Starting phenix.real_space_refine
on Fri Aug 22 21:47:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f76_28896/08_2025/8f76_28896.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f76_28896/08_2025/8f76_28896.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f76_28896/08_2025/8f76_28896.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f76_28896/08_2025/8f76_28896.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f76_28896/08_2025/8f76_28896.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f76_28896/08_2025/8f76_28896.cif"
  }
  resolution = 3.1
  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=   0.015 sd=   0.111
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: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    5195      2.51       5
     N    1428      2.21       5
     O    1490      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8170
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2363
          Classifications: {'peptide': 302}
          Link IDs: {'PTRANS': 14, 'TRANS': 287}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "X"
      Number of atoms: 1818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1818
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 5, 'TRANS': 210}
          Chain breaks: 4
    Chain: "Y"
      Number of atoms: 2594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2594
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "Z"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'PPI': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.17, per 1000 atoms: 0.27
  Number of scatterers: 8170
  At special positions: 0
  Unit cell: (82.62, 98.82, 136.89, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      57     16.00
     O    1490      8.00
     N    1428      7.00
     C    5195      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   4 " - pdb=" SG  CYS A 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  96 " - pdb=" SG  CYS A 178 " distance=2.03

  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: 0.59
  Conformation dependent library (CDL) restraints added in 504.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1956

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 11 sheets defined
      43.1% alpha, 21.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 48
      Proline residue:  A  29  - end of helix
      removed outlier: 3.932A  pdb=" N   SER A  32 " --> pdb=" O   PHE A  28 " (cutoff:3.500A)
      removed outlier: 4.959A  pdb=" N   VAL A  44 " --> pdb=" O   GLY A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 55
      removed outlier: 3.579A  pdb=" N   LEU A  54 " --> pdb=" O   GLU A  51 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   HIS A  55 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 51 through 55'
    Processing helix  chain 'A' and resid 56 through 87
      Proline residue:  A  78  - end of helix
    Processing helix  chain 'A' and resid 93 through 127
    Processing helix  chain 'A' and resid 130 through 135
    Processing helix  chain 'A' and resid 136 through 156
    Processing helix  chain 'A' and resid 156 through 163
      removed outlier: 3.924A  pdb=" N   LYS A 163 " --> pdb=" O   PRO A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 187
      removed outlier: 3.635A  pdb=" N   ALA A 187 " --> pdb=" O   MET A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 225
    Processing helix  chain 'A' and resid 229 through 263
      removed outlier: 3.529A  pdb=" N   ARG A 233 " --> pdb=" O   SER A 229 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
    Processing helix  chain 'A' and resid 268 through 281
      removed outlier: 3.984A  pdb=" N   ARG A 272 " --> pdb=" O   HIS A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 292
      Proline residue:  A 288  - end of helix
    Processing helix  chain 'A' and resid 295 through 305
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.710A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.980A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 15 through 40
    Processing helix  chain 'X' and resid 52 through 58
    Processing helix  chain 'X' and resid 233 through 240
      removed outlier: 4.065A  pdb=" N   ASN X 239 " --> pdb=" O   GLN X 236 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   ASP X 240 " --> pdb=" O   CYS X 237 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 265 through 279
    Processing helix  chain 'X' and resid 280 through 283
      removed outlier: 3.828A  pdb=" N   ARG X 283 " --> pdb=" O   ARG X 280 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'X' and resid 280 through 283'
    Processing helix  chain 'X' and resid 293 through 303
    Processing helix  chain 'X' and resid 307 through 312
      removed outlier: 4.142A  pdb=" N   TYR X 311 " --> pdb=" O   LYS X 307 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 313 through 318
      removed outlier: 3.520A  pdb=" N   TYR X 318 " --> pdb=" O   PHE X 315 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 331 through 351
      removed outlier: 4.178A  pdb=" N   THR X 335 " --> pdb=" O   ASP X 331 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 370 through 391
    Processing helix  chain 'Y' and resid 4 through 26
    Processing helix  chain 'Y' and resid 29 through 34
    Processing helix  chain 'Z' and resid 8 through 24
      removed outlier: 3.907A  pdb=" N   ASN Z  24 " --> pdb=" O   LYS Z  20 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 29 through 45
    Processing helix  chain 'Z' and resid 46 through 48
      No H-bonds generated for 'chain 'Z' and resid 46 through 48'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12
    Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AA3, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.726A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ASN N  35 " --> pdb=" O   ALA N  97 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'X' and resid 207 through 214
      removed outlier: 4.334A  pdb=" N   VAL X 224 " --> pdb=" O   LEU X  45 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ARG X  42 " --> pdb=" O   ALA X 243 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   ILE X 245 " --> pdb=" O   ARG X  42 " (cutoff:3.500A)
      removed outlier: 5.941A  pdb=" N   LEU X  44 " --> pdb=" O   ILE X 245 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   VAL X 247 " --> pdb=" O   LEU X  44 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   LEU X  46 " --> pdb=" O   VAL X 247 " (cutoff:3.500A)
      removed outlier: 8.197A  pdb=" N   ASP X 249 " --> pdb=" O   LEU X  46 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'Y' and resid 46 through 52
      removed outlier: 5.486A  pdb=" N   THR Y  47 " --> pdb=" O   ASN Y 340 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ASN Y 340 " --> pdb=" O   THR Y  47 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   PHE Y 335 " --> pdb=" O   SER Y 331 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   SER Y 331 " --> pdb=" O   PHE Y 335 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LYS Y 337 " --> pdb=" O   THR Y 329 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'Y' and resid 58 through 63
      removed outlier: 3.710A  pdb=" N   ALA Y  60 " --> pdb=" O   ALA Y  73 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LEU Y  70 " --> pdb=" O   TRP Y  82 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   ASP Y  83 " --> pdb=" O   LYS Y  89 " (cutoff:3.500A)
      removed outlier: 5.850A  pdb=" N   LYS Y  89 " --> pdb=" O   ASP Y  83 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'Y' and resid 100 through 105
      removed outlier: 6.631A  pdb=" N   GLY Y 115 " --> pdb=" O   MET Y 101 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   CYS Y 103 " --> pdb=" O   ALA Y 113 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   ALA Y 113 " --> pdb=" O   CYS Y 103 " (cutoff:3.500A)
      removed outlier: 5.097A  pdb=" N   TYR Y 105 " --> pdb=" O   TYR Y 111 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   TYR Y 111 " --> pdb=" O   TYR Y 105 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   GLY Y 116 " --> pdb=" O   ILE Y 120 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   ILE Y 120 " --> pdb=" O   GLY Y 116 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   ASN Y 125 " --> pdb=" O   VAL Y 135 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   VAL Y 135 " --> pdb=" O   ASN Y 125 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'Y' and resid 146 through 151
      removed outlier: 4.177A  pdb=" N   THR Y 165 " --> pdb=" O   SER Y 161 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   ASP Y 170 " --> pdb=" O   GLN Y 176 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   GLN Y 176 " --> pdb=" O   ASP Y 170 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'Y' and resid 187 through 192
      removed outlier: 4.564A  pdb=" N   SER Y 207 " --> pdb=" O   ALA Y 203 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ASP Y 212 " --> pdb=" O   CYS Y 218 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   CYS Y 218 " --> pdb=" O   ASP Y 212 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'Y' and resid 229 through 234
      removed outlier: 6.189A  pdb=" N   ASP Y 254 " --> pdb=" O   GLU Y 260 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   GLU Y 260 " --> pdb=" O   ASP Y 254 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'Y' and resid 273 through 278
      removed outlier: 3.835A  pdb=" N   SER Y 275 " --> pdb=" O   GLY Y 288 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ASP Y 298 " --> pdb=" O   ARG Y 304 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   ARG Y 304 " --> pdb=" O   ASP Y 298 " (cutoff:3.500A)

    444 hydrogen bonds defined for protein.
    1278 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.33

  Time building geometry restraints manager: 0.82 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: 2320
        1.34 -     1.45: 1421
        1.45 -     1.57: 4512
        1.57 -     1.69: 0
        1.69 -     1.81: 83
  Bond restraints: 8336
  Sorted by residual:
  bond pdb=" CG1 ILE X 285 "
       pdb=" CD1 ILE X 285 "
    ideal  model  delta    sigma   weight residual
    1.513  1.445  0.068 3.90e-02 6.57e+02 3.00e+00
  bond pdb=" CB  PHE A 101 "
       pdb=" CG  PHE A 101 "
    ideal  model  delta    sigma   weight residual
    1.502  1.540 -0.038 2.30e-02 1.89e+03 2.76e+00
  bond pdb=" C2  PPI A 401 "
       pdb=" C3  PPI A 401 "
    ideal  model  delta    sigma   weight residual
    1.519  1.487  0.032 2.00e-02 2.50e+03 2.52e+00
  bond pdb=" CB  THR Y 274 "
       pdb=" CG2 THR Y 274 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.48e+00
  bond pdb=" CA  THR Y  87 "
       pdb=" C   THR Y  87 "
    ideal  model  delta    sigma   weight residual
    1.523  1.541 -0.018 1.34e-02 5.57e+03 1.83e+00
  ... (remaining 8331 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 10927
        2.10 -     4.21: 292
        4.21 -     6.31: 46
        6.31 -     8.42: 17
        8.42 -    10.52: 5
  Bond angle restraints: 11287
  Sorted by residual:
  angle pdb=" C   THR Y  86 "
        pdb=" N   THR Y  87 "
        pdb=" CA  THR Y  87 "
      ideal   model   delta    sigma   weight residual
     121.54  128.77   -7.23 1.91e+00 2.74e-01 1.43e+01
  angle pdb=" CA  PRO A 283 "
        pdb=" C   PRO A 283 "
        pdb=" N   PRO A 284 "
      ideal   model   delta    sigma   weight residual
     117.93  122.25   -4.32 1.20e+00 6.94e-01 1.29e+01
  angle pdb=" C   TYR A 188 "
        pdb=" N   ALA A 189 "
        pdb=" CA  ALA A 189 "
      ideal   model   delta    sigma   weight residual
     121.54  128.36   -6.82 1.91e+00 2.74e-01 1.27e+01
  angle pdb=" N   PRO A 283 "
        pdb=" CA  PRO A 283 "
        pdb=" C   PRO A 283 "
      ideal   model   delta    sigma   weight residual
     110.70  114.92   -4.22 1.22e+00 6.72e-01 1.20e+01
  angle pdb=" CB  MET A  77 "
        pdb=" CG  MET A  77 "
        pdb=" SD  MET A  77 "
      ideal   model   delta    sigma   weight residual
     112.70  123.02  -10.32 3.00e+00 1.11e-01 1.18e+01
  ... (remaining 11282 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4450
       17.96 -    35.92: 428
       35.92 -    53.88: 78
       53.88 -    71.84: 10
       71.84 -    89.80: 10
  Dihedral angle restraints: 4976
    sinusoidal: 1957
      harmonic: 3019
  Sorted by residual:
  dihedral pdb=" CB  CYS A   4 "
           pdb=" SG  CYS A   4 "
           pdb=" SG  CYS A 168 "
           pdb=" CB  CYS A 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -136.74   50.74     1      1.00e+01 1.00e-02 3.52e+01
  dihedral pdb=" CA  ASN A  41 "
           pdb=" C   ASN A  41 "
           pdb=" N   CYS A  42 "
           pdb=" CA  CYS A  42 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.37  -25.63     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CA  ALA Y  60 "
           pdb=" C   ALA Y  60 "
           pdb=" N   MET Y  61 "
           pdb=" CA  MET Y  61 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.11   21.89     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 4973 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 906
       0.050 -    0.100: 281
       0.100 -    0.150: 80
       0.150 -    0.200: 14
       0.200 -    0.250: 4
  Chirality restraints: 1285
  Sorted by residual:
  chirality pdb=" CB  VAL X  57 "
            pdb=" CA  VAL X  57 "
            pdb=" CG1 VAL X  57 "
            pdb=" CG2 VAL X  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CA  TYR Y  59 "
            pdb=" N   TYR Y  59 "
            pdb=" C   TYR Y  59 "
            pdb=" CB  TYR Y  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CG  LEU Y 286 "
            pdb=" CB  LEU Y 286 "
            pdb=" CD1 LEU Y 286 "
            pdb=" CD2 LEU Y 286 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 1282 not shown)

  Planarity restraints: 1436
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  39 "    0.022 2.00e-02 2.50e+03   4.33e-02 1.87e+01
        pdb=" C   PHE A  39 "   -0.075 2.00e-02 2.50e+03
        pdb=" O   PHE A  39 "    0.028 2.00e-02 2.50e+03
        pdb=" N   GLY A  40 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR Y  59 "   -0.035 2.00e-02 2.50e+03   2.41e-02 1.16e+01
        pdb=" CG  TYR Y  59 "    0.057 2.00e-02 2.50e+03
        pdb=" CD1 TYR Y  59 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR Y  59 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR Y  59 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR Y  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR Y  59 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR Y  59 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 156 "    0.055 5.00e-02 4.00e+02   8.21e-02 1.08e+01
        pdb=" N   PRO A 157 "   -0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO A 157 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 157 "    0.046 5.00e-02 4.00e+02
  ... (remaining 1433 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1595
        2.78 -     3.31: 7488
        3.31 -     3.84: 14416
        3.84 -     4.37: 17192
        4.37 -     4.90: 29723
  Nonbonded interactions: 70414
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP N  50 "
            pdb=" OG  SER N  59 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   PRO N 100 "
            pdb=" OG  SER Y 227 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OG1 THR Y 274 "
            pdb=" O   VAL Y 315 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OG  SER Y 147 "
            pdb=" O   VAL Y 187 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   ILE Y  58 "
            pdb=" OG  SER Y 316 "
     model   vdw
     2.288 3.040
  ... (remaining 70409 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.220
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
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      :  0.005   0.068   8338  Z= 0.218
  Angle     :  0.853  10.521  11291  Z= 0.451
  Chirality :  0.055   0.250   1285
  Planarity :  0.007   0.082   1436
  Dihedral  : 14.684  89.799   3014
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.19 (0.24), residues: 1020
  helix: -0.63 (0.23), residues: 384
  sheet: -0.65 (0.33), residues: 220
  loop : -0.81 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG Y 197 
 TYR   0.057   0.003   TYR Y  59 
 PHE   0.036   0.002   PHE A 101 
 TRP   0.023   0.003   TRP Y  99 
 HIS   0.005   0.001   HIS X 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 8336)
  covalent geometry    : angle       0.85357 (11287)
  SS BOND              : bond        0.00127 (    2)
  SS BOND              : angle       0.37152 (    4)
  hydrogen bonds       : bond        0.13409 (  444)
  hydrogen bonds       : angle       7.28748 ( 1278)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.315 
Fit side-chains
REVERT: X   27 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6699 (mp0)
REVERT: X  292 ASN cc_start: 0.7635 (m110) cc_final: 0.7412 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1229
  time to fit residues: 18.5543
Evaluate side-chains
  101 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.0980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 171 ASN
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X  23 ASN
Y  88 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.151153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.117700 restraints weight = 9482.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 2.03
r_work: 0.3215 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.1137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8338  Z= 0.133
  Angle     :  0.524   5.728  11291  Z= 0.279
  Chirality :  0.042   0.150   1285
  Planarity :  0.004   0.065   1436
  Dihedral  :  4.958  78.615   1129
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  6.99 %
    Favored  : 92.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.01 (0.26), residues: 1020
  helix:  1.03 (0.26), residues: 380
  sheet: -0.63 (0.34), residues: 221
  loop : -0.48 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  72 
 TYR   0.024   0.001   TYR Y  59 
 PHE   0.018   0.001   PHE A 155 
 TRP   0.016   0.002   TRP Y 211 
 HIS   0.003   0.001   HIS X 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8336)
  covalent geometry    : angle       0.52413 (11287)
  SS BOND              : bond        0.00138 (    2)
  SS BOND              : angle       0.37955 (    4)
  hydrogen bonds       : bond        0.03987 (  444)
  hydrogen bonds       : angle       5.52877 ( 1278)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 114
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  190 ASP cc_start: 0.7623 (t70) cc_final: 0.7236 (t0)
REVERT: N   80 TYR cc_start: 0.7958 (m-80) cc_final: 0.7758 (m-80)
REVERT: X   54 SER cc_start: 0.7920 (m) cc_final: 0.7535 (p)
REVERT: Y   42 ARG cc_start: 0.6922 (tpt170) cc_final: 0.6575 (tpt170)
REVERT: Y  219 ARG cc_start: 0.7803 (mmt180) cc_final: 0.7496 (tpp80)
  outliers start: 5
  outliers final: 4
  residues processed: 116
  average time/residue: 0.1042
  time to fit residues: 15.7451
Evaluate side-chains
  114 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 110
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   77 ASN
Chi-restraints excluded: chain X residue  229 ASP
Chi-restraints excluded: chain Y residue   87 THR
Chi-restraints excluded: chain Y residue  189 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 81 optimal weight:    0.6980
   chunk 65 optimal weight:   10.0000
   chunk 97 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 86 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN
X 292 ASN
Y 175 GLN
Y 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.141567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.108263 restraints weight = 9517.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.01
r_work: 0.3033 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8338  Z= 0.216
  Angle     :  0.579   7.543  11291  Z= 0.305
  Chirality :  0.044   0.153   1285
  Planarity :  0.004   0.057   1436
  Dihedral  :  5.105  88.028   1129
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  9.70 %
    Favored  : 88.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.18 (0.27), residues: 1020
  helix:  1.28 (0.27), residues: 387
  sheet: -0.79 (0.33), residues: 220
  loop : -0.35 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG Y  19 
 TYR   0.029   0.002   TYR Y  59 
 PHE   0.017   0.002   PHE A 155 
 TRP   0.013   0.002   TRP Y 211 
 HIS   0.005   0.001   HIS X 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 8336)
  covalent geometry    : angle       0.57948 (11287)
  SS BOND              : bond        0.00189 (    2)
  SS BOND              : angle       0.43067 (    4)
  hydrogen bonds       : bond        0.04396 (  444)
  hydrogen bonds       : angle       5.52604 ( 1278)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 ASP cc_start: 0.7557 (t70) cc_final: 0.7115 (t0)
REVERT: X  220 HIS cc_start: 0.8652 (t-90) cc_final: 0.7799 (t-90)
REVERT: Y   42 ARG cc_start: 0.6891 (tpt170) cc_final: 0.6440 (tpt170)
REVERT: Y  138 GLU cc_start: 0.8143 (tp30) cc_final: 0.7810 (tp30)
REVERT: Z   31 SER cc_start: 0.7548 (m) cc_final: 0.7303 (m)
  outliers start: 16
  outliers final: 9
  residues processed: 128
  average time/residue: 0.1109
  time to fit residues: 18.5071
Evaluate side-chains
  119 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain X residue  229 ASP
Chi-restraints excluded: chain X residue  292 ASN
Chi-restraints excluded: chain Y residue  177 THR
Chi-restraints excluded: chain Y residue  189 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 99 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 38 optimal weight:    0.3980
   chunk 19 optimal weight:    0.7980
   chunk 97 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN
N  31 ASN
X 292 ASN
Y  32 GLN
Y 175 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.143251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.110104 restraints weight = 9659.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.03
r_work: 0.3132 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8338  Z= 0.143
  Angle     :  0.514   6.354  11291  Z= 0.271
  Chirality :  0.042   0.160   1285
  Planarity :  0.004   0.055   1436
  Dihedral  :  4.924  88.556   1129
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.18 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.38 (0.27), residues: 1020
  helix:  1.52 (0.27), residues: 388
  sheet: -0.74 (0.34), residues: 215
  loop : -0.28 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG Y 219 
 TYR   0.018   0.001   TYR A 197 
 PHE   0.018   0.001   PHE A 155 
 TRP   0.013   0.002   TRP Y 211 
 HIS   0.004   0.001   HIS X 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8336)
  covalent geometry    : angle       0.51391 (11287)
  SS BOND              : bond        0.00217 (    2)
  SS BOND              : angle       0.40450 (    4)
  hydrogen bonds       : bond        0.03949 (  444)
  hydrogen bonds       : angle       5.30939 ( 1278)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 ASP cc_start: 0.7539 (t70) cc_final: 0.7114 (t0)
REVERT: Z   31 SER cc_start: 0.7609 (m) cc_final: 0.7387 (m)
  outliers start: 18
  outliers final: 15
  residues processed: 117
  average time/residue: 0.1140
  time to fit residues: 17.6155
Evaluate side-chains
  119 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   77 ASN
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain X residue   54 SER
Chi-restraints excluded: chain X residue  229 ASP
Chi-restraints excluded: chain X residue  292 ASN
Chi-restraints excluded: chain Y residue   32 GLN
Chi-restraints excluded: chain Y residue  177 THR
Chi-restraints excluded: chain Y residue  186 ASP
Chi-restraints excluded: chain Y residue  189 SER
Chi-restraints excluded: chain Y residue  276 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 99 optimal weight:    7.9990
   chunk 46 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN
N  35 ASN
X  35 GLN
X 292 ASN
Y 175 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.141400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.108213 restraints weight = 9574.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 2.01
r_work: 0.3064 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8338  Z= 0.184
  Angle     :  0.534   7.022  11291  Z= 0.281
  Chirality :  0.043   0.170   1285
  Planarity :  0.004   0.054   1436
  Dihedral  :  4.933  88.773   1129
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 12.18 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.36 (0.27), residues: 1020
  helix:  1.53 (0.27), residues: 387
  sheet: -0.83 (0.33), residues: 222
  loop : -0.26 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG Y 219 
 TYR   0.018   0.002   TYR A 197 
 PHE   0.016   0.001   PHE A 155 
 TRP   0.012   0.002   TRP Y 211 
 HIS   0.004   0.001   HIS X 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 8336)
  covalent geometry    : angle       0.53429 (11287)
  SS BOND              : bond        0.00268 (    2)
  SS BOND              : angle       0.43209 (    4)
  hydrogen bonds       : bond        0.04056 (  444)
  hydrogen bonds       : angle       5.34014 ( 1278)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 ASP cc_start: 0.7565 (t70) cc_final: 0.7094 (t0)
REVERT: X  220 HIS cc_start: 0.8644 (t-170) cc_final: 0.8428 (t-90)
REVERT: Y   59 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.8243 (m-80)
REVERT: Y  138 GLU cc_start: 0.8184 (tp30) cc_final: 0.7786 (tp30)
REVERT: Z   31 SER cc_start: 0.7570 (m) cc_final: 0.7352 (m)
  outliers start: 27
  outliers final: 21
  residues processed: 125
  average time/residue: 0.1016
  time to fit residues: 16.7385
Evaluate side-chains
  129 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   77 ASN
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain X residue   54 SER
Chi-restraints excluded: chain X residue  229 ASP
Chi-restraints excluded: chain X residue  292 ASN
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue  146 LEU
Chi-restraints excluded: chain Y residue  177 THR
Chi-restraints excluded: chain Y residue  186 ASP
Chi-restraints excluded: chain Y residue  189 SER
Chi-restraints excluded: chain Y residue  228 ASP
Chi-restraints excluded: chain Y residue  275 SER
Chi-restraints excluded: chain Y residue  276 VAL
Chi-restraints excluded: chain Z residue   28 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0050
   chunk 44 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 94 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0980
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X  35 GLN
X 292 ASN
Y 175 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.144697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.112277 restraints weight = 9427.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 1.97
r_work: 0.3111 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8338  Z= 0.113
  Angle     :  0.488   6.211  11291  Z= 0.258
  Chirality :  0.041   0.159   1285
  Planarity :  0.004   0.056   1436
  Dihedral  :  4.769  87.887   1129
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 13.08 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.54 (0.27), residues: 1020
  helix:  1.73 (0.27), residues: 389
  sheet: -0.67 (0.33), residues: 212
  loop : -0.30 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y 219 
 TYR   0.016   0.001   TYR A 197 
 PHE   0.017   0.001   PHE A 155 
 TRP   0.015   0.002   TRP Y 169 
 HIS   0.003   0.001   HIS X 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 8336)
  covalent geometry    : angle       0.48833 (11287)
  SS BOND              : bond        0.00237 (    2)
  SS BOND              : angle       0.42332 (    4)
  hydrogen bonds       : bond        0.03693 (  444)
  hydrogen bonds       : angle       5.12084 ( 1278)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.345 
Fit side-chains
REVERT: A  190 ASP cc_start: 0.7519 (t70) cc_final: 0.7046 (t0)
REVERT: A  206 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7431 (mtm)
REVERT: N   32 TYR cc_start: 0.8951 (m-80) cc_final: 0.8578 (m-80)
REVERT: Y   59 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.8037 (m-80)
REVERT: Z   31 SER cc_start: 0.7445 (m) cc_final: 0.7229 (m)
  outliers start: 26
  outliers final: 20
  residues processed: 124
  average time/residue: 0.0896
  time to fit residues: 15.0905
Evaluate side-chains
  126 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   77 ASN
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain X residue   54 SER
Chi-restraints excluded: chain X residue  229 ASP
Chi-restraints excluded: chain X residue  292 ASN
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue  177 THR
Chi-restraints excluded: chain Y residue  189 SER
Chi-restraints excluded: chain Y residue  228 ASP
Chi-restraints excluded: chain Y residue  234 PHE
Chi-restraints excluded: chain Y residue  276 VAL
Chi-restraints excluded: chain Z residue   28 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0070
   chunk 77 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 64 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 98 optimal weight:    9.9990
   overall best weight:    1.1602

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X  35 GLN
** X 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X 292 ASN
Y  32 GLN
Y 175 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.138722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.105482 restraints weight = 9763.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 1.99
r_work: 0.3046 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8338  Z= 0.174
  Angle     :  0.522   7.049  11291  Z= 0.275
  Chirality :  0.043   0.145   1285
  Planarity :  0.004   0.053   1436
  Dihedral  :  4.876  89.270   1129
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 13.87 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.49 (0.27), residues: 1020
  helix:  1.73 (0.27), residues: 387
  sheet: -0.84 (0.32), residues: 225
  loop : -0.24 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y 219 
 TYR   0.016   0.002   TYR A 197 
 PHE   0.016   0.001   PHE A 155 
 TRP   0.011   0.001   TRP Y 211 
 HIS   0.004   0.001   HIS X 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8336)
  covalent geometry    : angle       0.52223 (11287)
  SS BOND              : bond        0.00277 (    2)
  SS BOND              : angle       0.42177 (    4)
  hydrogen bonds       : bond        0.03937 (  444)
  hydrogen bonds       : angle       5.22890 ( 1278)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 ASP cc_start: 0.7541 (t70) cc_final: 0.7060 (t0)
REVERT: A  206 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7498 (mtm)
REVERT: Y   59 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7993 (m-80)
REVERT: Y  138 GLU cc_start: 0.8190 (tp30) cc_final: 0.7837 (tp30)
REVERT: Z   31 SER cc_start: 0.7570 (m) cc_final: 0.7344 (m)
  outliers start: 28
  outliers final: 23
  residues processed: 127
  average time/residue: 0.1003
  time to fit residues: 16.6040
Evaluate side-chains
  136 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   77 ASN
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain X residue   54 SER
Chi-restraints excluded: chain X residue  229 ASP
Chi-restraints excluded: chain X residue  292 ASN
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue  146 LEU
Chi-restraints excluded: chain Y residue  177 THR
Chi-restraints excluded: chain Y residue  186 ASP
Chi-restraints excluded: chain Y residue  189 SER
Chi-restraints excluded: chain Y residue  228 ASP
Chi-restraints excluded: chain Y residue  234 PHE
Chi-restraints excluded: chain Y residue  275 SER
Chi-restraints excluded: chain Y residue  276 VAL
Chi-restraints excluded: chain Z residue   28 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 64 optimal weight:   10.0000
   chunk 53 optimal weight:    0.8980
   chunk 30 optimal weight:    6.9990
   chunk 88 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X  35 GLN
X 292 ASN
Y 175 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.142662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.110098 restraints weight = 9550.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 1.97
r_work: 0.3060 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8338  Z= 0.138
  Angle     :  0.505   6.697  11291  Z= 0.267
  Chirality :  0.042   0.164   1285
  Planarity :  0.004   0.054   1436
  Dihedral  :  4.828  88.961   1129
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 14.32 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.55 (0.27), residues: 1020
  helix:  1.79 (0.27), residues: 388
  sheet: -0.82 (0.33), residues: 225
  loop : -0.22 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y  19 
 TYR   0.016   0.001   TYR A 197 
 PHE   0.016   0.001   PHE A 155 
 TRP   0.013   0.002   TRP Y 169 
 HIS   0.003   0.001   HIS X 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8336)
  covalent geometry    : angle       0.50454 (11287)
  SS BOND              : bond        0.00254 (    2)
  SS BOND              : angle       0.42085 (    4)
  hydrogen bonds       : bond        0.03801 (  444)
  hydrogen bonds       : angle       5.15505 ( 1278)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A  190 ASP cc_start: 0.7507 (t70) cc_final: 0.7006 (t0)
REVERT: A  206 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7476 (mtm)
REVERT: Y   42 ARG cc_start: 0.6723 (tpt170) cc_final: 0.6358 (mmt180)
REVERT: Y   59 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.7988 (m-80)
REVERT: Z   31 SER cc_start: 0.7446 (m) cc_final: 0.7228 (m)
  outliers start: 27
  outliers final: 23
  residues processed: 121
  average time/residue: 0.1052
  time to fit residues: 16.9905
Evaluate side-chains
  128 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   77 ASN
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain X residue   54 SER
Chi-restraints excluded: chain X residue  229 ASP
Chi-restraints excluded: chain X residue  292 ASN
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue  146 LEU
Chi-restraints excluded: chain Y residue  177 THR
Chi-restraints excluded: chain Y residue  186 ASP
Chi-restraints excluded: chain Y residue  189 SER
Chi-restraints excluded: chain Y residue  228 ASP
Chi-restraints excluded: chain Y residue  234 PHE
Chi-restraints excluded: chain Y residue  275 SER
Chi-restraints excluded: chain Y residue  276 VAL
Chi-restraints excluded: chain Z residue   28 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 70 optimal weight:    0.0010
   chunk 9 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 65 optimal weight:    6.9990
   chunk 97 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X  35 GLN
X 292 ASN
Y 175 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.143259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.110805 restraints weight = 9548.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 1.96
r_work: 0.3099 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8338  Z= 0.129
  Angle     :  0.498   6.780  11291  Z= 0.263
  Chirality :  0.042   0.153   1285
  Planarity :  0.004   0.054   1436
  Dihedral  :  4.798  89.510   1129
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 14.32 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.62 (0.27), residues: 1020
  helix:  1.84 (0.27), residues: 388
  sheet: -0.73 (0.33), residues: 218
  loop : -0.21 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y  19 
 TYR   0.016   0.001   TYR A 197 
 PHE   0.015   0.001   PHE A 155 
 TRP   0.013   0.002   TRP Y 169 
 HIS   0.003   0.001   HIS X 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8336)
  covalent geometry    : angle       0.49827 (11287)
  SS BOND              : bond        0.00228 (    2)
  SS BOND              : angle       0.38187 (    4)
  hydrogen bonds       : bond        0.03731 (  444)
  hydrogen bonds       : angle       5.10592 ( 1278)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  190 ASP cc_start: 0.7528 (t70) cc_final: 0.7028 (t0)
REVERT: A  206 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7536 (mtm)
REVERT: Y   42 ARG cc_start: 0.6811 (tpt170) cc_final: 0.6429 (mmt180)
REVERT: Y   59 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.8044 (m-80)
REVERT: Z   31 SER cc_start: 0.7624 (m) cc_final: 0.7397 (m)
  outliers start: 26
  outliers final: 22
  residues processed: 123
  average time/residue: 0.1086
  time to fit residues: 17.7232
Evaluate side-chains
  128 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   77 ASN
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain X residue   54 SER
Chi-restraints excluded: chain X residue  229 ASP
Chi-restraints excluded: chain X residue  292 ASN
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue  177 THR
Chi-restraints excluded: chain Y residue  186 ASP
Chi-restraints excluded: chain Y residue  189 SER
Chi-restraints excluded: chain Y residue  228 ASP
Chi-restraints excluded: chain Y residue  234 PHE
Chi-restraints excluded: chain Y residue  275 SER
Chi-restraints excluded: chain Y residue  276 VAL
Chi-restraints excluded: chain Z residue   28 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 14 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    0.7980
   chunk 85 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X  35 GLN
X 292 ASN
Y 175 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.142463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.109904 restraints weight = 9531.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 1.96
r_work: 0.3087 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8338  Z= 0.148
  Angle     :  0.516   6.937  11291  Z= 0.269
  Chirality :  0.042   0.163   1285
  Planarity :  0.004   0.054   1436
  Dihedral  :  4.820  89.746   1129
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 14.54 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.58 (0.27), residues: 1020
  helix:  1.83 (0.27), residues: 388
  sheet: -0.81 (0.33), residues: 225
  loop : -0.20 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y  19 
 TYR   0.021   0.002   TYR A  34 
 PHE   0.015   0.001   PHE A 155 
 TRP   0.012   0.001   TRP Y 169 
 HIS   0.003   0.001   HIS X 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8336)
  covalent geometry    : angle       0.51570 (11287)
  SS BOND              : bond        0.00244 (    2)
  SS BOND              : angle       0.38576 (    4)
  hydrogen bonds       : bond        0.03798 (  444)
  hydrogen bonds       : angle       5.13146 ( 1278)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  190 ASP cc_start: 0.7513 (t70) cc_final: 0.7025 (t0)
REVERT: A  206 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7547 (mtm)
REVERT: N   80 TYR cc_start: 0.8405 (m-80) cc_final: 0.7962 (m-80)
REVERT: Y   59 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.8076 (m-80)
REVERT: Y  212 ASP cc_start: 0.7664 (t70) cc_final: 0.7393 (t0)
REVERT: Z   31 SER cc_start: 0.7596 (m) cc_final: 0.7367 (m)
  outliers start: 26
  outliers final: 22
  residues processed: 123
  average time/residue: 0.1003
  time to fit residues: 16.6363
Evaluate side-chains
  130 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   77 ASN
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain X residue   54 SER
Chi-restraints excluded: chain X residue  229 ASP
Chi-restraints excluded: chain X residue  292 ASN
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue  146 LEU
Chi-restraints excluded: chain Y residue  177 THR
Chi-restraints excluded: chain Y residue  186 ASP
Chi-restraints excluded: chain Y residue  189 SER
Chi-restraints excluded: chain Y residue  228 ASP
Chi-restraints excluded: chain Y residue  234 PHE
Chi-restraints excluded: chain Y residue  275 SER
Chi-restraints excluded: chain Y residue  276 VAL
Chi-restraints excluded: chain Z residue   28 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 5 optimal weight:    0.0770
   chunk 19 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 67 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.8940

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X  35 GLN
X 292 ASN
Y 175 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.142269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.109628 restraints weight = 9547.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.99
r_work: 0.3062 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8338  Z= 0.149
  Angle     :  0.509   6.942  11291  Z= 0.269
  Chirality :  0.042   0.162   1285
  Planarity :  0.004   0.054   1436
  Dihedral  :  4.816  88.928   1129
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 14.43 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.57 (0.27), residues: 1020
  helix:  1.84 (0.27), residues: 387
  sheet: -0.81 (0.33), residues: 225
  loop : -0.23 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y  19 
 TYR   0.016   0.001   TYR A 197 
 PHE   0.015   0.001   PHE X 212 
 TRP   0.012   0.001   TRP Y 169 
 HIS   0.003   0.001   HIS X 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 8336)
  covalent geometry    : angle       0.50926 (11287)
  SS BOND              : bond        0.00249 (    2)
  SS BOND              : angle       0.38539 (    4)
  hydrogen bonds       : bond        0.03818 (  444)
  hydrogen bonds       : angle       5.13890 ( 1278)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2312.37 seconds
wall clock time: 40 minutes 24.62 seconds (2424.62 seconds total)