Starting phenix.real_space_refine
on Fri Oct 10 17:00:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8itl_35706/10_2025/8itl_35706.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8itl_35706/10_2025/8itl_35706.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8itl_35706/10_2025/8itl_35706.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8itl_35706/10_2025/8itl_35706.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8itl_35706/10_2025/8itl_35706.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8itl_35706/10_2025/8itl_35706.cif"
  }
  resolution = 3.23
  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=  -0.002 sd=   0.093
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      43      5.16       5
     C    5024      2.51       5
     N    1421      2.21       5
     O    1466      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7954
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2139
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2139
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 6, 'TRANS': 271}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 159
          Unresolved non-hydrogen angles: 199
          Unresolved non-hydrogen dihedrals: 127
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 4, 'PHE:plan': 3, 'ASP:plan': 2, 'ARG:plan': 8, 'GLN:plan1': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 96
    Chain: "A"
      Number of atoms: 1875
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1875
          Classifications: {'peptide': 232}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "B"
      Number of atoms: 2567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2567
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 33
    Chain: "G"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 417
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "N"
      Number of atoms: 956
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 956
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 2.35, per 1000 atoms: 0.30
  Number of scatterers: 7954
  At special positions: 0
  Unit cell: (76.041, 102.816, 125.307, 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      43     16.00
     O    1466      8.00
     N    1421      7.00
     C    5024      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 180 " - pdb=" SG  CYS R 250 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.00

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 489.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1942

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 11 sheets defined
      43.4% alpha, 17.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'R' and resid 88 through 126
    Processing helix  chain 'R' and resid 131 through 158
      removed outlier: 3.890A  pdb=" N   LEU R 152 " --> pdb=" O   ALA R 148 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 175 through 211
      removed outlier: 3.854A  pdb=" N   TYR R 195 " --> pdb=" O   VAL R 191 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 219 through 245
      Proline residue:  R 231  - end of helix
      Proline residue:  R 237  - end of helix
    Processing helix  chain 'R' and resid 256 through 293
      removed outlier: 3.987A  pdb=" N   ILE R 262 " --> pdb=" O   ALA R 258 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ILE R 263 " --> pdb=" O   ILE R 259 " (cutoff:3.500A)
      Proline residue:  R 266  - end of helix
      removed outlier: 3.597A  pdb=" N   ARG R 292 " --> pdb=" O   LYS R 288 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 295 through 321
      removed outlier: 3.525A  pdb=" N   ARG R 302 " --> pdb=" O   ASP R 298 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU R 303 " --> pdb=" O   TYR R 299 " (cutoff:3.500A)
      Proline residue:  R 312  - end of helix
    Processing helix  chain 'R' and resid 332 through 356
      removed outlier: 3.792A  pdb=" N   ILE R 342 " --> pdb=" O   LEU R 338 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 360 through 379
    Processing helix  chain 'A' and resid 10 through 40
      removed outlier: 3.767A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 3.678A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 279
      removed outlier: 3.647A  pdb=" N   SER A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 285
      removed outlier: 4.284A  pdb=" N   ASP A 284 " --> pdb=" O   TRP A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 3.528A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 4.430A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.788A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.867A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223
      removed outlier: 7.219A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.986A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 214
    Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51
      removed outlier: 5.639A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.046A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.621A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ASN B 125 " --> pdb=" O   ARG B 134 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 150
      removed outlier: 5.008A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.775A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.510A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.775A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   TYR B 289 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 4 through 6
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.097A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)

    424 hydrogen bonds defined for protein.
    1221 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: 1.02 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: 2652
        1.34 -     1.46: 1957
        1.46 -     1.58: 3446
        1.58 -     1.70: 0
        1.70 -     1.83: 56
  Bond restraints: 8111
  Sorted by residual:
  bond pdb=" CA  PHE N 108 "
       pdb=" C   PHE N 108 "
    ideal  model  delta    sigma   weight residual
    1.528  1.490  0.037 1.35e-02 5.49e+03 7.71e+00
  bond pdb=" CA  MET A 221 "
       pdb=" C   MET A 221 "
    ideal  model  delta    sigma   weight residual
    1.523  1.498  0.025 1.21e-02 6.83e+03 4.15e+00
  bond pdb=" CA  GLU B 260 "
       pdb=" C   GLU B 260 "
    ideal  model  delta    sigma   weight residual
    1.526  1.504  0.023 1.37e-02 5.33e+03 2.76e+00
  bond pdb=" C   VAL R 311 "
       pdb=" N   PRO R 312 "
    ideal  model  delta    sigma   weight residual
    1.333  1.357 -0.023 1.44e-02 4.82e+03 2.64e+00
  bond pdb=" CA  ASN B 293 "
       pdb=" C   ASN B 293 "
    ideal  model  delta    sigma   weight residual
    1.530  1.513  0.017 1.08e-02 8.57e+03 2.57e+00
  ... (remaining 8106 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 10759
        1.65 -     3.30: 201
        3.30 -     4.95: 35
        4.95 -     6.59: 11
        6.59 -     8.24: 3
  Bond angle restraints: 11009
  Sorted by residual:
  angle pdb=" C   PHE A 312 "
        pdb=" N   PRO A 313 "
        pdb=" CA  PRO A 313 "
      ideal   model   delta    sigma   weight residual
     119.28  115.02    4.26 1.10e+00 8.26e-01 1.50e+01
  angle pdb=" N   ASP B 291 "
        pdb=" CA  ASP B 291 "
        pdb=" C   ASP B 291 "
      ideal   model   delta    sigma   weight residual
     113.15  108.61    4.54 1.19e+00 7.06e-01 1.46e+01
  angle pdb=" N   ASP N 109 "
        pdb=" CA  ASP N 109 "
        pdb=" C   ASP N 109 "
      ideal   model   delta    sigma   weight residual
     112.47  116.75   -4.28 1.24e+00 6.50e-01 1.19e+01
  angle pdb=" C   ASP B 195 "
        pdb=" N   THR B 196 "
        pdb=" CA  THR B 196 "
      ideal   model   delta    sigma   weight residual
     121.54  126.51   -4.97 1.91e+00 2.74e-01 6.78e+00
  angle pdb=" N   THR B  87 "
        pdb=" CA  THR B  87 "
        pdb=" CB  THR B  87 "
      ideal   model   delta    sigma   weight residual
     113.65  109.88    3.77 1.47e+00 4.63e-01 6.58e+00
  ... (remaining 11004 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 4343
       17.85 -    35.69: 370
       35.69 -    53.54: 76
       53.54 -    71.39: 3
       71.39 -    89.23: 17
  Dihedral angle restraints: 4809
    sinusoidal: 1805
      harmonic: 3004
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -9.28  -76.72     1      1.00e+01 1.00e-02 7.39e+01
  dihedral pdb=" CB  CYS R 180 "
           pdb=" SG  CYS R 180 "
           pdb=" SG  CYS R 250 "
           pdb=" CB  CYS R 250 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  164.32  -71.32     1      1.00e+01 1.00e-02 6.53e+01
  dihedral pdb=" CB  GLU B 215 "
           pdb=" CG  GLU B 215 "
           pdb=" CD  GLU B 215 "
           pdb=" OE1 GLU B 215 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.04  -88.04     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 4806 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 794
       0.034 -    0.068: 323
       0.068 -    0.102: 92
       0.102 -    0.135: 40
       0.135 -    0.169: 1
  Chirality restraints: 1250
  Sorted by residual:
  chirality pdb=" CA  ASP N 109 "
            pdb=" N   ASP N 109 "
            pdb=" C   ASP N 109 "
            pdb=" CB  ASP N 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.17e-01
  chirality pdb=" CA  VAL B 112 "
            pdb=" N   VAL B 112 "
            pdb=" C   VAL B 112 "
            pdb=" CB  VAL B 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.47e-01
  chirality pdb=" CA  VAL B 327 "
            pdb=" N   VAL B 327 "
            pdb=" C   VAL B 327 "
            pdb=" CB  VAL B 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.45e-01
  ... (remaining 1247 not shown)

  Planarity restraints: 1416
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 220 "    0.013 2.00e-02 2.50e+03   2.69e-02 7.25e+00
        pdb=" C   HIS A 220 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   HIS A 220 "    0.018 2.00e-02 2.50e+03
        pdb=" N   MET A 221 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 352 "   -0.009 2.00e-02 2.50e+03   1.83e-02 3.35e+00
        pdb=" C   VAL R 352 "    0.032 2.00e-02 2.50e+03
        pdb=" O   VAL R 352 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   SER R 353 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 311 "   -0.029 5.00e-02 4.00e+02   4.42e-02 3.13e+00
        pdb=" N   PRO R 312 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO R 312 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO R 312 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1413 not shown)

  Histogram of nonbonded interaction distances:
        1.86 -     2.47: 46
        2.47 -     3.08: 5482
        3.08 -     3.68: 11942
        3.68 -     4.29: 17092
        4.29 -     4.90: 29573
  Nonbonded interactions: 64135
  Sorted by model distance:
  nonbonded pdb=" CZ  PHE B 292 "
            pdb=" OD1 ASN B 313 "
     model   vdw
     1.862 3.340
  nonbonded pdb=" CD1 PHE B 292 "
            pdb=" C   ASN B 313 "
     model   vdw
     2.018 2.856
  nonbonded pdb=" CD2 PHE B 292 "
            pdb=" O   ASP B 312 "
     model   vdw
     2.125 3.340
  nonbonded pdb=" NZ  LYS B  57 "
            pdb=" OH  TYR B  59 "
     model   vdw
     2.128 3.120
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.157 3.040
  ... (remaining 64130 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:             1.490
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.760
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
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      :  0.004   0.079   8115  Z= 0.211
  Angle     :  0.608   8.243  11015  Z= 0.350
  Chirality :  0.042   0.169   1250
  Planarity :  0.003   0.044   1416
  Dihedral  : 14.366  89.234   2858
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  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: -0.13 (0.27), residues: 1019
  helix:  1.82 (0.26), residues: 410
  sheet: -1.08 (0.36), residues: 228
  loop : -1.55 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R  95 
 TYR   0.025   0.002   TYR N 115 
 PHE   0.015   0.002   PHE B 241 
 TRP   0.014   0.001   TRP R 197 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 8111)
  covalent geometry    : angle       0.60802 (11009)
  SS BOND              : bond        0.01804 (    3)
  SS BOND              : angle       0.83057 (    6)
  hydrogen bonds       : bond        0.14663 (  424)
  hydrogen bonds       : angle       5.96147 ( 1221)
  Misc. bond           : bond        0.07867 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.342 
Fit side-chains
REVERT: R   99 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7883 (mt-10)
REVERT: A  209 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6818 (mm-30)
REVERT: B  246 ASP cc_start: 0.7715 (m-30) cc_final: 0.7459 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0948
  time to fit residues: 16.7689
Evaluate side-chains
  102 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
R 373 HIS
A 371 ASN
B 313 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.196441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.155194 restraints weight = 9280.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3839 rms_B_bonded: 2.21
r_work: 0.3562 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.1106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8115  Z= 0.139
  Angle     :  0.540   9.650  11015  Z= 0.284
  Chirality :  0.042   0.157   1250
  Planarity :  0.004   0.060   1416
  Dihedral  :  4.104  19.069   1132
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  8.50 %
    Favored  : 90.52 %
  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:  0.35 (0.28), residues: 1019
  helix:  2.34 (0.26), residues: 408
  sheet: -0.94 (0.36), residues: 224
  loop : -1.36 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.013   0.001   TYR R 195 
 PHE   0.025   0.002   PHE B 292 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8111)
  covalent geometry    : angle       0.53922 (11009)
  SS BOND              : bond        0.00078 (    3)
  SS BOND              : angle       0.99872 (    6)
  hydrogen bonds       : bond        0.04187 (  424)
  hydrogen bonds       : angle       4.44308 ( 1221)
  Misc. bond           : bond        0.00732 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.359 
Fit side-chains
REVERT: R   99 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8340 (mt-10)
REVERT: B  118 ASP cc_start: 0.7947 (t0) cc_final: 0.7710 (t0)
REVERT: B  246 ASP cc_start: 0.8109 (m-30) cc_final: 0.7850 (m-30)
  outliers start: 8
  outliers final: 6
  residues processed: 109
  average time/residue: 0.1081
  time to fit residues: 15.7931
Evaluate side-chains
  98 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  177 LEU
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  313 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 7 optimal weight:   20.0000
   chunk 32 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0670
   chunk 9 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0030
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.5128

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

Flipped N/Q/H residues before XYZ refinement:
B 293 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.199956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.157859 restraints weight = 9222.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 2.22
r_work: 0.3554 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.1389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8115  Z= 0.115
  Angle     :  0.498  10.294  11015  Z= 0.261
  Chirality :  0.040   0.154   1250
  Planarity :  0.004   0.058   1416
  Dihedral  :  3.868  19.011   1132
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 11.70 %
    Favored  : 87.07 %
  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:  0.37 (0.28), residues: 1019
  helix:  2.29 (0.26), residues: 422
  sheet: -0.73 (0.36), residues: 215
  loop : -1.56 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 214 
 TYR   0.012   0.001   TYR R 195 
 PHE   0.025   0.001   PHE B 292 
 TRP   0.011   0.001   TRP R 197 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 8111)
  covalent geometry    : angle       0.49736 (11009)
  SS BOND              : bond        0.00128 (    3)
  SS BOND              : angle       0.82454 (    6)
  hydrogen bonds       : bond        0.03864 (  424)
  hydrogen bonds       : angle       4.14246 ( 1221)
  Misc. bond           : bond        0.00535 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.306 
Fit side-chains
REVERT: R   99 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8299 (mt-10)
REVERT: R  113 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6517 (mp)
REVERT: R  145 MET cc_start: 0.7376 (tpp) cc_final: 0.7098 (tpp)
REVERT: R  335 PHE cc_start: 0.5923 (p90) cc_final: 0.5401 (p90)
REVERT: A  221 MET cc_start: 0.7290 (tpp) cc_final: 0.6996 (mmm)
REVERT: B  175 GLN cc_start: 0.7943 (pm20) cc_final: 0.7652 (pm20)
REVERT: N   87 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7971 (mttm)
  outliers start: 10
  outliers final: 8
  residues processed: 102
  average time/residue: 0.0954
  time to fit residues: 13.3966
Evaluate side-chains
  96 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  113 LEU
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain N residue   35 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 34 optimal weight:    0.4980
   chunk 100 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 81 optimal weight:    0.0870
   chunk 19 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   chunk 1 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.5960

-------------------------------------------------------------------------------
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 = 0.4259 r_free = 0.4259 target = 0.198946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.157114 restraints weight = 9364.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3841 rms_B_bonded: 2.21
r_work: 0.3572 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8115  Z= 0.120
  Angle     :  0.496  10.867  11015  Z= 0.259
  Chirality :  0.040   0.155   1250
  Planarity :  0.004   0.057   1416
  Dihedral  :  3.829  18.843   1132
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.56 %
    Favored  : 85.34 %
  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: 1019
  helix:  2.49 (0.26), residues: 414
  sheet: -0.77 (0.36), residues: 216
  loop : -1.46 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 214 
 TYR   0.012   0.001   TYR R 195 
 PHE   0.020   0.001   PHE R 335 
 TRP   0.011   0.001   TRP R 197 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8111)
  covalent geometry    : angle       0.49591 (11009)
  SS BOND              : bond        0.00171 (    3)
  SS BOND              : angle       0.84438 (    6)
  hydrogen bonds       : bond        0.03769 (  424)
  hydrogen bonds       : angle       4.03939 ( 1221)
  Misc. bond           : bond        0.00654 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.336 
Fit side-chains
REVERT: R   99 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8326 (mt-10)
REVERT: R  335 PHE cc_start: 0.5933 (p90) cc_final: 0.5376 (p90)
REVERT: A   21 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6879 (mt-10)
REVERT: A   60 MET cc_start: 0.6861 (ptt) cc_final: 0.6329 (ptt)
REVERT: A  221 MET cc_start: 0.7336 (tpp) cc_final: 0.7094 (mmm)
REVERT: B  175 GLN cc_start: 0.7923 (pm20) cc_final: 0.7556 (pm20)
REVERT: N   87 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7987 (mttm)
  outliers start: 17
  outliers final: 11
  residues processed: 105
  average time/residue: 0.0966
  time to fit residues: 13.9294
Evaluate side-chains
  101 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  177 LEU
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  245 TYR
Chi-restraints excluded: chain R residue  263 ILE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain N residue   35 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 58 optimal weight:    0.3980
   chunk 94 optimal weight:    0.0000
   overall best weight:    0.6584

-------------------------------------------------------------------------------
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 = 0.4274 r_free = 0.4274 target = 0.200924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.159525 restraints weight = 9395.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 2.28
r_work: 0.3553 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8115  Z= 0.129
  Angle     :  0.543  15.100  11015  Z= 0.273
  Chirality :  0.041   0.154   1250
  Planarity :  0.004   0.057   1416
  Dihedral  :  3.832  18.618   1132
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 14.41 %
    Favored  : 83.50 %
  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:  0.46 (0.27), residues: 1019
  helix:  2.46 (0.26), residues: 414
  sheet: -0.79 (0.36), residues: 217
  loop : -1.47 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 214 
 TYR   0.012   0.001   TYR R 195 
 PHE   0.019   0.001   PHE R 335 
 TRP   0.011   0.001   TRP R 197 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8111)
  covalent geometry    : angle       0.54311 (11009)
  SS BOND              : bond        0.00189 (    3)
  SS BOND              : angle       0.86503 (    6)
  hydrogen bonds       : bond        0.03810 (  424)
  hydrogen bonds       : angle       4.04187 ( 1221)
  Misc. bond           : bond        0.00583 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.311 
Fit side-chains
REVERT: R   99 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8333 (mt-10)
REVERT: R  335 PHE cc_start: 0.5819 (p90) cc_final: 0.5270 (p90)
REVERT: R  341 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7532 (mt-10)
REVERT: R  358 PHE cc_start: 0.6469 (OUTLIER) cc_final: 0.6016 (m-10)
REVERT: A  221 MET cc_start: 0.7350 (tpp) cc_final: 0.7114 (mmm)
REVERT: B  175 GLN cc_start: 0.7889 (pm20) cc_final: 0.7597 (pm20)
REVERT: N   87 LYS cc_start: 0.8241 (mtmm) cc_final: 0.7995 (mttm)
  outliers start: 17
  outliers final: 14
  residues processed: 106
  average time/residue: 0.0968
  time to fit residues: 14.1522
Evaluate side-chains
  107 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 SER
Chi-restraints excluded: chain R residue  177 LEU
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  245 TYR
Chi-restraints excluded: chain R residue  263 ILE
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain N residue   35 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0870
   chunk 44 optimal weight:    0.5980
   chunk 82 optimal weight:    0.8980
   chunk 79 optimal weight:    3.9990
   overall best weight:    0.7160

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.198108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.157088 restraints weight = 9357.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 2.23
r_work: 0.3554 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8115  Z= 0.133
  Angle     :  0.522  11.733  11015  Z= 0.268
  Chirality :  0.041   0.155   1250
  Planarity :  0.004   0.055   1416
  Dihedral  :  3.830  18.581   1132
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.52 %
    Favored  : 82.02 %
  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:  0.45 (0.27), residues: 1019
  helix:  2.47 (0.26), residues: 413
  sheet: -0.87 (0.35), residues: 221
  loop : -1.42 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 214 
 TYR   0.011   0.001   TYR R 356 
 PHE   0.019   0.001   PHE R 335 
 TRP   0.012   0.001   TRP R 197 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8111)
  covalent geometry    : angle       0.52195 (11009)
  SS BOND              : bond        0.00204 (    3)
  SS BOND              : angle       0.88623 (    6)
  hydrogen bonds       : bond        0.03799 (  424)
  hydrogen bonds       : angle       4.02246 ( 1221)
  Misc. bond           : bond        0.00617 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.261 
Fit side-chains
REVERT: R   99 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8322 (mt-10)
REVERT: R  341 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7550 (mt-10)
REVERT: R  358 PHE cc_start: 0.6478 (OUTLIER) cc_final: 0.5960 (m-10)
REVERT: A   21 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6758 (mt-10)
REVERT: A  221 MET cc_start: 0.7309 (tpp) cc_final: 0.7084 (mmm)
REVERT: B   59 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7827 (m-80)
REVERT: B   90 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8552 (m)
REVERT: B  175 GLN cc_start: 0.7866 (pm20) cc_final: 0.7580 (pm20)
REVERT: N   87 LYS cc_start: 0.8312 (mtmm) cc_final: 0.8059 (mttm)
  outliers start: 20
  outliers final: 14
  residues processed: 111
  average time/residue: 0.0806
  time to fit residues: 12.5702
Evaluate side-chains
  110 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 SER
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  245 TYR
Chi-restraints excluded: chain R residue  263 ILE
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   48 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 89 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 84 optimal weight:    9.9990
   chunk 77 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.4218 r_free = 0.4218 target = 0.195441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.153686 restraints weight = 9422.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 2.24
r_work: 0.3514 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8115  Z= 0.183
  Angle     :  0.573  12.109  11015  Z= 0.292
  Chirality :  0.042   0.158   1250
  Planarity :  0.004   0.059   1416
  Dihedral  :  4.060  20.437   1132
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.52 %
    Favored  : 81.65 %
  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:  0.29 (0.27), residues: 1019
  helix:  2.28 (0.26), residues: 412
  sheet: -0.93 (0.35), residues: 221
  loop : -1.45 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 369 
 TYR   0.014   0.001   TYR R 356 
 PHE   0.018   0.002   PHE R 335 
 TRP   0.016   0.001   TRP R 197 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 8111)
  covalent geometry    : angle       0.57237 (11009)
  SS BOND              : bond        0.00267 (    3)
  SS BOND              : angle       1.09322 (    6)
  hydrogen bonds       : bond        0.04168 (  424)
  hydrogen bonds       : angle       4.13288 ( 1221)
  Misc. bond           : bond        0.00701 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.304 
Fit side-chains
REVERT: R  335 PHE cc_start: 0.5885 (p90) cc_final: 0.5304 (p90)
REVERT: R  358 PHE cc_start: 0.6549 (OUTLIER) cc_final: 0.5976 (m-10)
REVERT: A   21 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6802 (mt-10)
REVERT: A   60 MET cc_start: 0.6873 (ptt) cc_final: 0.6554 (ptt)
REVERT: A  221 MET cc_start: 0.7338 (tpp) cc_final: 0.7108 (mmm)
REVERT: B   59 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.7848 (m-80)
REVERT: B   90 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8580 (m)
REVERT: B  175 GLN cc_start: 0.7955 (pm20) cc_final: 0.7614 (pm20)
REVERT: B  234 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.7835 (m-80)
REVERT: N   87 LYS cc_start: 0.8342 (mtmm) cc_final: 0.8080 (mttm)
  outliers start: 23
  outliers final: 15
  residues processed: 112
  average time/residue: 0.0818
  time to fit residues: 12.9515
Evaluate side-chains
  108 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 SER
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  210 VAL
Chi-restraints excluded: chain R residue  245 TYR
Chi-restraints excluded: chain R residue  263 ILE
Chi-restraints excluded: chain R residue  279 ILE
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain N residue   35 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 63 optimal weight:    0.4980
   chunk 81 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 21 optimal weight:    0.1980
   chunk 5 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4242 r_free = 0.4242 target = 0.198184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.157039 restraints weight = 9389.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 2.23
r_work: 0.3553 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8115  Z= 0.124
  Angle     :  0.525  12.040  11015  Z= 0.268
  Chirality :  0.041   0.184   1250
  Planarity :  0.004   0.056   1416
  Dihedral  :  3.891  18.979   1132
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 16.50 %
    Favored  : 81.40 %
  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:  0.41 (0.27), residues: 1019
  helix:  2.39 (0.26), residues: 413
  sheet: -0.88 (0.35), residues: 221
  loop : -1.40 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  19 
 TYR   0.013   0.001   TYR R 195 
 PHE   0.017   0.001   PHE R 335 
 TRP   0.012   0.001   TRP N  47 
 HIS   0.002   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8111)
  covalent geometry    : angle       0.52453 (11009)
  SS BOND              : bond        0.00202 (    3)
  SS BOND              : angle       0.87693 (    6)
  hydrogen bonds       : bond        0.03764 (  424)
  hydrogen bonds       : angle       4.00856 ( 1221)
  Misc. bond           : bond        0.00607 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: R  335 PHE cc_start: 0.5734 (p90) cc_final: 0.5196 (p90)
REVERT: R  341 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7469 (mt-10)
REVERT: R  358 PHE cc_start: 0.6605 (OUTLIER) cc_final: 0.5906 (m-10)
REVERT: A   21 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6799 (mt-10)
REVERT: A   60 MET cc_start: 0.6797 (ptt) cc_final: 0.6507 (ptt)
REVERT: A  221 MET cc_start: 0.7274 (tpp) cc_final: 0.7061 (mmm)
REVERT: B   59 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.7873 (m-80)
REVERT: B   90 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8545 (m)
REVERT: B  118 ASP cc_start: 0.7814 (t0) cc_final: 0.7593 (t0)
REVERT: B  175 GLN cc_start: 0.7869 (pm20) cc_final: 0.7573 (pm20)
REVERT: N   87 LYS cc_start: 0.8334 (mtmm) cc_final: 0.8092 (mttm)
  outliers start: 17
  outliers final: 12
  residues processed: 106
  average time/residue: 0.0916
  time to fit residues: 13.6481
Evaluate side-chains
  108 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 SER
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  245 TYR
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain N residue   35 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0050
   chunk 54 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.197513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.156348 restraints weight = 9352.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 2.24
r_work: 0.3543 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8115  Z= 0.134
  Angle     :  0.537  11.796  11015  Z= 0.272
  Chirality :  0.041   0.227   1250
  Planarity :  0.004   0.057   1416
  Dihedral  :  3.889  19.334   1132
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 16.87 %
    Favored  : 81.03 %
  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:  0.43 (0.27), residues: 1019
  helix:  2.38 (0.26), residues: 413
  sheet: -0.79 (0.35), residues: 219
  loop : -1.40 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  19 
 TYR   0.012   0.001   TYR R 195 
 PHE   0.018   0.001   PHE R 335 
 TRP   0.013   0.001   TRP N  47 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8111)
  covalent geometry    : angle       0.53632 (11009)
  SS BOND              : bond        0.00212 (    3)
  SS BOND              : angle       0.88882 (    6)
  hydrogen bonds       : bond        0.03774 (  424)
  hydrogen bonds       : angle       4.02398 ( 1221)
  Misc. bond           : bond        0.00610 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: R  335 PHE cc_start: 0.5688 (p90) cc_final: 0.5168 (p90)
REVERT: R  341 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7385 (mt-10)
REVERT: R  358 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.5912 (m-10)
REVERT: A   21 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6828 (mt-10)
REVERT: A   60 MET cc_start: 0.6851 (ptt) cc_final: 0.6559 (ptt)
REVERT: A  221 MET cc_start: 0.7276 (tpp) cc_final: 0.7060 (mmm)
REVERT: A  311 TYR cc_start: 0.6952 (m-80) cc_final: 0.6695 (m-80)
REVERT: B   59 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.7916 (m-80)
REVERT: B   90 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8579 (m)
REVERT: B  118 ASP cc_start: 0.7822 (t0) cc_final: 0.7601 (t0)
REVERT: B  175 GLN cc_start: 0.7907 (pm20) cc_final: 0.7580 (pm20)
REVERT: B  234 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.7876 (m-80)
REVERT: N   87 LYS cc_start: 0.8334 (mtmm) cc_final: 0.8089 (mttm)
  outliers start: 17
  outliers final: 12
  residues processed: 107
  average time/residue: 0.0873
  time to fit residues: 13.0537
Evaluate side-chains
  110 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 SER
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  245 TYR
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain N residue   35 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 88 optimal weight:    0.0970
   chunk 58 optimal weight:    0.4980
   chunk 70 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0770
   chunk 23 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0980
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.3336

-------------------------------------------------------------------------------
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 = 0.4266 r_free = 0.4266 target = 0.200622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.160317 restraints weight = 9354.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3856 rms_B_bonded: 2.18
r_work: 0.3591 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8115  Z= 0.101
  Angle     :  0.514  12.142  11015  Z= 0.259
  Chirality :  0.040   0.204   1250
  Planarity :  0.003   0.054   1416
  Dihedral  :  3.720  18.361   1132
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 17.86 %
    Favored  : 80.54 %
  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:  0.56 (0.27), residues: 1019
  helix:  2.47 (0.26), residues: 415
  sheet: -0.73 (0.35), residues: 219
  loop : -1.34 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  19 
 TYR   0.013   0.001   TYR R 195 
 PHE   0.017   0.001   PHE R 335 
 TRP   0.011   0.001   TRP N  47 
 HIS   0.002   0.000   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 8111)
  covalent geometry    : angle       0.51350 (11009)
  SS BOND              : bond        0.00158 (    3)
  SS BOND              : angle       0.73924 (    6)
  hydrogen bonds       : bond        0.03462 (  424)
  hydrogen bonds       : angle       3.92056 ( 1221)
  Misc. bond           : bond        0.00526 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  252 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6447 (pt0)
REVERT: R  335 PHE cc_start: 0.5575 (p90) cc_final: 0.5065 (p90)
REVERT: R  341 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7461 (mt-10)
REVERT: R  358 PHE cc_start: 0.6764 (OUTLIER) cc_final: 0.6073 (m-80)
REVERT: A   21 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6861 (mt-10)
REVERT: A   60 MET cc_start: 0.6735 (ptt) cc_final: 0.6458 (ptt)
REVERT: A  221 MET cc_start: 0.7266 (tpp) cc_final: 0.7037 (mmm)
REVERT: A  311 TYR cc_start: 0.6891 (m-80) cc_final: 0.6671 (m-80)
REVERT: B   59 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.7852 (m-80)
REVERT: B  234 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8019 (m-80)
REVERT: N   87 LYS cc_start: 0.8320 (mtmm) cc_final: 0.8102 (mttm)
  outliers start: 13
  outliers final: 9
  residues processed: 109
  average time/residue: 0.0967
  time to fit residues: 14.4511
Evaluate side-chains
  104 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  245 TYR
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   35 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 4 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 77 optimal weight:    0.5980
   chunk 40 optimal weight:    8.9990
   chunk 45 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.4227 r_free = 0.4227 target = 0.196371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.155192 restraints weight = 9352.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3807 rms_B_bonded: 2.23
r_work: 0.3531 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8115  Z= 0.165
  Angle     :  0.567  12.527  11015  Z= 0.287
  Chirality :  0.042   0.206   1250
  Planarity :  0.004   0.058   1416
  Dihedral  :  3.939  20.042   1132
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 17.73 %
    Favored  : 80.30 %
  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:  0.46 (0.27), residues: 1019
  helix:  2.35 (0.26), residues: 414
  sheet: -0.78 (0.35), residues: 219
  loop : -1.33 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG N  19 
 TYR   0.012   0.001   TYR R 356 
 PHE   0.017   0.002   PHE R 335 
 TRP   0.015   0.001   TRP R 197 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 8111)
  covalent geometry    : angle       0.56657 (11009)
  SS BOND              : bond        0.00233 (    3)
  SS BOND              : angle       0.96771 (    6)
  hydrogen bonds       : bond        0.03912 (  424)
  hydrogen bonds       : angle       4.06317 ( 1221)
  Misc. bond           : bond        0.00641 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2061.33 seconds
wall clock time: 36 minutes 5.55 seconds (2165.55 seconds total)