Starting phenix.real_space_refine
on Tue Mar  3 14:12:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d9k_27264/03_2026/8d9k_27264.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d9k_27264/03_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_27264/03_2026/8d9k_27264.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d9k_27264/03_2026/8d9k_27264.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d9k_27264/03_2026/8d9k_27264.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d9k_27264/03_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-5986/lib/python3.9/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: 1.32, per 1000 atoms: 0.23
  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: 0.70
  Conformation dependent library (CDL) restraints added in 175.8 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: 0.65
  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: 1.12

  Time building geometry restraints manager: 0.89 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: 3340
       19.18 -    38.35: 148
       38.35 -    57.53: 72
       57.53 -    76.70: 81
       76.70 -    95.88: 2
  Dihedral angle restraints: 3643
    sinusoidal: 2071
      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 3640 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:             0.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.870
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
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  : 16.349  95.877   2627
  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
  covalent geometry    : bond        0.00130 ( 5973)
  covalent geometry    : angle       0.36620 ( 8408)
  hydrogen bonds       : bond        0.14102 (  224)
  hydrogen bonds       : angle       4.94949 (  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  : 0.168 
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: 0.0673
  time to fit residues: 4.5889
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  : 0.139 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
A 147 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.045178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.032494 restraints weight = 33488.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.033566 restraints weight = 15883.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.034268 restraints weight = 10169.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.034741 restraints weight = 7675.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.035033 restraints weight = 6418.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2701
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2701 r_free = 0.2701    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 = 0.2692 r_free = 0.2692    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2692
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.2479

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= 0.295
  Angle     :  0.621   5.933   8408  Z= 0.314
  Chirality :  0.040   0.142    989
  Planarity :  0.003   0.021    831
  Dihedral  : 19.339  97.000   1620
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  8.97 %
    Favored  : 89.10 %
  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:  1.28 (0.38), residues: 534
  helix:  1.74 (0.57), residues: 91
  sheet:  1.57 (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 248 
 TYR   0.008   0.001   TYR A 150 
 PHE   0.011   0.002   PHE B 271 
 TRP   0.017   0.002   TRP A 206 
 HIS   0.010   0.002   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00618 ( 5973)
  covalent geometry    : angle       0.62121 ( 8408)
  hydrogen bonds       : bond        0.05081 (  224)
  hydrogen bonds       : angle       4.74501 (  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  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 TYR cc_start: 0.9572 (t80) cc_final: 0.9331 (t80)
REVERT: A  147 ASN cc_start: 0.9631 (m110) cc_final: 0.9398 (m-40)
REVERT: A  175 ILE cc_start: 0.9594 (mt) cc_final: 0.9309 (tp)
REVERT: B   71 LYS cc_start: 0.9419 (tmtt) cc_final: 0.9178 (tppt)
REVERT: B   87 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8644 (tt)
REVERT: B  147 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8637 (ptp)
REVERT: B  169 ILE cc_start: 0.9637 (mt) cc_final: 0.9428 (mm)
  outliers start: 9
  outliers final: 3
  residues processed: 35
  average time/residue: 0.0624
  time to fit residues: 3.0430
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  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  151 VAL
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:    2.9990
   chunk 2 optimal weight:   10.0000
   chunk 34 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 20 optimal weight:    6.9990
   chunk 59 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 48 optimal weight:    7.9990
   overall best weight:    4.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.043807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.031439 restraints weight = 33048.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.032506 restraints weight = 15519.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.033190 restraints weight = 9923.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.033627 restraints weight = 7488.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.033807 restraints weight = 6285.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2682
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2682 r_free = 0.2682    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 = 0.2682 r_free = 0.2682    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2682
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   5973  Z= 0.229
  Angle     :  0.525   4.704   8408  Z= 0.270
  Chirality :  0.039   0.186    989
  Planarity :  0.003   0.025    831
  Dihedral  : 19.329  96.568   1620
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  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:  1.02 (0.38), residues: 534
  helix:  1.69 (0.57), residues: 94
  sheet:  1.32 (0.38), residues: 178
  loop : -0.12 (0.41), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  99 
 TYR   0.007   0.001   TYR A 150 
 PHE   0.011   0.001   PHE A 166 
 TRP   0.014   0.001   TRP A 206 
 HIS   0.003   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 5973)
  covalent geometry    : angle       0.52473 ( 8408)
  hydrogen bonds       : bond        0.04391 (  224)
  hydrogen bonds       : angle       4.49781 (  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
  36 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 26
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A   95 SER cc_start: 0.9298 (t) cc_final: 0.8988 (p)
REVERT: A  115 TYR cc_start: 0.9565 (t80) cc_final: 0.9030 (t80)
REVERT: A  175 ILE cc_start: 0.9590 (mt) cc_final: 0.9261 (tp)
REVERT: B   71 LYS cc_start: 0.9464 (tmtt) cc_final: 0.9260 (tppt)
REVERT: B   87 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8777 (tt)
  outliers start: 10
  outliers final: 3
  residues processed: 33
  average time/residue: 0.0816
  time to fit residues: 3.6966
Evaluate side-chains
  20 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain B residue   87 LEU
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:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    3.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.043532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2608 r_free = 0.2608 target = 0.031160 restraints weight = 33287.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.032204 restraints weight = 15643.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.032909 restraints weight = 10030.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.033362 restraints weight = 7572.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.033584 restraints weight = 6345.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.2670
-------------------------------------------------------------------------------
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 = 0.2671 r_free = 0.2671    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2671
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.3394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   5973  Z= 0.198
  Angle     :  0.499   4.718   8408  Z= 0.256
  Chirality :  0.038   0.214    989
  Planarity :  0.003   0.032    831
  Dihedral  : 19.311  96.893   1620
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  :  9.83 %
    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:  0.97 (0.38), residues: 534
  helix:  1.77 (0.57), residues: 97
  sheet:  1.31 (0.39), residues: 176
  loop : -0.24 (0.41), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  21 
 TYR   0.006   0.001   TYR B  38 
 PHE   0.012   0.001   PHE A 166 
 TRP   0.011   0.001   TRP A 206 
 HIS   0.002   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 5973)
  covalent geometry    : angle       0.49864 ( 8408)
  hydrogen bonds       : bond        0.04237 (  224)
  hydrogen bonds       : angle       4.34142 (  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
  30 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 18
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 SER cc_start: 0.9290 (t) cc_final: 0.8977 (p)
REVERT: A  115 TYR cc_start: 0.9563 (t80) cc_final: 0.9082 (t80)
REVERT: A  175 ILE cc_start: 0.9595 (mt) cc_final: 0.9255 (tp)
REVERT: B   71 LYS cc_start: 0.9463 (tmtt) cc_final: 0.9213 (tppt)
  outliers start: 12
  outliers final: 6
  residues processed: 29
  average time/residue: 0.0738
  time to fit residues: 2.9238
Evaluate side-chains
  22 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 16
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
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  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:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    4.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.043577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.031149 restraints weight = 34314.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.032153 restraints weight = 16605.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.032852 restraints weight = 10883.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.033232 restraints weight = 8314.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.033575 restraints weight = 7118.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2678
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2678 r_free = 0.2678    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 = 0.2678 r_free = 0.2678    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2678
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.3727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   5973  Z= 0.225
  Angle     :  0.525   8.555   8408  Z= 0.266
  Chirality :  0.039   0.221    989
  Planarity :  0.003   0.033    831
  Dihedral  : 19.374  97.230   1620
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  :  9.40 %
    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:  0.80 (0.38), residues: 534
  helix:  1.53 (0.55), residues: 97
  sheet:  1.21 (0.39), residues: 177
  loop : -0.32 (0.41), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  99 
 TYR   0.005   0.001   TYR A 150 
 PHE   0.011   0.001   PHE A 166 
 TRP   0.006   0.001   TRP B 216 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 5973)
  covalent geometry    : angle       0.52458 ( 8408)
  hydrogen bonds       : bond        0.04409 (  224)
  hydrogen bonds       : angle       4.37762 (  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
  29 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 17
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 SER cc_start: 0.9303 (t) cc_final: 0.8997 (p)
REVERT: A  115 TYR cc_start: 0.9560 (t80) cc_final: 0.9099 (t80)
REVERT: A  175 ILE cc_start: 0.9579 (mt) cc_final: 0.9298 (tp)
  outliers start: 12
  outliers final: 8
  residues processed: 28
  average time/residue: 0.0931
  time to fit residues: 3.4834
Evaluate side-chains
  24 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 16
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
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  180 ILE
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  249 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 26 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 57 optimal weight:   20.0000
   chunk 59 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 54 optimal weight:   20.0000
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    4.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.043671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.031066 restraints weight = 34354.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.032068 restraints weight = 16385.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.032756 restraints weight = 10651.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.033179 restraints weight = 8125.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.033501 restraints weight = 6894.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2676
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    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 = 0.2677 r_free = 0.2677    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2677
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.3966

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= 0.212
  Angle     :  0.519   7.249   8408  Z= 0.263
  Chirality :  0.039   0.234    989
  Planarity :  0.003   0.032    831
  Dihedral  : 19.379  97.384   1620
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  :  9.40 %
    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:  0.68 (0.38), residues: 534
  helix:  1.52 (0.55), residues: 97
  sheet:  1.15 (0.39), residues: 175
  loop : -0.43 (0.41), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  99 
 TYR   0.005   0.001   TYR A  50 
 PHE   0.011   0.001   PHE A 166 
 TRP   0.012   0.001   TRP A 206 
 HIS   0.003   0.001   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 5973)
  covalent geometry    : angle       0.51874 ( 8408)
  hydrogen bonds       : bond        0.04364 (  224)
  hydrogen bonds       : angle       4.34226 (  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
  29 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 17
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 SER cc_start: 0.9298 (t) cc_final: 0.9019 (p)
REVERT: A  115 TYR cc_start: 0.9551 (t80) cc_final: 0.9344 (t80)
REVERT: A  175 ILE cc_start: 0.9582 (mt) cc_final: 0.9241 (tp)
  outliers start: 12
  outliers final: 9
  residues processed: 28
  average time/residue: 0.0738
  time to fit residues: 2.9299
Evaluate side-chains
  25 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 16
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
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  145 LEU
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  249 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 18 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 39 optimal weight:    8.9990
   chunk 42 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 27 optimal weight:    0.5980
   chunk 21 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    2.5188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.044736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.032473 restraints weight = 33499.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.033513 restraints weight = 16036.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.034220 restraints weight = 10243.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.034680 restraints weight = 7702.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.034944 restraints weight = 6408.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2717
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2717 r_free = 0.2717    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 = 0.2717 r_free = 0.2717    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2717
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.3889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   5973  Z= 0.133
  Angle     :  0.461   7.227   8408  Z= 0.234
  Chirality :  0.038   0.227    989
  Planarity :  0.003   0.029    831
  Dihedral  : 19.252  96.215   1620
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 8.43
  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:  0.71 (0.38), residues: 534
  helix:  1.69 (0.57), residues: 97
  sheet:  1.10 (0.39), residues: 173
  loop : -0.41 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  21 
 TYR   0.003   0.001   TYR B  38 
 PHE   0.013   0.001   PHE A 166 
 TRP   0.006   0.001   TRP B 344 
 HIS   0.003   0.001   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 5973)
  covalent geometry    : angle       0.46063 ( 8408)
  hydrogen bonds       : bond        0.03963 (  224)
  hydrogen bonds       : angle       4.10889 (  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
  26 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 SER cc_start: 0.9163 (t) cc_final: 0.8940 (p)
REVERT: A  147 ASN cc_start: 0.9473 (m110) cc_final: 0.9198 (m-40)
REVERT: A  175 ILE cc_start: 0.9518 (mt) cc_final: 0.9167 (tp)
REVERT: B  122 LYS cc_start: 0.9147 (mtpt) cc_final: 0.8486 (mtpt)
  outliers start: 5
  outliers final: 4
  residues processed: 26
  average time/residue: 0.0942
  time to fit residues: 3.2661
Evaluate side-chains
  22 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 18
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  200 GLN
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:   10.0000
   chunk 4 optimal weight:    0.0870
   chunk 8 optimal weight:    0.0980
   chunk 43 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 57 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 56 optimal weight:   10.0000
   overall best weight:    0.4958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.045959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.033665 restraints weight = 32422.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.034753 restraints weight = 15662.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.035482 restraints weight = 10020.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.035962 restraints weight = 7518.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.036232 restraints weight = 6265.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2766
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2766 r_free = 0.2766    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 = 0.2765 r_free = 0.2765    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2765
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.3678

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= 0.081
  Angle     :  0.453   7.135   8408  Z= 0.225
  Chirality :  0.038   0.202    989
  Planarity :  0.003   0.025    831
  Dihedral  : 18.989  93.496   1620
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 5.71
  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:  0.88 (0.37), residues: 534
  helix:  1.76 (0.57), residues: 96
  sheet:  1.29 (0.39), residues: 167
  loop : -0.29 (0.39), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 214 
 TYR   0.004   0.001   TYR A 115 
 PHE   0.012   0.001   PHE A 166 
 TRP   0.014   0.001   TRP B 344 
 HIS   0.004   0.001   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00171 ( 5973)
  covalent geometry    : angle       0.45272 ( 8408)
  hydrogen bonds       : bond        0.03707 (  224)
  hydrogen bonds       : angle       3.86926 (  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
  26 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 SER cc_start: 0.9053 (t) cc_final: 0.8805 (p)
REVERT: A  115 TYR cc_start: 0.9437 (t80) cc_final: 0.9211 (t80)
REVERT: A  147 ASN cc_start: 0.9448 (m110) cc_final: 0.9180 (m-40)
REVERT: B   38 TYR cc_start: 0.8852 (t80) cc_final: 0.8327 (t80)
REVERT: B  122 LYS cc_start: 0.9019 (mtpt) cc_final: 0.8717 (ptpt)
  outliers start: 5
  outliers final: 4
  residues processed: 26
  average time/residue: 0.0978
  time to fit residues: 3.3970
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  : 0.169 
-------------------------------------------------------------------------------
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  192 SER
Chi-restraints excluded: chain B residue  200 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 1 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 39 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    4.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.043727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.031539 restraints weight = 33481.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.032566 restraints weight = 16359.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.033249 restraints weight = 10590.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.033669 restraints weight = 8027.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.033983 restraints weight = 6756.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2696
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2696 r_free = 0.2696    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 = 0.2696 r_free = 0.2696    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2696
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.3956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5973  Z= 0.211
  Angle     :  0.523   7.112   8408  Z= 0.263
  Chirality :  0.038   0.195    989
  Planarity :  0.003   0.027    831
  Dihedral  : 19.147  95.812   1620
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  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:  0.79 (0.38), residues: 534
  helix:  1.86 (0.58), residues: 97
  sheet:  1.19 (0.39), residues: 171
  loop : -0.42 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  99 
 TYR   0.005   0.001   TYR A  50 
 PHE   0.011   0.001   PHE A 166 
 TRP   0.013   0.001   TRP B 344 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 5973)
  covalent geometry    : angle       0.52259 ( 8408)
  hydrogen bonds       : bond        0.04320 (  224)
  hydrogen bonds       : angle       4.15784 (  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
  24 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 SER cc_start: 0.9332 (t) cc_final: 0.8990 (p)
REVERT: A  175 ILE cc_start: 0.9642 (mm) cc_final: 0.9285 (tp)
REVERT: B  200 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.8046 (mp10)
  outliers start: 5
  outliers final: 4
  residues processed: 23
  average time/residue: 0.1059
  time to fit residues: 3.2312
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  : 0.191 
-------------------------------------------------------------------------------
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  192 SER
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  335 LYS
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:    8.9990
   chunk 20 optimal weight:    9.9990
   chunk 2 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 36 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 14 optimal weight:    9.9990
   chunk 57 optimal weight:   20.0000
   overall best weight:    7.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.042615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.030381 restraints weight = 35363.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.031381 restraints weight = 17029.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.032066 restraints weight = 11016.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.032413 restraints weight = 8365.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.032720 restraints weight = 7173.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2640
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2640 r_free = 0.2640    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 = 0.2639 r_free = 0.2639    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.4625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.047   5973  Z= 0.362
  Angle     :  0.690   7.400   8408  Z= 0.349
  Chirality :  0.042   0.200    989
  Planarity :  0.004   0.033    831
  Dihedral  : 19.461  98.691   1620
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 10.47 %
    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:  0.37 (0.37), residues: 534
  helix:  1.63 (0.59), residues: 88
  sheet:  0.78 (0.38), residues: 177
  loop : -0.57 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  99 
 TYR   0.013   0.001   TYR A 115 
 PHE   0.011   0.002   PHE B 251 
 TRP   0.009   0.002   TRP B 216 
 HIS   0.006   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00753 ( 5973)
  covalent geometry    : angle       0.68958 ( 8408)
  hydrogen bonds       : bond        0.05802 (  224)
  hydrogen bonds       : angle       4.86229 (  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
  24 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 16
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  175 ILE cc_start: 0.9708 (mm) cc_final: 0.9380 (tp)
REVERT: B  200 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8142 (mp10)
  outliers start: 8
  outliers final: 4
  residues processed: 22
  average time/residue: 0.0984
  time to fit residues: 2.8410
Evaluate side-chains
  21 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 16
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
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  192 SER
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  335 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 36 optimal weight:    0.4980
   chunk 55 optimal weight:   20.0000
   chunk 35 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 24 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.8780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.044549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.032422 restraints weight = 32557.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.033471 restraints weight = 15812.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.034187 restraints weight = 10172.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.034615 restraints weight = 7647.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.034914 restraints weight = 6420.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    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 = 0.2724 r_free = 0.2724    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2724
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.4241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5973  Z= 0.097
  Angle     :  0.500   7.782   8408  Z= 0.253
  Chirality :  0.039   0.192    989
  Planarity :  0.003   0.025    831
  Dihedral  : 19.246  95.292   1620
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 11.32 %
    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:  0.58 (0.37), residues: 534
  helix:  1.60 (0.57), residues: 96
  sheet:  1.02 (0.39), residues: 171
  loop : -0.48 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 119 
 TYR   0.004   0.001   TYR B  38 
 PHE   0.013   0.001   PHE A 166 
 TRP   0.013   0.001   TRP B 344 
 HIS   0.005   0.001   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 5973)
  covalent geometry    : angle       0.49983 ( 8408)
  hydrogen bonds       : bond        0.04238 (  224)
  hydrogen bonds       : angle       4.23765 (  540)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 866.61 seconds
wall clock time: 15 minutes 43.52 seconds (943.52 seconds total)