492.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2654
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2654 r_free = 0.2654    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 = 0.2655 r_free = 0.2655    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2655
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.3480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6026  Z= 0.161
  Angle     :  0.500   4.741   8487  Z= 0.256
  Chirality :  0.038   0.157   1002
  Planarity :  0.003   0.021    837
  Dihedral  : 10.560  81.543   1370
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 11.25
  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:  0.64 (0.36), residues: 541
  helix:  1.71 (0.58), residues: 91
  sheet:  0.96 (0.38), residues: 184
  loop : -0.39 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  99 
 TYR   0.007   0.001   TYR B 361 
 PHE   0.010   0.001   PHE B  88 
 TRP   0.012   0.001   TRP B  93 
 HIS   0.008   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.16 ( 6026)
  covalent geometry    : angle       0.50046 /  0.26 ( 8487)
  hydrogen bonds       : bond        0.04314 /  2.87 (  212)
  hydrogen bonds       : angle       4.12148 /  2.77 (  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  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.8888 (mtm) cc_final: 0.8337 (mtm)
REVERT: B  166 ASP cc_start: 0.9227 (m-30) cc_final: 0.9007 (m-30)
REVERT: A   27 SER cc_start: 0.9627 (m) cc_final: 0.9382 (t)
REVERT: A   44 MET cc_start: 0.6752 (tmm) cc_final: 0.5708 (tmm)
REVERT: A  115 TYR cc_start: 0.9602 (t80) cc_final: 0.9095 (t80)
REVERT: A  157 MET cc_start: 0.9229 (ttm) cc_final: 0.8886 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0739
  time to fit residues: 3.6662
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 11 optimal weight:    0.0870
   chunk 57 optimal weight:   20.0000
   chunk 5 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 3 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 38 optimal weight:    0.6980
   chunk 9 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 14 optimal weight:    8.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    4.1564

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.035958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2547 r_free = 0.2547 target = 0.026891 restraints weight = 49681.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.027966 restraints weight = 24971.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.028675 restraints weight = 16074.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.029081 restraints weight = 11908.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.029549 restraints weight = 9831.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.2624
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    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 = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.3844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6026  Z= 0.178
  Angle     :  0.517   4.717   8487  Z= 0.265
  Chirality :  0.038   0.137   1002
  Planarity :  0.003   0.022    837
  Dihedral  : 10.708  81.578   1370
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  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:  0.52 (0.36), residues: 541
  helix:  1.59 (0.57), residues: 91
  sheet:  0.84 (0.38), residues: 183
  loop : -0.42 (0.37), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  99 
 TYR   0.009   0.001   TYR B 361 
 PHE   0.017   0.002   PHE B  88 
 TRP   0.013   0.002   TRP A 206 
 HIS   0.008   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.18 ( 6026)
  covalent geometry    : angle       0.51675 /  0.26 ( 8487)
  hydrogen bonds       : bond        0.04632 /  3.08 (  212)
  hydrogen bonds       : angle       4.18811 /  2.81 (  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
  35 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  166 ASP cc_start: 0.9415 (m-30) cc_final: 0.9107 (m-30)
REVERT: A   44 MET cc_start: 0.6907 (tmm) cc_final: 0.5975 (tmm)
REVERT: A  115 TYR cc_start: 0.9595 (t80) cc_final: 0.9054 (t80)
REVERT: A  142 MET cc_start: 0.9723 (mmm) cc_final: 0.9496 (mmm)
REVERT: A  157 MET cc_start: 0.9240 (ttm) cc_final: 0.8940 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0777
  time to fit residues: 3.6439
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  : 0.151 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   chunk 45 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   chunk 4 optimal weight:    9.9990
   chunk 52 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 3 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    4.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.035550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2528 r_free = 0.2528 target = 0.026697 restraints weight = 50080.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2564 r_free = 0.2564 target = 0.027732 restraints weight = 25582.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2590 r_free = 0.2590 target = 0.028450 restraints weight = 16653.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2608 r_free = 0.2608 target = 0.028963 restraints weight = 12252.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.029342 restraints weight = 9822.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.2602
-------------------------------------------------------------------------------
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 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2603
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.4177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6026  Z= 0.203
  Angle     :  0.548   5.542   8487  Z= 0.281
  Chirality :  0.039   0.151   1002
  Planarity :  0.003   0.022    837
  Dihedral  : 10.894  81.657   1370
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  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:  0.44 (0.36), residues: 541
  helix:  1.51 (0.57), residues: 91
  sheet:  0.78 (0.38), residues: 181
  loop : -0.44 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 168 
 TYR   0.011   0.001   TYR A 186 
 PHE   0.018   0.002   PHE B 297 
 TRP   0.014   0.002   TRP A 206 
 HIS   0.007   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00414 /  0.20 ( 6026)
  covalent geometry    : angle       0.54765 /  0.28 ( 8487)
  hydrogen bonds       : bond        0.05089 /  3.40 (  212)
  hydrogen bonds       : angle       4.34143 /  2.94 (  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
  32 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.9013 (mtm) cc_final: 0.8529 (mtm)
REVERT: B  148 LEU cc_start: 0.9601 (mt) cc_final: 0.9373 (mt)
REVERT: B  168 LYS cc_start: 0.9086 (mmmm) cc_final: 0.8620 (mmmm)
REVERT: A   44 MET cc_start: 0.7078 (tmm) cc_final: 0.6112 (tmm)
REVERT: A  115 TYR cc_start: 0.9592 (t80) cc_final: 0.9030 (t80)
REVERT: A  157 MET cc_start: 0.9260 (ttm) cc_final: 0.9028 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0654
  time to fit residues: 2.9786
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  : 0.212 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 16 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 24 optimal weight:    8.9990
   chunk 48 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 30 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 0 optimal weight:    9.9990
   overall best weight:    1.3982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.2909 r_free = 0.2909 target = 0.037347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2592 r_free = 0.2592 target = 0.028221 restraints weight = 47849.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.029325 restraints weight = 23953.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.030120 restraints weight = 15240.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.030632 restraints weight = 11101.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.031038 restraints weight = 8915.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2665
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2665 r_free = 0.2665    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2665 r_free = 0.2665    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2665
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.4068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6026  Z= 0.095
  Angle     :  0.485   4.961   8487  Z= 0.242
  Chirality :  0.038   0.201   1002
  Planarity :  0.002   0.023    837
  Dihedral  : 10.434  81.580   1370
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  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:  0.68 (0.37), residues: 541
  helix:  1.83 (0.57), residues: 91
  sheet:  1.00 (0.39), residues: 181
  loop : -0.39 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 158 
 TYR   0.010   0.001   TYR A 186 
 PHE   0.014   0.001   PHE B  88 
 TRP   0.017   0.001   TRP A 206 
 HIS   0.012   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00204 /  0.09 ( 6026)
  covalent geometry    : angle       0.48475 /  0.24 ( 8487)
  hydrogen bonds       : bond        0.03465 /  2.21 (  212)
  hydrogen bonds       : angle       3.92331 /  2.62 (  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
  42 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.9037 (mtm) cc_final: 0.8561 (mtm)
REVERT: B  166 ASP cc_start: 0.9506 (m-30) cc_final: 0.9243 (m-30)
REVERT: B  168 LYS cc_start: 0.9109 (mmmm) cc_final: 0.8631 (mmmm)
REVERT: A   44 MET cc_start: 0.6841 (tmm) cc_final: 0.5902 (tmm)
REVERT: A  115 TYR cc_start: 0.9550 (t80) cc_final: 0.8968 (t80)
REVERT: A  140 ASN cc_start: 0.9575 (t0) cc_final: 0.9329 (t0)
REVERT: A  142 MET cc_start: 0.9513 (mmm) cc_final: 0.9231 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0541
  time to fit residues: 3.4157
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  : 0.184 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 59 optimal weight:   20.0000
   chunk 39 optimal weight:    9.9990
   chunk 18 optimal weight:   20.0000
   chunk 55 optimal weight:   20.0000
   chunk 16 optimal weight:    9.9990
   chunk 28 optimal weight:    0.8980
   chunk 21 optimal weight:    7.9990
   overall best weight:    4.1786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.2859 r_free = 0.2859 target = 0.035632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2536 r_free = 0.2536 target = 0.026763 restraints weight = 49136.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2572 r_free = 0.2572 target = 0.027807 restraints weight = 24817.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2599 r_free = 0.2599 target = 0.028544 restraints weight = 15990.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.029071 restraints weight = 11692.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2632 r_free = 0.2632 target = 0.029439 restraints weight = 9308.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2615
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2615 r_free = 0.2615    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 = 0.2615 r_free = 0.2615    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2615
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.4376

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= 0.174
  Angle     :  0.524   5.435   8487  Z= 0.267
  Chirality :  0.038   0.144   1002
  Planarity :  0.003   0.022    837
  Dihedral  : 10.754  80.822   1370
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.58 (0.37), residues: 541
  helix:  1.76 (0.58), residues: 91
  sheet:  0.79 (0.39), residues: 183
  loop : -0.35 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  99 
 TYR   0.007   0.001   TYR A  50 
 PHE   0.018   0.002   PHE B  88 
 TRP   0.016   0.002   TRP A 206 
 HIS   0.010   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.17 ( 6026)
  covalent geometry    : angle       0.52384 /  0.27 ( 8487)
  hydrogen bonds       : bond        0.04617 /  3.06 (  212)
  hydrogen bonds       : angle       4.18327 /  2.83 (  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  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.9021 (mtm) cc_final: 0.8539 (mtm)
REVERT: B  148 LEU cc_start: 0.9600 (mt) cc_final: 0.9376 (mt)
REVERT: B  168 LYS cc_start: 0.9067 (mmmm) cc_final: 0.8618 (mmmm)
REVERT: A   44 MET cc_start: 0.7078 (tmm) cc_final: 0.6079 (tmm)
REVERT: A  115 TYR cc_start: 0.9595 (t80) cc_final: 0.9037 (t80)
REVERT: A  140 ASN cc_start: 0.9531 (t0) cc_final: 0.9323 (t0)
REVERT: A  142 MET cc_start: 0.9547 (mmm) cc_final: 0.9323 (mmm)
REVERT: A  184 TYR cc_start: 0.9207 (m-80) cc_final: 0.8937 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0548
  time to fit residues: 2.7963
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  : 0.282 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 51 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   chunk 18 optimal weight:    8.9990
   chunk 28 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.035703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2535 r_free = 0.2535 target = 0.026846 restraints weight = 49414.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2572 r_free = 0.2572 target = 0.027898 restraints weight = 24811.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2599 r_free = 0.2599 target = 0.028645 restraints weight = 15929.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.029164 restraints weight = 11641.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.029509 restraints weight = 9263.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.2612
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2613
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2613 r_free = 0.2613    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 = 0.2613 r_free = 0.2613    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2613
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.4610

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= 0.169
  Angle     :  0.529   5.934   8487  Z= 0.269
  Chirality :  0.038   0.132   1002
  Planarity :  0.003   0.023    837
  Dihedral  : 10.862  81.412   1370
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.57 (0.37), residues: 541
  helix:  1.76 (0.57), residues: 91
  sheet:  0.70 (0.38), residues: 184
  loop : -0.28 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 170 
 TYR   0.007   0.001   TYR A 186 
 PHE   0.018   0.002   PHE B  88 
 TRP   0.017   0.002   TRP A 206 
 HIS   0.009   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.17 ( 6026)
  covalent geometry    : angle       0.52907 /  0.27 ( 8487)
  hydrogen bonds       : bond        0.04511 /  2.99 (  212)
  hydrogen bonds       : angle       4.17685 /  2.82 (  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
  32 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.9059 (mtm) cc_final: 0.8672 (mtt)
REVERT: B  148 LEU cc_start: 0.9645 (mt) cc_final: 0.9390 (mt)
REVERT: B  168 LYS cc_start: 0.9074 (mmmm) cc_final: 0.8626 (mmmm)
REVERT: A   44 MET cc_start: 0.7101 (tmm) cc_final: 0.6114 (tmm)
REVERT: A  115 TYR cc_start: 0.9587 (t80) cc_final: 0.9012 (t80)
REVERT: A  142 MET cc_start: 0.9551 (mmm) cc_final: 0.9312 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0592
  time to fit residues: 2.8175
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  : 0.185 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 54 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 53 optimal weight:    6.9990
   chunk 42 optimal weight:    8.9990
   chunk 55 optimal weight:   20.0000
   chunk 1 optimal weight:    0.9990
   chunk 25 optimal weight:    9.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.035047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2516 r_free = 0.2516 target = 0.026327 restraints weight = 51711.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2551 r_free = 0.2551 target = 0.027336 restraints weight = 26378.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2578 r_free = 0.2578 target = 0.028045 restraints weight = 17138.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.028569 restraints weight = 12601.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2611 r_free = 0.2611 target = 0.028920 restraints weight = 10070.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.2584
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2586
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2586 r_free = 0.2586    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 = 0.2586 r_free = 0.2586    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2586
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.4926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6026  Z= 0.202
  Angle     :  0.564   6.931   8487  Z= 0.288
  Chirality :  0.039   0.132   1002
  Planarity :  0.003   0.022    837
  Dihedral  : 11.217  84.446   1370
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  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:  0.37 (0.37), residues: 541
  helix:  1.55 (0.56), residues: 91
  sheet:  0.47 (0.38), residues: 188
  loop : -0.31 (0.40), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 170 
 TYR   0.008   0.001   TYR A  50 
 PHE   0.019   0.002   PHE B  88 
 TRP   0.018   0.002   TRP B 252 
 HIS   0.009   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00416 /  0.20 ( 6026)
  covalent geometry    : angle       0.56419 /  0.29 ( 8487)
  hydrogen bonds       : bond        0.05197 /  3.50 (  212)
  hydrogen bonds       : angle       4.35640 /  2.95 (  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  : 0.185 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 MET cc_start: 0.9117 (mtm) cc_final: 0.8752 (mtt)
REVERT: B  148 LEU cc_start: 0.9667 (mt) cc_final: 0.9375 (mt)
REVERT: B  168 LYS cc_start: 0.9089 (mmmm) cc_final: 0.8634 (mmmm)
REVERT: A   44 MET cc_start: 0.7195 (tmm) cc_final: 0.6245 (tmm)
REVERT: A  115 TYR cc_start: 0.9569 (t80) cc_final: 0.9011 (t80)
REVERT: A  142 MET cc_start: 0.9546 (mmm) cc_final: 0.9315 (mmm)
REVERT: A  184 TYR cc_start: 0.9202 (m-80) cc_final: 0.8828 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0647
  time to fit residues: 3.0816
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  : 0.186 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 33 optimal weight:   20.0000
   chunk 2 optimal weight:    0.0970
   chunk 36 optimal weight:    6.9990
   chunk 40 optimal weight:    8.9990
   chunk 53 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 43 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    4.2186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.035284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2528 r_free = 0.2528 target = 0.026619 restraints weight = 50373.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.027614 restraints weight = 25913.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2589 r_free = 0.2589 target = 0.028330 restraints weight = 16911.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.028854 restraints weight = 12436.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.029196 restraints weight = 9948.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2595
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2595 r_free = 0.2595    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 = 0.2595 r_free = 0.2595    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2595
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.5007

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= 0.178
  Angle     :  0.537   6.549   8487  Z= 0.275
  Chirality :  0.038   0.135   1002
  Planarity :  0.003   0.022    837
  Dihedral  : 11.184  85.338   1370
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.41 (0.37), residues: 541
  helix:  1.59 (0.56), residues: 91
  sheet:  0.52 (0.38), residues: 186
  loop : -0.31 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 170 
 TYR   0.006   0.001   TYR A  50 
 PHE   0.018   0.002   PHE B  88 
 TRP   0.018   0.002   TRP A 206 
 HIS   0.008   0.001   HIS A 233 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.18 ( 6026)
  covalent geometry    : angle       0.53725 /  0.27 ( 8487)
  hydrogen bonds       : bond        0.04717 /  3.14 (  212)
  hydrogen bonds       : angle       4.31690 /  2.90 (  510)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 900.33 seconds
wall clock time: 16 minutes 24.50 seconds (984.50 seconds total)