Starting phenix.real_space_refine
on Thu Jul  2 02:26:59 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8d9k_27264/07_2026/8d9k_27264.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d9k_27264/07_2026/8d9k_27264.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d9k_27264/07_2026/8d9k_27264.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d9k_27264/07_2026/8d9k_27264.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8d9k_27264/07_2026/8d9k_27264.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8d9k_27264/07_2026/8d9k_27264.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d9k_27264/07_2026/8d9k_27264.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d9k_27264/07_2026/8d9k_27264.cif"
  }
  resolution = 3.72
  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=   0.006 sd=   0.030
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      21      5.16       5
     C    3387      2.51       5
     N     993      2.21       5
     O    1242      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: 5708
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1740
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 15, 'TRANS': 198}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2578
          Classifications: {'peptide': 332}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 321}
          Chain breaks: 3
    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': 2, 'rna3p_pur': 28, 'rna3p_pyr': 29}
          Link IDs: {'rna2p': 8, 'rna3p': 56}
          Chain breaks: 1
  Residues with excluded nonbonded symmetry interactions: 43
    residue:
      pdb=" N   TYR A  37 " occ=0.88
      ... (10 atoms not shown)
      pdb=" OH  TYR A  37 " occ=0.88
    residue:
      pdb=" N   GLU A  43 " occ=0.83
      ... (7 atoms not shown)
      pdb=" OE2 GLU A  43 " occ=0.83
    residue:
      pdb=" N   ASP A  45 " occ=0.96
      ... (6 atoms not shown)
      pdb=" OD2 ASP A  45 " occ=0.96
    residue:
      pdb=" N   TYR A  50 " occ=0.90
      ... (10 atoms not shown)
      pdb=" OH  TYR A  50 " occ=0.90
    residue:
      pdb=" N   GLU A  52 " occ=0.87
      ... (7 atoms not shown)
      pdb=" OE2 GLU A  52 " occ=0.87
    residue:
      pdb=" N   PHE A  53 " occ=0.93
      ... (9 atoms not shown)
      pdb=" CZ  PHE A  53 " occ=0.93
    residue:
      pdb=" N   PHE A  54 " occ=0.88
      ... (9 atoms not shown)
      pdb=" CZ  PHE A  54 " occ=0.88
    residue:
      pdb=" N   GLU A  79 " occ=0.85
      ... (7 atoms not shown)
      pdb=" OE2 GLU A  79 " occ=0.85
    residue:
      pdb=" N   LYS A 111 " occ=0.98
      ... (7 atoms not shown)
      pdb=" NZ  LYS A 111 " occ=0.98
    residue:
      pdb=" N   ARG A 121 " occ=0.88
      ... (9 atoms not shown)
      pdb=" NH2 ARG A 121 " occ=0.88
    residue:
      pdb=" N   ARG A 138 " occ=0.99
      ... (9 atoms not shown)
      pdb=" NH2 ARG A 138 " occ=0.99
    residue:
      pdb=" N   MET A 142 " occ=0.86
      ... (6 atoms not shown)
      pdb=" CE  MET A 142 " occ=0.86
    ... (remaining 31 not shown)
  Time building chain proxies: 1.48, per 1000 atoms: 0.26
  Number of scatterers: 5708
  At special positions: 0
  Unit cell: (64.74, 100.845, 110.805, 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      21     16.00
     P      65     15.00
     O    1242      8.00
     N     993      7.00
     C    3387      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: 0.47
  Conformation dependent library (CDL) restraints added in 157.9 milliseconds
  

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1016

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 8 sheets defined
      22.7% alpha, 31.9% beta
      27 base pairs and 29 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 88 through 95
    Processing helix  chain 'A' and resid 109 through 126
    Processing helix  chain 'A' and resid 140 through 149
      removed outlier: 3.844A  pdb=" N   LEU A 145 " --> pdb=" O   ALA A 141 " (cutoff:3.500A)
      Proline residue:  A 146  - end of helix
    Processing helix  chain 'A' and resid 177 through 187
      removed outlier: 3.629A  pdb=" N   ALA A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLU A 183 " --> pdb=" O   THR A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 214
    Processing helix  chain 'A' and resid 221 through 226
      removed outlier: 4.069A  pdb=" N   SER A 226 " --> pdb=" O   GLU A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 238
      removed outlier: 3.728A  pdb=" N   HIS A 233 " --> pdb=" O   PRO A 229 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   GLY A 235 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   THR A 236 " --> pdb=" O   GLY A 232 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   THR A 238 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 248
    Processing helix  chain 'B' and resid 229 through 233
      removed outlier: 3.604A  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 343 through 348
      removed outlier: 4.398A  pdb=" N   LEU B 347 " --> pdb=" O   ASN B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 359
      removed outlier: 3.975A  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 sheet with id=AA1, first strand: chain 'A' and resid 134 through 138
      removed outlier: 5.498A  pdb=" N   VAL A  78 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 7.753A  pdb=" N   LEU A 104 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   PHE A  80 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 8.075A  pdb=" N   LEU A 106 " --> pdb=" O   PHE A  80 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ASP A  82 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   GLU A  79 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 5.548A  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: 5.865A  pdb=" N   PHE A 159 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   ILE A  83 " --> pdb=" O   PHE A 159 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   THR A 155 " --> pdb=" O   LEU A 193 " (cutoff:3.500A)
      removed outlier: 8.244A  pdb=" N   TYR A 195 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   MET A 157 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
      removed outlier: 8.186A  pdb=" N   ILE A 197 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   PHE A 159 " --> pdb=" O   ILE A 197 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   GLY A 192 " --> pdb=" O   ARG A 258 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   ILE A 255 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 6 through 10
    Processing sheet with id=AA3, first strand: chain 'B' and resid 67 through 69
      removed outlier: 6.463A  pdb=" N   LEU B  85 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   VAL B  98 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   LEU B  87 " --> pdb=" O   LEU B  96 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110
      removed outlier: 3.655A  pdb=" N   ALA B 107 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ASP B 125 " --> pdb=" O   ASP B 121 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   VAL B 126 " --> pdb=" O   GLU B 141 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 153
      removed outlier: 3.951A  pdb=" N   ASP B 150 " --> pdb=" O   ALA B 163 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ILE B 169 " --> pdb=" O   CYS B 184 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   TRP B 173 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   ILE B 180 " --> pdb=" O   TRP B 173 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 196
      removed outlier: 3.854A  pdb=" N   ARG B 193 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   THR B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   LEU B 213 " --> pdb=" O   CYS B 226 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   CYS B 226 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   LEU B 215 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 252
      removed outlier: 3.836A  pdb=" N   ARG B 248 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   CYS B 262 " --> pdb=" O   VAL B 267 " (cutoff:3.500A)
      removed outlier: 5.472A  pdb=" N   VAL B 267 " --> pdb=" O   CYS B 262 " (cutoff:3.500A)
      removed outlier: 5.605A  pdb=" N   GLN B 272 " --> pdb=" O   TYR B 282 " (cutoff:3.500A)
      removed outlier: 5.222A  pdb=" N   TYR B 282 " --> pdb=" O   GLN B 272 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   ASP B 274 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   LEU B 280 " --> pdb=" O   ASP B 274 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 292 through 298
      removed outlier: 3.981A  pdb=" N   ASP B 294 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)

    155 hydrogen bonds defined for protein.
    426 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      69 hydrogen bonds
      114 hydrogen bond angles
      0 basepair planarities
      27 basepair parallelities
      29 stacking parallelities
  Total time for adding SS restraints: 1.00

  Time building geometry restraints manager: 0.63 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: 1574
        1.34 -     1.45: 1394
        1.45 -     1.57: 2850
        1.57 -     1.69: 128
        1.69 -     1.81: 27
  Bond restraints: 5973
  Sorted by residual:
  bond pdb=" CG  PRO B  92 "
       pdb=" CD  PRO B  92 "
    ideal  model  delta    sigma   weight residual
    1.512  1.492  0.020 2.70e-02 1.37e+03 5.36e-01
  bond pdb=" N   PHE A 166 "
       pdb=" CA  PHE A 166 "
    ideal  model  delta    sigma   weight residual
    1.462  1.472 -0.010 1.54e-02 4.22e+03 4.02e-01
  bond pdb=" CA  PHE A 166 "
       pdb=" CB  PHE A 166 "
    ideal  model  delta    sigma   weight residual
    1.530  1.539 -0.009 1.54e-02 4.22e+03 3.50e-01
  bond pdb=" N   GLU B 114 "
       pdb=" CA  GLU B 114 "
    ideal  model  delta    sigma   weight residual
    1.461  1.470 -0.009 1.52e-02 4.33e+03 3.14e-01
  bond pdb=" CA  GLU B 167 "
       pdb=" CB  GLU B 167 "
    ideal  model  delta    sigma   weight residual
    1.530  1.539 -0.009 1.69e-02 3.50e+03 2.79e-01
  ... (remaining 5968 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.01: 8254
        1.01 -     2.02: 108
        2.02 -     3.03: 37
        3.03 -     4.04: 5
        4.04 -     5.06: 4
  Bond angle restraints: 8408
  Sorted by residual:
  angle pdb=" C   TYR B 361 "
        pdb=" N   LYS B 362 "
        pdb=" CA  LYS B 362 "
      ideal   model   delta    sigma   weight residual
     121.70  126.76   -5.06 1.80e+00 3.09e-01 7.89e+00
  angle pdb=" C   ASP B 166 "
        pdb=" N   GLU B 167 "
        pdb=" CA  GLU B 167 "
      ideal   model   delta    sigma   weight residual
     121.54  125.67   -4.13 1.91e+00 2.74e-01 4.68e+00
  angle pdb=" C   SER B 113 "
        pdb=" N   GLU B 114 "
        pdb=" CA  GLU B 114 "
      ideal   model   delta    sigma   weight residual
     122.07  124.77   -2.70 1.43e+00 4.89e-01 3.57e+00
  angle pdb=" C   HIS A 165 "
        pdb=" N   PHE A 166 "
        pdb=" CA  PHE A 166 "
      ideal   model   delta    sigma   weight residual
     122.08  124.50   -2.42 1.47e+00 4.63e-01 2.71e+00
  angle pdb=" CA  GLU B 167 "
        pdb=" CB  GLU B 167 "
        pdb=" CG  GLU B 167 "
      ideal   model   delta    sigma   weight residual
     114.10  117.33   -3.23 2.00e+00 2.50e-01 2.60e+00
  ... (remaining 8403 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.18: 3258
       19.18 -    38.35: 111
       38.35 -    57.53: 15
       57.53 -    76.70: 1
       76.70 -    95.88: 2
  Dihedral angle restraints: 3387
    sinusoidal: 1815
      harmonic: 1572
  Sorted by residual:
  dihedral pdb=" CA  LEU B  35 "
           pdb=" CB  LEU B  35 "
           pdb=" CG  LEU B  35 "
           pdb=" CD1 LEU B  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  134.67   45.33     3      1.50e+01 4.44e-03 8.15e+00
  dihedral pdb=" CA  LEU A 104 "
           pdb=" CB  LEU A 104 "
           pdb=" CG  LEU A 104 "
           pdb=" CD1 LEU A 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  140.47   39.53     3      1.50e+01 4.44e-03 7.01e+00
  dihedral pdb=" O4'   A C   7 "
           pdb=" C1'   A C   7 "
           pdb=" N9    A C   7 "
           pdb=" C4    A C   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -142.86   36.86     1      1.70e+01 3.46e-03 6.64e+00
  ... (remaining 3384 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 687
       0.025 -    0.049: 181
       0.049 -    0.074: 52
       0.074 -    0.098: 33
       0.098 -    0.123: 36
  Chirality restraints: 989
  Sorted by residual:
  chirality pdb=" CA  VAL B  98 "
            pdb=" N   VAL B  98 "
            pdb=" C   VAL B  98 "
            pdb=" CB  VAL B  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.78e-01
  chirality pdb=" CA  ILE B 160 "
            pdb=" N   ILE B 160 "
            pdb=" C   ILE B 160 "
            pdb=" CB  ILE B 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.71e-01
  chirality pdb=" CA  VAL B  16 "
            pdb=" N   VAL B  16 "
            pdb=" C   VAL B  16 "
            pdb=" CB  VAL B  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.64e-01
  ... (remaining 986 not shown)

  Planarity restraints: 831
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  59 "   -0.013 2.00e-02 2.50e+03   6.11e-03 1.12e+00
        pdb=" N9    G C  59 "    0.015 2.00e-02 2.50e+03
        pdb=" C8    G C  59 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    G C  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G C  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G C  59 "    0.002 2.00e-02 2.50e+03
        pdb=" O6    G C  59 "   -0.004 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 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    G C  59 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 228 "   -0.016 5.00e-02 4.00e+02   2.39e-02 9.11e-01
        pdb=" N   PRO A 229 "    0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO A 229 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 229 "   -0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 318 "   -0.015 5.00e-02 4.00e+02   2.23e-02 7.97e-01
        pdb=" N   PRO B 319 "    0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO B 319 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO B 319 "   -0.012 5.00e-02 4.00e+02
  ... (remaining 828 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1350
        2.80 -     3.32: 5002
        3.32 -     3.85: 10049
        3.85 -     4.37: 11700
        4.37 -     4.90: 18273
  Nonbonded interactions: 46374
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS B 187 "
            pdb=" OG  SER B 208 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OG  SER B 146 "
            pdb=" OD2 ASP B 166 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OP1   U C  60 "
            pdb=" N4    C C  61 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" O6    G C  10 "
            pdb=" N2    G C  45 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" OG1 THR B 188 "
            pdb=" OD2 ASP B 210 "
     model   vdw
     2.311 3.040
  ... (remaining 46369 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:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.000
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
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      :  0.001   0.020   5973  Z= 0.065
  Angle     :  0.366   5.055   8408  Z= 0.182
  Chirality :  0.034   0.123    989
  Planarity :  0.002   0.024    831
  Dihedral  :  9.120  95.877   2371
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  5.77 %
    Favored  : 93.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.53 (0.38), residues: 534
  helix:  1.29 (0.58), residues: 103
  sheet:  1.77 (0.39), residues: 185
  loop :  0.37 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 318 
 TYR   0.004   0.001   TYR B 361 
 PHE   0.009   0.001   PHE A 166 
 TRP   0.006   0.001   TRP A 206 
 HIS   0.002   0.000   HIS A 210 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00130 /  0.07 ( 5973)
  covalent geometry    : angle       0.36620 /  0.18 ( 8408)
  hydrogen bonds       : bond        0.14102 /  9.15 (  224)
  hydrogen bonds       : angle       4.94949 /  3.36 (  540)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 SER cc_start: 0.9241 (t) cc_final: 0.8861 (p)
REVERT: A  114 ASP cc_start: 0.9260 (t0) cc_final: 0.9017 (t0)
REVERT: A  115 TYR cc_start: 0.9439 (t80) cc_final: 0.8910 (t80)
REVERT: A  118 ASP cc_start: 0.9329 (m-30) cc_final: 0.9065 (m-30)
REVERT: A  175 ILE cc_start: 0.9475 (mt) cc_final: 0.9114 (tp)
REVERT: B   71 LYS cc_start: 0.9030 (tmtt) cc_final: 0.8744 (tppt)
REVERT: B  122 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8545 (ttpp)
  outliers start: 3
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0810
  time to fit residues: 5.4931
Evaluate side-chains
  20 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:   20.0000
   chunk 24 optimal weight:    8.9990
   chunk 48 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    9.9990
   chunk 58 optimal weight:   10.0000
   overall best weight:    5.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 147 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.045279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.032630 restraints weight = 33424.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.033693 restraints weight = 16055.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.034400 restraints weight = 10375.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.034834 restraints weight = 7842.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.035133 restraints weight = 6624.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2702
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 13 (19 function evaluations)
r_final: 0.2694
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   5973  Z= 0.296
  Angle     :  0.623   6.328   8408  Z= 0.314
  Chirality :  0.040   0.147    989
  Planarity :  0.003   0.024    831
  Dihedral  :  9.801  97.426   1364
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  8.76 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.25 (0.38), residues: 534
  helix:  1.75 (0.57), residues: 91
  sheet:  1.53 (0.39), residues: 179
  loop :  0.06 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  99 
 TYR   0.009   0.001   TYR A 150 
 PHE   0.011   0.002   PHE B 271 
 TRP   0.017   0.002   TRP A 206 
 HIS   0.011   0.002   HIS B 187 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00610 /  0.30 ( 5973)
  covalent geometry    : angle       0.62272 /  0.31 ( 8408)
  hydrogen bonds       : bond        0.05128 /  3.35 (  224)
  hydrogen bonds       : angle       4.74259 /  3.19 (  540)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 TYR cc_start: 0.9559 (t80) cc_final: 0.9321 (t80)
REVERT: A  147 ASN cc_start: 0.9627 (m110) cc_final: 0.9400 (m-40)
REVERT: A  175 ILE cc_start: 0.9595 (mt) cc_final: 0.9318 (tp)
REVERT: B   71 LYS cc_start: 0.9423 (tmtt) cc_final: 0.9195 (tppt)
REVERT: B   87 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8672 (tt)
REVERT: B  147 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8715 (ptp)
REVERT: B  169 ILE cc_start: 0.9673 (mt) cc_final: 0.9462 (mm)
  outliers start: 9
  outliers final: 3
  residues processed: 34
  average time/residue: 0.0758
  time to fit residues: 3.5520
Evaluate side-chains
  22 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 17
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  192 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 56 optimal weight:   20.0000
   chunk 30 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 32 optimal weight:    8.9990
   chunk 19 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   overall best weight:    4.9990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.043734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.031220 restraints weight = 33377.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.032267 restraints weight = 15712.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.032964 restraints weight = 10141.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.033397 restraints weight = 7655.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.033691 restraints weight = 6460.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2672
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 8 (15 function evaluations)
r_final: 0.2672
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   5973  Z= 0.236
  Angle     :  0.529   4.787   8408  Z= 0.272
  Chirality :  0.039   0.175    989
  Planarity :  0.003   0.026    831
  Dihedral  :  9.970  97.113   1364
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 10.04 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.98 (0.38), residues: 534
  helix:  1.73 (0.57), residues: 94
  sheet:  1.27 (0.39), residues: 178
  loop : -0.15 (0.41), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 138 
 TYR   0.007   0.001   TYR A 150 
 PHE   0.011   0.001   PHE A 166 
 TRP   0.013   0.001   TRP A 206 
 HIS   0.004   0.001   HIS B 187 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00495 /  0.24 ( 5973)
  covalent geometry    : angle       0.52914 /  0.27 ( 8408)
  hydrogen bonds       : bond        0.04439 /  2.94 (  224)
  hydrogen bonds       : angle       4.54454 /  3.08 (  540)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 25
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A   95 SER cc_start: 0.9310 (t) cc_final: 0.8991 (p)
REVERT: A  115 TYR cc_start: 0.9571 (t80) cc_final: 0.9031 (t80)
REVERT: A  175 ILE cc_start: 0.9589 (mt) cc_final: 0.9254 (tp)
REVERT: B   71 LYS cc_start: 0.9474 (tmtt) cc_final: 0.9268 (tppt)
  outliers start: 10
  outliers final: 3
  residues processed: 33
  average time/residue: 0.0746
  time to fit residues: 3.4834
Evaluate side-chains
  18 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 15
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  192 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 56 optimal weight:   20.0000
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 19 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 58 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    2.3988

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.044520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.032031 restraints weight = 33066.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.033114 restraints weight = 15602.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.033789 restraints weight = 10011.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.034268 restraints weight = 7637.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.034529 restraints weight = 6388.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2703
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2703 r_free = 0.2703    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2703 r_free = 0.2703    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2703
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5973  Z= 0.129
  Angle     :  0.460   8.790   8408  Z= 0.234
  Chirality :  0.038   0.183    989
  Planarity :  0.003   0.025    831
  Dihedral  :  9.691  95.941   1364
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 10.68 %
    Favored  : 87.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.08 (0.38), residues: 534
  helix:  1.79 (0.57), residues: 97
  sheet:  1.36 (0.39), residues: 172
  loop : -0.10 (0.41), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 119 
 TYR   0.005   0.001   TYR B  38 
 PHE   0.012   0.001   PHE A 166 
 TRP   0.009   0.001   TRP A 206 
 HIS   0.003   0.001   HIS B 187 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.13 ( 5973)
  covalent geometry    : angle       0.46020 /  0.23 ( 8408)
  hydrogen bonds       : bond        0.03736 /  2.51 (  224)
  hydrogen bonds       : angle       4.20277 /  2.84 (  540)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 20
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A   95 SER cc_start: 0.9214 (t) cc_final: 0.8913 (p)
REVERT: A  115 TYR cc_start: 0.9538 (t80) cc_final: 0.9294 (t80)
REVERT: A  147 ASN cc_start: 0.9531 (m110) cc_final: 0.9251 (m-40)
REVERT: A  175 ILE cc_start: 0.9588 (mt) cc_final: 0.9248 (tp)
REVERT: B   71 LYS cc_start: 0.9459 (tmtt) cc_final: 0.9230 (tppt)
  outliers start: 8
  outliers final: 5
  residues processed: 27
  average time/residue: 0.0735
  time to fit residues: 2.7607
Evaluate side-chains
  23 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 18
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  192 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   chunk 45 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 30 optimal weight:    8.9990
   chunk 51 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   chunk 5 optimal weight:   10.0000
   overall best weight:    4.1788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.043230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.030856 restraints weight = 33850.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.031892 restraints weight = 15819.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.032590 restraints weight = 10114.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.032976 restraints weight = 7639.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.033316 restraints weight = 6498.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2671
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2671 r_free = 0.2671    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2671 r_free = 0.2671    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2671
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.3514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   5973  Z= 0.208
  Angle     :  0.507   6.588   8408  Z= 0.258
  Chirality :  0.038   0.183    989
  Planarity :  0.003   0.031    831
  Dihedral  :  9.839  97.218   1364
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  9.62 %
    Favored  : 88.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.88 (0.38), residues: 534
  helix:  1.69 (0.57), residues: 97
  sheet:  1.16 (0.38), residues: 178
  loop : -0.23 (0.41), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  21 
 TYR   0.005   0.001   TYR B  38 
 PHE   0.010   0.001   PHE A 166 
 TRP   0.008   0.001   TRP A 206 
 HIS   0.003   0.001   HIS B 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00436 /  0.21 ( 5973)
  covalent geometry    : angle       0.50704 /  0.26 ( 8408)
  hydrogen bonds       : bond        0.04283 /  2.88 (  224)
  hydrogen bonds       : angle       4.32368 /  2.91 (  540)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 18
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 SER cc_start: 0.9358 (t) cc_final: 0.8986 (p)
REVERT: A  115 TYR cc_start: 0.9563 (t80) cc_final: 0.9323 (t80)
REVERT: A  175 ILE cc_start: 0.9590 (mt) cc_final: 0.9308 (tp)
REVERT: B   71 LYS cc_start: 0.9476 (tmtt) cc_final: 0.9223 (tppt)
  outliers start: 10
  outliers final: 7
  residues processed: 27
  average time/residue: 0.0610
  time to fit residues: 2.2984
Evaluate side-chains
  24 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 17
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  168 LYS
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  200 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 25 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 57 optimal weight:   10.0000
   chunk 59 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 50 optimal weight:   10.0000
   chunk 54 optimal weight:   20.0000
   chunk 16 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    4.9990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.042769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.030459 restraints weight = 34192.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.031490 restraints weight = 16109.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.032166 restraints weight = 10379.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.032621 restraints weight = 7868.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.032885 restraints weight = 6599.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2643
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2643 r_free = 0.2643    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2643 r_free = 0.2643    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2643
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.4050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   5973  Z= 0.241
  Angle     :  0.556   6.855   8408  Z= 0.280
  Chirality :  0.039   0.189    989
  Planarity :  0.003   0.033    831
  Dihedral  : 10.255  98.048   1364
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 10.26 %
    Favored  : 88.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.61 (0.37), residues: 534
  helix:  1.59 (0.57), residues: 94
  sheet:  1.06 (0.38), residues: 174
  loop : -0.46 (0.40), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  99 
 TYR   0.006   0.001   TYR A  50 
 PHE   0.011   0.002   PHE A 166 
 TRP   0.010   0.001   TRP A 206 
 HIS   0.003   0.001   HIS B 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00505 /  0.24 ( 5973)
  covalent geometry    : angle       0.55619 /  0.28 ( 8408)
  hydrogen bonds       : bond        0.04598 /  3.04 (  224)
  hydrogen bonds       : angle       4.41754 /  2.99 (  540)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 17
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A   95 SER cc_start: 0.9345 (t) cc_final: 0.9093 (p)
REVERT: A  115 TYR cc_start: 0.9565 (t80) cc_final: 0.9353 (t80)
REVERT: A  175 ILE cc_start: 0.9592 (mt) cc_final: 0.9272 (tp)
  outliers start: 8
  outliers final: 5
  residues processed: 24
  average time/residue: 0.0573
  time to fit residues: 1.9010
Evaluate side-chains
  22 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 17
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  192 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0270
   chunk 39 optimal weight:    9.9990
   chunk 42 optimal weight:    6.9990
   chunk 47 optimal weight:    8.9990
   chunk 51 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.9642

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.045360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.033219 restraints weight = 32859.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.034284 restraints weight = 15664.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.034983 restraints weight = 9988.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.035421 restraints weight = 7476.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.035728 restraints weight = 6270.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2750
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2750
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.3821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5973  Z= 0.090
  Angle     :  0.468   6.510   8408  Z= 0.235
  Chirality :  0.038   0.209    989
  Planarity :  0.003   0.027    831
  Dihedral  :  9.864  95.803   1364
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 10.04 %
    Favored  : 88.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.71 (0.37), residues: 534
  helix:  1.72 (0.57), residues: 97
  sheet:  1.23 (0.38), residues: 164
  loop : -0.46 (0.39), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 214 
 TYR   0.004   0.001   TYR B  38 
 PHE   0.012   0.001   PHE A 166 
 TRP   0.009   0.001   TRP B 344 
 HIS   0.004   0.001   HIS B 144 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00185 /  0.09 ( 5973)
  covalent geometry    : angle       0.46767 /  0.23 ( 8408)
  hydrogen bonds       : bond        0.03733 /  2.40 (  224)
  hydrogen bonds       : angle       4.09067 /  2.76 (  540)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 23
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A   95 SER cc_start: 0.9118 (t) cc_final: 0.8859 (p)
REVERT: A  147 ASN cc_start: 0.9474 (m110) cc_final: 0.9197 (m-40)
REVERT: B   38 TYR cc_start: 0.8908 (t80) cc_final: 0.8498 (t80)
  outliers start: 8
  outliers final: 4
  residues processed: 29
  average time/residue: 0.0574
  time to fit residues: 2.3357
Evaluate side-chains
  24 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  168 LYS
Chi-restraints excluded: chain B residue  192 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:   20.0000
   chunk 55 optimal weight:   20.0000
   chunk 4 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 24 optimal weight:    0.0870
   chunk 12 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    4.4166

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.043664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.031388 restraints weight = 33758.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.032402 restraints weight = 16261.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.033088 restraints weight = 10561.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.033462 restraints weight = 8043.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.033806 restraints weight = 6886.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2689
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2689 r_free = 0.2689    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2690 r_free = 0.2690    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.2690
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.4077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   5973  Z= 0.214
  Angle     :  0.548   8.656   8408  Z= 0.273
  Chirality :  0.040   0.246    989
  Planarity :  0.003   0.030    831
  Dihedral  : 10.027  97.221   1364
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 10.90 %
    Favored  : 87.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.63 (0.37), residues: 534
  helix:  1.62 (0.56), residues: 97
  sheet:  1.07 (0.38), residues: 169
  loop : -0.45 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  21 
 TYR   0.005   0.001   TYR A  50 
 PHE   0.010   0.001   PHE A 166 
 TRP   0.007   0.001   TRP B 216 
 HIS   0.003   0.001   HIS B 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00451 /  0.21 ( 5973)
  covalent geometry    : angle       0.54840 /  0.27 ( 8408)
  hydrogen bonds       : bond        0.04316 /  2.87 (  224)
  hydrogen bonds       : angle       4.30853 /  2.90 (  540)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A   95 SER cc_start: 0.9347 (t) cc_final: 0.9003 (p)
REVERT: A  175 ILE cc_start: 0.9653 (mm) cc_final: 0.9352 (tp)
REVERT: B   38 TYR cc_start: 0.8935 (t80) cc_final: 0.8527 (t80)
  outliers start: 7
  outliers final: 5
  residues processed: 29
  average time/residue: 0.0559
  time to fit residues: 2.2970
Evaluate side-chains
  24 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  168 LYS
Chi-restraints excluded: chain B residue  192 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 18 optimal weight:    0.0060
   chunk 41 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 51 optimal weight:    8.9990
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 52 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    2.1802

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.045120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.032967 restraints weight = 33117.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.034021 restraints weight = 15972.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.034729 restraints weight = 10211.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.035104 restraints weight = 7674.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.035452 restraints weight = 6514.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2735
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2735 r_free = 0.2735    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2734 r_free = 0.2734    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2734
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.4005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5973  Z= 0.123
  Angle     :  0.486   8.054   8408  Z= 0.243
  Chirality :  0.038   0.182    989
  Planarity :  0.003   0.027    831
  Dihedral  :  9.923  96.224   1364
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.11 %
    Favored  : 87.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.65 (0.37), residues: 534
  helix:  1.68 (0.57), residues: 97
  sheet:  1.05 (0.38), residues: 170
  loop : -0.43 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  21 
 TYR   0.015   0.001   TYR A 115 
 PHE   0.012   0.001   PHE A 166 
 TRP   0.008   0.001   TRP B 344 
 HIS   0.003   0.001   HIS B 144 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 ( 5973)
  covalent geometry    : angle       0.48641 /  0.24 ( 8408)
  hydrogen bonds       : bond        0.03869 /  2.54 (  224)
  hydrogen bonds       : angle       4.08439 /  2.75 (  540)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A   95 SER cc_start: 0.9191 (t) cc_final: 0.8931 (p)
REVERT: A  147 ASN cc_start: 0.9487 (m110) cc_final: 0.9182 (m-40)
REVERT: A  175 ILE cc_start: 0.9667 (mm) cc_final: 0.9335 (tp)
REVERT: B   38 TYR cc_start: 0.8843 (t80) cc_final: 0.8064 (t80)
  outliers start: 6
  outliers final: 5
  residues processed: 27
  average time/residue: 0.0661
  time to fit residues: 2.5567
Evaluate side-chains
  25 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   chunk 2 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 57 optimal weight:   10.0000
   overall best weight:    1.9586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.045225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.032939 restraints weight = 33298.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.034006 restraints weight = 16102.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.034719 restraints weight = 10337.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.035160 restraints weight = 7773.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.035477 restraints weight = 6513.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2793
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2793 r_free = 0.2793    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2793 r_free = 0.2793    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2793
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.3992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5973  Z= 0.114
  Angle     :  0.479   8.150   8408  Z= 0.239
  Chirality :  0.038   0.172    989
  Planarity :  0.003   0.026    831
  Dihedral  :  9.864  95.772   1364
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 11.11 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.70 (0.37), residues: 534
  helix:  1.71 (0.57), residues: 97
  sheet:  1.01 (0.38), residues: 171
  loop : -0.35 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 104 
 TYR   0.003   0.001   TYR A 115 
 PHE   0.011   0.001   PHE A 166 
 TRP   0.011   0.001   TRP B 344 
 HIS   0.003   0.001   HIS B 144 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.11 ( 5973)
  covalent geometry    : angle       0.47891 /  0.24 ( 8408)
  hydrogen bonds       : bond        0.03797 /  2.50 (  224)
  hydrogen bonds       : angle       3.97697 /  2.67 (  540)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A   95 SER cc_start: 0.9146 (t) cc_final: 0.8917 (p)
REVERT: A  147 ASN cc_start: 0.9442 (m110) cc_final: 0.9159 (m-40)
REVERT: B   38 TYR cc_start: 0.8860 (t80) cc_final: 0.8104 (t80)
  outliers start: 5
  outliers final: 5
  residues processed: 25
  average time/residue: 0.0575
  time to fit residues: 2.0145
Evaluate side-chains
  25 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 3 optimal weight:    0.0670
   chunk 11 optimal weight:    1.9990
   chunk 44 optimal weight:    8.9990
   chunk 36 optimal weight:    7.9990
   chunk 55 optimal weight:   20.0000
   chunk 35 optimal weight:    1.9990
   chunk 50 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0870
   chunk 15 optimal weight:   10.0000
   overall best weight:    2.0302

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.045388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.033231 restraints weight = 32654.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.034295 restraints weight = 15819.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.034998 restraints weight = 10135.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.035431 restraints weight = 7619.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.035728 restraints weight = 6381.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2787
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2788
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.3974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5973  Z= 0.116
  Angle     :  0.476   8.249   8408  Z= 0.238
  Chirality :  0.038   0.170    989
  Planarity :  0.003   0.025    831
  Dihedral  :  9.844  95.718   1364
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 10.90 %
    Favored  : 88.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.69 (0.37), residues: 534
  helix:  1.70 (0.57), residues: 97
  sheet:  1.00 (0.38), residues: 171
  loop : -0.34 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 214 
 TYR   0.015   0.001   TYR A 115 
 PHE   0.012   0.001   PHE B  22 
 TRP   0.007   0.001   TRP B 344 
 HIS   0.003   0.001   HIS B 144 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.12 ( 5973)
  covalent geometry    : angle       0.47634 /  0.24 ( 8408)
  hydrogen bonds       : bond        0.03805 /  2.49 (  224)
  hydrogen bonds       : angle       3.94919 /  2.65 (  540)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 760.35 seconds
wall clock time: 13 minutes 55.07 seconds (835.07 seconds total)