Starting phenix.real_space_refine
on Fri Aug 22 17:00:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8geb_29964/08_2025/8geb_29964.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8geb_29964/08_2025/8geb_29964.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8geb_29964/08_2025/8geb_29964.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8geb_29964/08_2025/8geb_29964.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8geb_29964/08_2025/8geb_29964.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8geb_29964/08_2025/8geb_29964.cif"
  }
  resolution = 3.6
  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=  -0.001 sd=   0.028
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      36      5.16       5
     C    4017      2.51       5
     N    1091      2.21       5
     O    1079      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  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: 6223
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1650
          Classifications: {'peptide': 233}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 79}
          Link IDs: {'PTRANS': 6, 'TRANS': 226}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 299
          Unresolved non-hydrogen angles: 364
          Unresolved non-hydrogen dihedrals: 238
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 12, 'ASN:plan1': 2, 'GLU:plan': 17, 'ASP:plan': 11, 'PHE:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 198
    Chain: "B"
      Number of atoms: 2301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2301
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 77}
          Link IDs: {'PTRANS': 5, 'TRANS': 323}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 227
          Unresolved non-hydrogen angles: 287
          Unresolved non-hydrogen dihedrals: 167
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'ARG:plan': 7, 'GLN:plan1': 6, 'GLU:plan': 6, 'ASN:plan1': 6, 'ASP:plan': 19}
          Unresolved non-hydrogen planarities: 158
    Chain: "G"
      Number of atoms: 319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 319
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 84
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "R"
      Number of atoms: 1938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 1938
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 97}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 330
          Unresolved non-hydrogen angles: 416
          Unresolved non-hydrogen dihedrals: 267
          Unresolved non-hydrogen chiralities: 36
          Planarities with less than four sites: {'TRP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 9, 'GLN:plan1': 8, 'ASP:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 6, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 162
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.90, per 1000 atoms: 0.31
  Number of scatterers: 6223
  At special positions: 0
  Unit cell: (68.9, 98.58, 127.2, 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      36     16.00
     O    1079      8.00
     N    1091      7.00
     C    4017      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " 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: 0.56
  Conformation dependent library (CDL) restraints added in 434.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1694

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      47.5% alpha, 16.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 4.420A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 233 through 237
      removed outlier: 4.043A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.735A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.641A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.326A  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 8 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.522A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 14 through 24
      removed outlier: 3.546A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.683A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   MET R  40 " --> pdb=" O   MET R  36 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 3.895A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 171
      Proline residue:  R 168  - end of helix
      removed outlier: 3.506A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 270 through 298
      removed outlier: 4.111A  pdb=" N   CYS R 285 " --> pdb=" O   THR R 281 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.169A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 318
    Processing helix  chain 'R' and resid 321 through 327
      removed outlier: 3.611A  pdb=" N   ILE R 325 " --> pdb=" O   PHE R 321 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 329 through 340
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214
      removed outlier: 6.848A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.683A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 50
      removed outlier: 5.914A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   THR B 329 " --> pdb=" O   LYS B 337 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 61
      removed outlier: 7.102A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.507A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.523A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.310A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   CYS B 166 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.807A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.187A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.790A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.272A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)

    373 hydrogen bonds defined for protein.
    1086 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: 0.97

  Time building geometry restraints manager: 0.72 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: 1987
        1.34 -     1.45: 886
        1.45 -     1.57: 3436
        1.57 -     1.69: 1
        1.69 -     1.81: 48
  Bond restraints: 6358
  Sorted by residual:
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.575 -0.052 2.00e-02 2.50e+03 6.78e+00
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.449 -0.052 2.00e-02 2.50e+03 6.77e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.441 -0.047 2.00e-02 2.50e+03 5.49e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 2.00e-02 2.50e+03 4.89e+00
  bond pdb=" CA  ALA B  73 "
       pdb=" CB  ALA B  73 "
    ideal  model  delta    sigma   weight residual
    1.532  1.496  0.035 1.82e-02 3.02e+03 3.79e+00
  ... (remaining 6353 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 8572
        1.70 -     3.41: 121
        3.41 -     5.11: 13
        5.11 -     6.82: 6
        6.82 -     8.52: 2
  Bond angle restraints: 8714
  Sorted by residual:
  angle pdb=" N   ILE B 269 "
        pdb=" CA  ILE B 269 "
        pdb=" C   ILE B 269 "
      ideal   model   delta    sigma   weight residual
     109.34  117.26   -7.92 2.08e+00 2.31e-01 1.45e+01
  angle pdb=" CB  MET B 188 "
        pdb=" CG  MET B 188 "
        pdb=" SD  MET B 188 "
      ideal   model   delta    sigma   weight residual
     112.70  104.18    8.52 3.00e+00 1.11e-01 8.06e+00
  angle pdb=" N   CYS B 271 "
        pdb=" CA  CYS B 271 "
        pdb=" C   CYS B 271 "
      ideal   model   delta    sigma   weight residual
     110.59  114.37   -3.78 1.45e+00 4.76e-01 6.79e+00
  angle pdb=" N   SER B  74 "
        pdb=" CA  SER B  74 "
        pdb=" C   SER B  74 "
      ideal   model   delta    sigma   weight residual
     109.85  113.95   -4.10 1.58e+00 4.01e-01 6.73e+00
  angle pdb=" C   VAL R 295 "
        pdb=" N   HIS R 296 "
        pdb=" CA  HIS R 296 "
      ideal   model   delta    sigma   weight residual
     121.14  116.74    4.40 1.75e+00 3.27e-01 6.31e+00
  ... (remaining 8709 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.71: 3352
       16.71 -    33.41: 249
       33.41 -    50.12: 45
       50.12 -    66.82: 9
       66.82 -    83.53: 2
  Dihedral angle restraints: 3657
    sinusoidal: 1051
      harmonic: 2606
  Sorted by residual:
  dihedral pdb=" CA  ILE R 298 "
           pdb=" C   ILE R 298 "
           pdb=" N   GLN R 299 "
           pdb=" CA  GLN R 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.25   16.75     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  MET B 262 "
           pdb=" C   MET B 262 "
           pdb=" N   THR B 263 "
           pdb=" CA  THR B 263 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.40   16.60     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.49   16.51     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 3654 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 650
       0.030 -    0.060: 273
       0.060 -    0.090: 84
       0.090 -    0.121: 41
       0.121 -    0.151: 2
  Chirality restraints: 1050
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.55   -0.15 2.00e-01 2.50e+01 5.68e-01
  chirality pdb=" CA  ILE A 288 "
            pdb=" N   ILE A 288 "
            pdb=" C   ILE A 288 "
            pdb=" CB  ILE A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.41e-01
  chirality pdb=" CA  ILE A 244 "
            pdb=" N   ILE A 244 "
            pdb=" C   ILE A 244 "
            pdb=" CB  ILE A 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.62e-01
  ... (remaining 1047 not shown)

  Planarity restraints: 1106
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 322 "    0.029 5.00e-02 4.00e+02   4.37e-02 3.06e+00
        pdb=" N   PRO R 323 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO R 323 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO R 323 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "   -0.020 5.00e-02 4.00e+02   2.95e-02 1.39e+00
        pdb=" N   PRO B 194 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 320 "    0.018 5.00e-02 4.00e+02   2.73e-02 1.19e+00
        pdb=" N   PRO A 321 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 321 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 321 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1103 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 2190
        2.85 -     3.36: 5967
        3.36 -     3.87: 10203
        3.87 -     4.39: 10707
        4.39 -     4.90: 19725
  Nonbonded interactions: 48792
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP R 113 "
            pdb=" OH  TYR R 316 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" OG  SER B 279 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" NH1 ARG B 137 "
            pdb=" O   ILE B 171 "
     model   vdw
     2.373 3.120
  nonbonded pdb=" OD1 ASP R 113 "
            pdb=" OAM G1I R 501 "
     model   vdw
     2.375 3.040
  nonbonded pdb=" O   ARG A 283 "
            pdb=" NH1 ARG A 356 "
     model   vdw
     2.380 3.120
  ... (remaining 48787 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.160
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.140
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
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      :  0.003   0.052   6359  Z= 0.163
  Angle     :  0.520   8.519   8716  Z= 0.275
  Chirality :  0.040   0.151   1050
  Planarity :  0.003   0.044   1106
  Dihedral  : 12.499  83.527   1960
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  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:  1.44 (0.29), residues: 875
  helix:  2.72 (0.26), residues: 396
  sheet:  0.15 (0.41), residues: 162
  loop : -0.95 (0.32), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  49 
 TYR   0.011   0.001   TYR R 199 
 PHE   0.007   0.001   PHE A 212 
 TRP   0.017   0.001   TRP A 281 
 HIS   0.006   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6358)
  covalent geometry    : angle       0.52000 ( 8714)
  SS BOND              : bond        0.00379 (    1)
  SS BOND              : angle       0.28311 (    2)
  hydrogen bonds       : bond        0.13781 (  373)
  hydrogen bonds       : angle       5.93691 ( 1086)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.279 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.0653
  time to fit residues: 8.0872
Evaluate side-chains
  64 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.123162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.105820 restraints weight = 10754.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.108603 restraints weight = 6477.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.110269 restraints weight = 4576.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.111698 restraints weight = 3643.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.112206 restraints weight = 3034.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.1130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   6359  Z= 0.237
  Angle     :  0.546   5.828   8716  Z= 0.295
  Chirality :  0.042   0.143   1050
  Planarity :  0.004   0.045   1106
  Dihedral  :  4.679  31.062    959
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 11.00 %
    Favored  : 86.60 %
  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:  1.18 (0.29), residues: 875
  helix:  2.49 (0.26), residues: 399
  sheet: -0.01 (0.40), residues: 161
  loop : -1.07 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  49 
 TYR   0.015   0.002   TYR R 199 
 PHE   0.015   0.002   PHE B 235 
 TRP   0.013   0.002   TRP B 169 
 HIS   0.008   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00559 ( 6358)
  covalent geometry    : angle       0.54569 ( 8714)
  SS BOND              : bond        0.00825 (    1)
  SS BOND              : angle       0.73411 (    2)
  hydrogen bonds       : bond        0.04253 (  373)
  hydrogen bonds       : angle       4.76363 ( 1086)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.243 
Fit side-chains
REVERT: B  233 CYS cc_start: 0.8329 (t) cc_final: 0.8077 (t)
REVERT: B  258 ASP cc_start: 0.8388 (t70) cc_final: 0.8161 (t0)
REVERT: R   58 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8380 (mp)
  outliers start: 12
  outliers final: 11
  residues processed: 80
  average time/residue: 0.0569
  time to fit residues: 6.8796
Evaluate side-chains
  78 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   48 VAL
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 60 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 85 optimal weight:    0.6980
   chunk 20 optimal weight:    0.4980
   chunk 77 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 72 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.126214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.109000 restraints weight = 10686.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.111884 restraints weight = 6334.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.113841 restraints weight = 4426.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.115040 restraints weight = 3425.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.116135 restraints weight = 2877.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.1209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6359  Z= 0.134
  Angle     :  0.452   5.508   8716  Z= 0.246
  Chirality :  0.040   0.200   1050
  Planarity :  0.003   0.043   1106
  Dihedral  :  4.388  28.207    959
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.40 %
    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:  1.39 (0.29), residues: 875
  helix:  2.77 (0.25), residues: 393
  sheet:  0.16 (0.41), residues: 156
  loop : -1.07 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  49 
 TYR   0.012   0.001   TYR R 199 
 PHE   0.009   0.001   PHE A 212 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6358)
  covalent geometry    : angle       0.45208 ( 8714)
  SS BOND              : bond        0.00411 (    1)
  SS BOND              : angle       0.46351 (    2)
  hydrogen bonds       : bond        0.03660 (  373)
  hydrogen bonds       : angle       4.41023 ( 1086)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.248 
Fit side-chains
REVERT: B  233 CYS cc_start: 0.8267 (t) cc_final: 0.7988 (t)
REVERT: B  258 ASP cc_start: 0.8242 (t70) cc_final: 0.7979 (t0)
REVERT: R   58 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8373 (mp)
  outliers start: 11
  outliers final: 7
  residues processed: 79
  average time/residue: 0.0575
  time to fit residues: 6.8828
Evaluate side-chains
  77 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 81 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.124204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.106251 restraints weight = 10475.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.109362 restraints weight = 5994.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.111432 restraints weight = 4107.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.112852 restraints weight = 3168.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.113601 restraints weight = 2622.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6359  Z= 0.137
  Angle     :  0.446   5.495   8716  Z= 0.243
  Chirality :  0.040   0.207   1050
  Planarity :  0.003   0.043   1106
  Dihedral  :  4.245  28.361    959
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 17.40 %
    Favored  : 79.80 %
  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:  1.40 (0.29), residues: 875
  helix:  2.81 (0.25), residues: 393
  sheet: -0.03 (0.40), residues: 164
  loop : -1.02 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R  63 
 TYR   0.013   0.001   TYR R 199 
 PHE   0.009   0.001   PHE A 212 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6358)
  covalent geometry    : angle       0.44641 ( 8714)
  SS BOND              : bond        0.00421 (    1)
  SS BOND              : angle       0.40366 (    2)
  hydrogen bonds       : bond        0.03543 (  373)
  hydrogen bonds       : angle       4.23094 ( 1086)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.8959 (mtpt) cc_final: 0.8723 (ttmm)
REVERT: B   82 TRP cc_start: 0.8094 (OUTLIER) cc_final: 0.7307 (m-90)
REVERT: B  233 CYS cc_start: 0.8253 (t) cc_final: 0.7956 (t)
REVERT: B  258 ASP cc_start: 0.8213 (t70) cc_final: 0.7983 (t0)
  outliers start: 14
  outliers final: 10
  residues processed: 79
  average time/residue: 0.0559
  time to fit residues: 6.7091
Evaluate side-chains
  77 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 34 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.122696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.105446 restraints weight = 11012.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.108249 restraints weight = 6599.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.110150 restraints weight = 4625.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.111365 restraints weight = 3608.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.111964 restraints weight = 3045.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6359  Z= 0.206
  Angle     :  0.513   6.836   8716  Z= 0.276
  Chirality :  0.041   0.209   1050
  Planarity :  0.003   0.042   1106
  Dihedral  :  4.417  28.587    959
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.40 %
    Favored  : 79.40 %
  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:  1.17 (0.29), residues: 875
  helix:  2.62 (0.25), residues: 393
  sheet: -0.20 (0.40), residues: 158
  loop : -1.09 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R  63 
 TYR   0.015   0.002   TYR R 199 
 PHE   0.015   0.001   PHE B 235 
 TRP   0.011   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 6358)
  covalent geometry    : angle       0.51250 ( 8714)
  SS BOND              : bond        0.00729 (    1)
  SS BOND              : angle       0.70426 (    2)
  hydrogen bonds       : bond        0.03917 (  373)
  hydrogen bonds       : angle       4.37738 ( 1086)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.8999 (mtpt) cc_final: 0.8753 (ttmm)
REVERT: B   82 TRP cc_start: 0.8179 (OUTLIER) cc_final: 0.7495 (m-10)
REVERT: B  233 CYS cc_start: 0.8318 (t) cc_final: 0.8109 (t)
REVERT: B  258 ASP cc_start: 0.8265 (t70) cc_final: 0.8042 (t0)
  outliers start: 16
  outliers final: 14
  residues processed: 79
  average time/residue: 0.0654
  time to fit residues: 7.4109
Evaluate side-chains
  81 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   48 VAL
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  324 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 74 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 79 optimal weight:    0.6980
   chunk 23 optimal weight:   10.0000
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 318 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.121905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.103924 restraints weight = 10509.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.106935 restraints weight = 6077.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.108795 restraints weight = 4209.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.110342 restraints weight = 3292.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.111253 restraints weight = 2725.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6359  Z= 0.174
  Angle     :  0.484   6.886   8716  Z= 0.260
  Chirality :  0.040   0.207   1050
  Planarity :  0.003   0.042   1106
  Dihedral  :  4.357  29.166    959
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 17.40 %
    Favored  : 78.80 %
  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:  1.17 (0.29), residues: 875
  helix:  2.68 (0.26), residues: 393
  sheet: -0.30 (0.41), residues: 158
  loop : -1.11 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  49 
 TYR   0.013   0.001   TYR R 199 
 PHE   0.011   0.001   PHE B 235 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 6358)
  covalent geometry    : angle       0.48379 ( 8714)
  SS BOND              : bond        0.00560 (    1)
  SS BOND              : angle       0.56775 (    2)
  hydrogen bonds       : bond        0.03710 (  373)
  hydrogen bonds       : angle       4.28514 ( 1086)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8757 (ttmm)
REVERT: B   82 TRP cc_start: 0.8146 (OUTLIER) cc_final: 0.7459 (m-10)
REVERT: B  258 ASP cc_start: 0.8228 (t70) cc_final: 0.8026 (t0)
REVERT: R  316 TYR cc_start: 0.8027 (m-10) cc_final: 0.7754 (m-10)
  outliers start: 19
  outliers final: 15
  residues processed: 87
  average time/residue: 0.0577
  time to fit residues: 7.5044
Evaluate side-chains
  84 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  324 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0870
   chunk 47 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0050
   chunk 49 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    0.2980
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.3572

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.126080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.108306 restraints weight = 10363.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.111403 restraints weight = 5932.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.113549 restraints weight = 4086.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.115036 restraints weight = 3122.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.116078 restraints weight = 2561.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6359  Z= 0.097
  Angle     :  0.427   6.467   8716  Z= 0.232
  Chirality :  0.039   0.219   1050
  Planarity :  0.003   0.040   1106
  Dihedral  :  4.072  29.797    959
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 19.00 %
    Favored  : 77.80 %
  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:  1.38 (0.29), residues: 875
  helix:  2.95 (0.26), residues: 393
  sheet: -0.33 (0.40), residues: 165
  loop : -1.07 (0.33), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  49 
 TYR   0.011   0.001   TYR R 199 
 PHE   0.010   0.001   PHE A 212 
 TRP   0.017   0.001   TRP A 281 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 6358)
  covalent geometry    : angle       0.42734 ( 8714)
  SS BOND              : bond        0.00137 (    1)
  SS BOND              : angle       0.24674 (    2)
  hydrogen bonds       : bond        0.03253 (  373)
  hydrogen bonds       : angle       3.97339 ( 1086)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.8953 (mtpt) cc_final: 0.8672 (ttmm)
REVERT: B   82 TRP cc_start: 0.8048 (OUTLIER) cc_final: 0.7285 (m-10)
REVERT: B  234 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8452 (t80)
  outliers start: 16
  outliers final: 11
  residues processed: 89
  average time/residue: 0.0546
  time to fit residues: 7.3901
Evaluate side-chains
  84 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0000
   chunk 18 optimal weight:    2.9990
   chunk 80 optimal weight:    0.2980
   chunk 5 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.125115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.107382 restraints weight = 10455.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.110440 restraints weight = 5997.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.112377 restraints weight = 4121.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.113976 restraints weight = 3198.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.114882 restraints weight = 2618.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6359  Z= 0.122
  Angle     :  0.460   6.362   8716  Z= 0.249
  Chirality :  0.040   0.218   1050
  Planarity :  0.003   0.041   1106
  Dihedral  :  4.054  29.745    959
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 19.80 %
    Favored  : 77.00 %
  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:  1.43 (0.29), residues: 875
  helix:  2.95 (0.26), residues: 393
  sheet: -0.29 (0.40), residues: 164
  loop : -0.98 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  49 
 TYR   0.012   0.001   TYR R 199 
 PHE   0.009   0.001   PHE A 212 
 TRP   0.018   0.001   TRP A 281 
 HIS   0.002   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6358)
  covalent geometry    : angle       0.45969 ( 8714)
  SS BOND              : bond        0.00302 (    1)
  SS BOND              : angle       0.22748 (    2)
  hydrogen bonds       : bond        0.03356 (  373)
  hydrogen bonds       : angle       3.94824 ( 1086)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.8961 (mtpt) cc_final: 0.8687 (ttmm)
REVERT: B   82 TRP cc_start: 0.8067 (OUTLIER) cc_final: 0.7381 (m-10)
  outliers start: 16
  outliers final: 14
  residues processed: 82
  average time/residue: 0.0554
  time to fit residues: 7.0012
Evaluate side-chains
  83 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  324 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 81 optimal weight:    0.5980
   chunk 5 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 58 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 52 optimal weight:    0.3980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3632 r_free = 0.3632 target = 0.126599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.109617 restraints weight = 10877.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.112461 restraints weight = 6394.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.114498 restraints weight = 4439.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.115831 restraints weight = 3408.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.116792 restraints weight = 2826.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6359  Z= 0.127
  Angle     :  0.464   6.645   8716  Z= 0.252
  Chirality :  0.040   0.219   1050
  Planarity :  0.003   0.041   1106
  Dihedral  :  4.046  30.034    959
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 20.60 %
    Favored  : 76.60 %
  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:  1.40 (0.29), residues: 875
  helix:  2.90 (0.26), residues: 393
  sheet: -0.28 (0.40), residues: 163
  loop : -0.99 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  49 
 TYR   0.012   0.001   TYR R 199 
 PHE   0.009   0.001   PHE A 212 
 TRP   0.015   0.001   TRP A 281 
 HIS   0.002   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6358)
  covalent geometry    : angle       0.46394 ( 8714)
  SS BOND              : bond        0.00344 (    1)
  SS BOND              : angle       0.28819 (    2)
  hydrogen bonds       : bond        0.03426 (  373)
  hydrogen bonds       : angle       3.95978 ( 1086)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8672 (ttmm)
REVERT: B   82 TRP cc_start: 0.8117 (OUTLIER) cc_final: 0.7398 (m-10)
  outliers start: 14
  outliers final: 13
  residues processed: 81
  average time/residue: 0.0571
  time to fit residues: 7.0165
Evaluate side-chains
  81 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  324 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 61 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 86 optimal weight:    0.0020
   overall best weight:    0.6788

-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.126441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.109300 restraints weight = 10808.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.112088 restraints weight = 6420.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.113931 restraints weight = 4511.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.115449 restraints weight = 3527.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.116236 restraints weight = 2917.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6359  Z= 0.129
  Angle     :  0.469   6.587   8716  Z= 0.255
  Chirality :  0.040   0.221   1050
  Planarity :  0.003   0.041   1106
  Dihedral  :  4.047  30.272    959
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 20.80 %
    Favored  : 76.20 %
  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:  1.40 (0.29), residues: 875
  helix:  2.83 (0.26), residues: 399
  sheet: -0.20 (0.41), residues: 158
  loop : -1.01 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  49 
 TYR   0.013   0.001   TYR R 199 
 PHE   0.009   0.001   PHE A 212 
 TRP   0.015   0.001   TRP A 281 
 HIS   0.002   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6358)
  covalent geometry    : angle       0.46938 ( 8714)
  SS BOND              : bond        0.00352 (    1)
  SS BOND              : angle       0.33492 (    2)
  hydrogen bonds       : bond        0.03412 (  373)
  hydrogen bonds       : angle       3.95509 ( 1086)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.8972 (mtpt) cc_final: 0.8677 (ttmm)
REVERT: B   82 TRP cc_start: 0.8128 (OUTLIER) cc_final: 0.7476 (m-10)
  outliers start: 15
  outliers final: 13
  residues processed: 80
  average time/residue: 0.0592
  time to fit residues: 7.1737
Evaluate side-chains
  81 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  324 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 52 optimal weight:    0.5980
   chunk 61 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0270
   chunk 36 optimal weight:    0.1980
   chunk 43 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.4838

-------------------------------------------------------------------------------
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 = 0.3630 r_free = 0.3630 target = 0.125575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.108008 restraints weight = 10465.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.111125 restraints weight = 5945.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.113058 restraints weight = 4050.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.114680 restraints weight = 3137.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.115631 restraints weight = 2557.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6359  Z= 0.110
  Angle     :  0.454   6.789   8716  Z= 0.246
  Chirality :  0.040   0.222   1050
  Planarity :  0.003   0.040   1106
  Dihedral  :  3.974  30.372    959
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 20.40 %
    Favored  : 76.60 %
  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:  1.44 (0.29), residues: 875
  helix:  2.98 (0.26), residues: 393
  sheet: -0.35 (0.40), residues: 162
  loop : -0.97 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 197 
 TYR   0.012   0.001   TYR R 199 
 PHE   0.009   0.001   PHE A 212 
 TRP   0.013   0.001   TRP A 281 
 HIS   0.002   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 6358)
  covalent geometry    : angle       0.45409 ( 8714)
  SS BOND              : bond        0.00229 (    1)
  SS BOND              : angle       0.17725 (    2)
  hydrogen bonds       : bond        0.03287 (  373)
  hydrogen bonds       : angle       3.86846 ( 1086)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1090.63 seconds
wall clock time: 19 minutes 33.75 seconds (1173.75 seconds total)