Starting phenix.real_space_refine
on Mon May 12 04:42:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fls_29285/05_2025/8fls_29285.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fls_29285/05_2025/8fls_29285.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fls_29285/05_2025/8fls_29285.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fls_29285/05_2025/8fls_29285.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fls_29285/05_2025/8fls_29285.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fls_29285/05_2025/8fls_29285.cif"
  }
  resolution = 3.09
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.077
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      54      5.16       5
     C    5637      2.51       5
     N    1543      2.21       5
     O    1610      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8844
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1900
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 6, 'TRANS': 226}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "B"
      Number of atoms: 2542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2542
          Classifications: {'peptide': 337}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "G"
      Number of atoms: 383
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 383
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "N"
      Number of atoms: 953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 953
          Classifications: {'peptide': 126}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "P"
      Number of atoms: 266
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 266
          Classifications: {'peptide': 32}
          Link IDs: {'TRANS': 31}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'AIB:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 2800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2800
          Classifications: {'peptide': 362}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 11, 'TRANS': 350}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 187
          Unresolved non-hydrogen angles: 227
          Unresolved non-hydrogen dihedrals: 155
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 115
  Time building chain proxies: 5.24, per 1000 atoms: 0.59
  Number of scatterers: 8844
  At special positions: 0
  Unit cell: (73.1, 96.9, 170.85, 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      54     16.00
     O    1610      8.00
     N    1543      7.00
     C    5637      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.01
    Simple disulfide: pdb=" SG  CYS R  48 " - pdb=" SG  CYS R 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 108 " - pdb=" SG  CYS R 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 131 " - pdb=" SG  CYS R 170 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 281 " - pdb=" SG  CYS R 351 " 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: 2.11
  Conformation dependent library (CDL) restraints added in 972.7 milliseconds
  

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2146

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 12 sheets defined
      43.5% alpha, 18.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.720A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 51
    Processing helix  chain 'A' and resid 52 through 63
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.997A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.631A  pdb=" N   ALA A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.544A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.867A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 5 through 25
      removed outlier: 3.553A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.827A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 25
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'P' and resid 2 through 32
    Processing helix  chain 'R' and resid 33 through 54
    Processing helix  chain 'R' and resid 168 through 172
      removed outlier: 3.688A  pdb=" N   LYS R 172 " --> pdb=" O   GLU R 169 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 212
      removed outlier: 3.958A  pdb=" N   ARG R 181 " --> pdb=" O   GLU R 177 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   PHE R 212 " --> pdb=" O   ILE R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 244
    Processing helix  chain 'R' and resid 278 through 312
      removed outlier: 3.562A  pdb=" N   ARG R 282 " --> pdb=" O   TYR R 278 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ALA R 284 " --> pdb=" O   GLY R 280 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 316 through 319
    Processing helix  chain 'R' and resid 320 through 347
      Proline residue:  R 332  - end of helix
    Processing helix  chain 'R' and resid 357 through 359
      No H-bonds generated for 'chain 'R' and resid 357 through 359'
    Processing helix  chain 'R' and resid 360 through 391
      Proline residue:  R 366  - end of helix
      removed outlier: 3.716A  pdb=" N   ILE R 381 " --> pdb=" O   LEU R 377 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 400 through 418
      Proline residue:  R 415  - end of helix
    Processing helix  chain 'R' and resid 420 through 425
      removed outlier: 4.001A  pdb=" N   PHE R 424 " --> pdb=" O   HIS R 420 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 434 through 460
      removed outlier: 4.548A  pdb=" N   GLY R 452 " --> pdb=" O   ASN R 448 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   PHE R 453 " --> pdb=" O   SER R 449 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 463 through 478
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.378A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.514A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.353A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.445A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.045A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.720A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.669A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63
      removed outlier: 3.864A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.873A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.788A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.608A  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: 3.505A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.977A  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: 6.977A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.098A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.157A  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: 3.573A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.613A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.434A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112
    Processing sheet with id=AB3, first strand: chain 'R' and resid 125 through 130
      removed outlier: 3.560A  pdb=" N   GLU R 125 " --> pdb=" O   CYS R 148 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   CYS R 148 " --> pdb=" O   GLU R 125 " (cutoff:3.500A)

    472 hydrogen bonds defined for protein.
    1341 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: 2.66

  Time building geometry restraints manager: 2.48 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.32: 1484
        1.32 -     1.44: 2523
        1.44 -     1.57: 4960
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 9041
  Sorted by residual:
  bond pdb=" CA  SER B 331 "
       pdb=" CB  SER B 331 "
    ideal  model  delta    sigma   weight residual
    1.532  1.479  0.053 1.68e-02 3.54e+03 9.89e+00
  bond pdb=" C   PRO N 100 "
       pdb=" O   PRO N 100 "
    ideal  model  delta    sigma   weight residual
    1.237  1.199  0.038 1.26e-02 6.30e+03 9.31e+00
  bond pdb=" N   THR N 111 "
       pdb=" CA  THR N 111 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.033 1.10e-02 8.26e+03 9.27e+00
  bond pdb=" N   VAL B  71 "
       pdb=" CA  VAL B  71 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.035 1.14e-02 7.69e+03 9.22e+00
  bond pdb=" N   VAL B 315 "
       pdb=" CA  VAL B 315 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.033 1.10e-02 8.26e+03 8.75e+00
  ... (remaining 9036 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 11701
        1.53 -     3.06: 472
        3.06 -     4.59: 83
        4.59 -     6.13: 18
        6.13 -     7.66: 5
  Bond angle restraints: 12279
  Sorted by residual:
  angle pdb=" N   HIS R 223 "
        pdb=" CA  HIS R 223 "
        pdb=" C   HIS R 223 "
      ideal   model   delta    sigma   weight residual
     110.97  105.65    5.32 1.09e+00 8.42e-01 2.38e+01
  angle pdb=" N   VAL R 365 "
        pdb=" CA  VAL R 365 "
        pdb=" CB  VAL R 365 "
      ideal   model   delta    sigma   weight residual
     110.50  113.45   -2.95 6.30e-01 2.52e+00 2.19e+01
  angle pdb=" C   PHE R 335 "
        pdb=" CA  PHE R 335 "
        pdb=" CB  PHE R 335 "
      ideal   model   delta    sigma   weight residual
     110.85  118.51   -7.66 1.70e+00 3.46e-01 2.03e+01
  angle pdb=" N   ASP B  76 "
        pdb=" CA  ASP B  76 "
        pdb=" C   ASP B  76 "
      ideal   model   delta    sigma   weight residual
     113.15  108.12    5.03 1.19e+00 7.06e-01 1.78e+01
  angle pdb=" N   ASP B 333 "
        pdb=" CA  ASP B 333 "
        pdb=" C   ASP B 333 "
      ideal   model   delta    sigma   weight residual
     113.15  108.15    5.00 1.19e+00 7.06e-01 1.77e+01
  ... (remaining 12274 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 4805
       17.73 -    35.47: 407
       35.47 -    53.20: 76
       53.20 -    70.94: 17
       70.94 -    88.67: 7
  Dihedral angle restraints: 5312
    sinusoidal: 1989
      harmonic: 3323
  Sorted by residual:
  dihedral pdb=" C   PHE R 335 "
           pdb=" N   PHE R 335 "
           pdb=" CA  PHE R 335 "
           pdb=" CB  PHE R 335 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.96   14.36     0      2.50e+00 1.60e-01 3.30e+01
  dihedral pdb=" CB  CYS R 281 "
           pdb=" SG  CYS R 281 "
           pdb=" SG  CYS R 351 "
           pdb=" CB  CYS R 351 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.66  -45.66     1      1.00e+01 1.00e-02 2.89e+01
  dihedral pdb=" CA  LEU A 291 "
           pdb=" C   LEU A 291 "
           pdb=" N   ASN A 292 "
           pdb=" CA  ASN A 292 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.43  -24.57     0      5.00e+00 4.00e-02 2.42e+01
  ... (remaining 5309 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 1279
       0.095 -    0.190: 86
       0.190 -    0.285: 12
       0.285 -    0.379: 1
       0.379 -    0.474: 1
  Chirality restraints: 1379
  Sorted by residual:
  chirality pdb=" CA  PHE R 335 "
            pdb=" N   PHE R 335 "
            pdb=" C   PHE R 335 "
            pdb=" CB  PHE R 335 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.62e+00
  chirality pdb=" CA  LYS B  57 "
            pdb=" N   LYS B  57 "
            pdb=" C   LYS B  57 "
            pdb=" CB  LYS B  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.19e+00
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.28 2.00e-01 2.50e+01 1.97e+00
  ... (remaining 1376 not shown)

  Planarity restraints: 1563
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 427 "    0.060 5.00e-02 4.00e+02   9.13e-02 1.33e+01
        pdb=" N   PRO R 428 "   -0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO R 428 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO R 428 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS R 360 "    0.012 2.00e-02 2.50e+03   2.47e-02 6.08e+00
        pdb=" C   LYS R 360 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   LYS R 360 "    0.016 2.00e-02 2.50e+03
        pdb=" N   TRP R 361 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "   -0.040 5.00e-02 4.00e+02   6.16e-02 6.07e+00
        pdb=" N   PRO G  49 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1560 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1654
        2.77 -     3.30: 8570
        3.30 -     3.84: 15321
        3.84 -     4.37: 18156
        4.37 -     4.90: 31472
  Nonbonded interactions: 75173
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU P   4 "
            pdb=" OH  TYR R 195 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OD1 ASP P  17 "
            pdb=" NH2 ARG P  20 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" O   ASP B 163 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   ALA A  48 "
            pdb=" OG  SER A  51 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" NH2 ARG B   8 "
            pdb=" OE1 GLN N 120 "
     model   vdw
     2.309 3.120
  ... (remaining 75168 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.350
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6616
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9047  Z= 0.279
  Angle     :  0.701   7.657  12291  Z= 0.454
  Chirality :  0.054   0.474   1379
  Planarity :  0.005   0.091   1563
  Dihedral  : 14.012  88.671   3148
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  1.00 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.25), residues: 1119
  helix:  2.25 (0.24), residues: 432
  sheet: -0.60 (0.34), residues: 209
  loop : -0.02 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 339 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.023   0.002   PHE R 447 
 TYR   0.011   0.001   TYR R 296 
 ARG   0.007   0.000   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13608 (  472)
  hydrogen bonds       : angle       5.89755 ( 1341)
  SS BOND              : bond        0.00860 (    6)
  SS BOND              : angle       1.32742 (   12)
  covalent geometry    : bond        0.00433 ( 9041)
  covalent geometry    : angle       0.69972 (12279)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.943 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.7052 (t80)
REVERT: N  105 ARG cc_start: 0.7528 (ttt90) cc_final: 0.7215 (tmt170)
  outliers start: 10
  outliers final: 4
  residues processed: 136
  average time/residue: 0.2550
  time to fit residues: 45.8077
Evaluate side-chains
  120 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 115
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain R residue  363 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 84 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 57 optimal weight:    0.3980
   chunk 45 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 101 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
B 220 GLN
N  31 ASN
** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.192232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.154048 restraints weight = 9547.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 1.70
r_work: 0.3590 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3461 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.0879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9047  Z= 0.123
  Angle     :  0.508   6.306  12291  Z= 0.275
  Chirality :  0.041   0.193   1379
  Planarity :  0.004   0.068   1563
  Dihedral  :  4.735  53.654   1252
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  7.44 %
    Favored  : 91.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.25), residues: 1119
  helix:  2.61 (0.24), residues: 433
  sheet: -0.68 (0.34), residues: 211
  loop : -0.02 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.036   0.001   PHE R 335 
 TYR   0.030   0.001   TYR R 191 
 ARG   0.005   0.000   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04093 (  472)
  hydrogen bonds       : angle       4.64888 ( 1341)
  SS BOND              : bond        0.00322 (    6)
  SS BOND              : angle       0.84905 (   12)
  covalent geometry    : bond        0.00265 ( 9041)
  covalent geometry    : angle       0.50712 (12279)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.7730 (mtpt) cc_final: 0.7385 (tttm)
REVERT: A  299 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6029 (mp0)
REVERT: B   59 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7388 (t80)
REVERT: N   34 MET cc_start: 0.8451 (mmm) cc_final: 0.8242 (mmm)
REVERT: N  105 ARG cc_start: 0.8053 (ttt90) cc_final: 0.7024 (tmt170)
  outliers start: 10
  outliers final: 6
  residues processed: 124
  average time/residue: 0.2552
  time to fit residues: 42.2603
Evaluate side-chains
  117 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain R residue  363 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0010
   chunk 24 optimal weight:    6.9990
   chunk 21 optimal weight:    0.2980
   chunk 88 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 81 optimal weight:    0.1980
   chunk 93 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.3986

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

Flipped N/Q/H residues before XYZ refinement:
** R 374 ASN ** 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 = 0.4145 r_free = 0.4145 target = 0.195308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.157432 restraints weight = 9664.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 1.78
r_work: 0.3724 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3589 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.1232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   9047  Z= 0.099
  Angle     :  0.462   6.285  12291  Z= 0.250
  Chirality :  0.040   0.160   1379
  Planarity :  0.004   0.053   1563
  Dihedral  :  4.362  48.957   1250
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  8.88 %
    Favored  : 89.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.26), residues: 1119
  helix:  2.90 (0.24), residues: 432
  sheet: -0.52 (0.34), residues: 211
  loop :  0.07 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 339 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.030   0.001   PHE R 335 
 TYR   0.029   0.001   TYR R 191 
 ARG   0.006   0.000   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03636 (  472)
  hydrogen bonds       : angle       4.34746 ( 1341)
  SS BOND              : bond        0.00247 (    6)
  SS BOND              : angle       0.69109 (   12)
  covalent geometry    : bond        0.00203 ( 9041)
  covalent geometry    : angle       0.46145 (12279)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.7673 (mtpt) cc_final: 0.7395 (ttpp)
REVERT: A  299 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6416 (mt-10)
REVERT: B   59 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.7418 (t80)
REVERT: B  215 GLU cc_start: 0.6626 (mm-30) cc_final: 0.6071 (mm-30)
REVERT: N  105 ARG cc_start: 0.8010 (ttt90) cc_final: 0.6932 (tmt170)
REVERT: R  335 PHE cc_start: 0.6339 (p90) cc_final: 0.6041 (p90)
  outliers start: 12
  outliers final: 8
  residues processed: 136
  average time/residue: 0.2353
  time to fit residues: 42.7604
Evaluate side-chains
  126 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain R residue  302 GLU
Chi-restraints excluded: chain R residue  430 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 83 optimal weight:   30.0000
   chunk 26 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** R 374 ASN ** 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 = 0.4040 r_free = 0.4040 target = 0.185489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.147762 restraints weight = 9685.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 1.69
r_work: 0.3506 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   9047  Z= 0.235
  Angle     :  0.611   9.493  12291  Z= 0.324
  Chirality :  0.045   0.252   1379
  Planarity :  0.005   0.065   1563
  Dihedral  :  4.905  50.477   1247
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 11.43 %
    Favored  : 87.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.25), residues: 1119
  helix:  2.24 (0.25), residues: 439
  sheet: -0.74 (0.33), residues: 218
  loop : -0.18 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 211 
 HIS   0.009   0.002   HIS A 357 
 PHE   0.028   0.002   PHE R 335 
 TYR   0.032   0.002   TYR R 191 
 ARG   0.005   0.001   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04548 (  472)
  hydrogen bonds       : angle       4.79241 ( 1341)
  SS BOND              : bond        0.00558 (    6)
  SS BOND              : angle       1.19853 (   12)
  covalent geometry    : bond        0.00553 ( 9041)
  covalent geometry    : angle       0.61020 (12279)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 1.028 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.7648 (mtpt) cc_final: 0.7342 (ttpp)
REVERT: A  299 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.5866 (mp0)
REVERT: B   59 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7478 (t80)
REVERT: N  105 ARG cc_start: 0.8082 (ttt90) cc_final: 0.7027 (tmt170)
  outliers start: 13
  outliers final: 11
  residues processed: 114
  average time/residue: 0.2512
  time to fit residues: 38.5260
Evaluate side-chains
  115 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue  363 ILE
Chi-restraints excluded: chain R residue  430 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 39 optimal weight:    0.0870
   chunk 81 optimal weight:    0.0370
   chunk 82 optimal weight:   10.0000
   chunk 68 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 109 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   chunk 95 optimal weight:    0.9980
   overall best weight:    0.5436

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

Flipped N/Q/H residues before XYZ refinement:
** R 374 ASN ** 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 = 0.4091 r_free = 0.4091 target = 0.191132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.153503 restraints weight = 9580.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3720 rms_B_bonded: 1.69
r_work: 0.3600 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3472 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   9047  Z= 0.105
  Angle     :  0.473   6.339  12291  Z= 0.255
  Chirality :  0.040   0.167   1379
  Planarity :  0.004   0.054   1563
  Dihedral  :  4.355  47.342   1247
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 12.43 %
    Favored  : 86.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.26), residues: 1119
  helix:  2.75 (0.25), residues: 432
  sheet: -0.53 (0.33), residues: 213
  loop : -0.04 (0.30), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 298 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.028   0.001   PHE R 335 
 TYR   0.027   0.001   TYR R 191 
 ARG   0.006   0.000   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03653 (  472)
  hydrogen bonds       : angle       4.38263 ( 1341)
  SS BOND              : bond        0.00241 (    6)
  SS BOND              : angle       0.55427 (   12)
  covalent geometry    : bond        0.00224 ( 9041)
  covalent geometry    : angle       0.47247 (12279)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.873 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.7752 (mtpt) cc_final: 0.7445 (ttpp)
REVERT: A  278 ASN cc_start: 0.8486 (m110) cc_final: 0.8258 (m110)
REVERT: A  299 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6187 (mp0)
REVERT: B   59 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.7330 (t80)
REVERT: N  105 ARG cc_start: 0.8004 (ttt90) cc_final: 0.6993 (tmt170)
REVERT: R  335 PHE cc_start: 0.6374 (p90) cc_final: 0.6030 (p90)
  outliers start: 14
  outliers final: 7
  residues processed: 127
  average time/residue: 0.2337
  time to fit residues: 40.3221
Evaluate side-chains
  123 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain R residue  302 GLU
Chi-restraints excluded: chain R residue  363 ILE
Chi-restraints excluded: chain R residue  430 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 57 optimal weight:    8.9990
   chunk 87 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 15 optimal weight:    0.5980
   chunk 92 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0170
   chunk 72 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.9020

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

Flipped N/Q/H residues before XYZ refinement:
** R 374 ASN ** 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 = 0.4077 r_free = 0.4077 target = 0.189474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.153797 restraints weight = 9593.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 1.66
r_work: 0.3565 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3434 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9047  Z= 0.132
  Angle     :  0.498   6.430  12291  Z= 0.267
  Chirality :  0.041   0.257   1379
  Planarity :  0.004   0.055   1563
  Dihedral  :  4.323  47.366   1246
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 12.99 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.26), residues: 1119
  helix:  2.74 (0.25), residues: 432
  sheet: -0.54 (0.32), residues: 225
  loop :  0.03 (0.31), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 211 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.028   0.001   PHE R 335 
 TYR   0.027   0.001   TYR R 191 
 ARG   0.006   0.000   ARG R 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03811 (  472)
  hydrogen bonds       : angle       4.41161 ( 1341)
  SS BOND              : bond        0.00329 (    6)
  SS BOND              : angle       0.74703 (   12)
  covalent geometry    : bond        0.00296 ( 9041)
  covalent geometry    : angle       0.49774 (12279)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.870 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.7679 (mtpt) cc_final: 0.7376 (ttpp)
REVERT: A  278 ASN cc_start: 0.8462 (m110) cc_final: 0.8178 (m110)
REVERT: A  299 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6143 (mp0)
REVERT: B   59 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.7445 (t80)
REVERT: N  105 ARG cc_start: 0.8037 (ttt90) cc_final: 0.6982 (tmt170)
REVERT: R  335 PHE cc_start: 0.6387 (p90) cc_final: 0.6018 (p90)
  outliers start: 15
  outliers final: 12
  residues processed: 126
  average time/residue: 0.2371
  time to fit residues: 40.2904
Evaluate side-chains
  130 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain R residue  302 GLU
Chi-restraints excluded: chain R residue  363 ILE
Chi-restraints excluded: chain R residue  430 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 107 optimal weight:    0.0870
   chunk 108 optimal weight:    0.8980
   chunk 81 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0030
   chunk 78 optimal weight:   50.0000
   chunk 56 optimal weight:   10.0000
   overall best weight:    0.5368

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

Flipped N/Q/H residues before XYZ refinement:
** R 374 ASN ** 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 = 0.4101 r_free = 0.4101 target = 0.190839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.153472 restraints weight = 9618.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 1.78
r_work: 0.3595 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3461 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9047  Z= 0.105
  Angle     :  0.467   6.354  12291  Z= 0.252
  Chirality :  0.040   0.258   1379
  Planarity :  0.003   0.052   1563
  Dihedral  :  4.156  46.547   1246
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 13.54 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.26), residues: 1119
  helix:  2.99 (0.25), residues: 425
  sheet: -0.41 (0.32), residues: 223
  loop :  0.11 (0.31), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 211 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.028   0.001   PHE R 335 
 TYR   0.026   0.001   TYR R 191 
 ARG   0.004   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03562 (  472)
  hydrogen bonds       : angle       4.29681 ( 1341)
  SS BOND              : bond        0.00363 (    6)
  SS BOND              : angle       1.01875 (   12)
  covalent geometry    : bond        0.00225 ( 9041)
  covalent geometry    : angle       0.46662 (12279)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 1.008 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.7615 (mtpt) cc_final: 0.7315 (ttpp)
REVERT: A  278 ASN cc_start: 0.8424 (m110) cc_final: 0.8121 (m110)
REVERT: B   59 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.7408 (t80)
REVERT: N  105 ARG cc_start: 0.8018 (ttt90) cc_final: 0.6885 (tmt170)
REVERT: R  335 PHE cc_start: 0.6235 (p90) cc_final: 0.5891 (p90)
REVERT: R  447 PHE cc_start: 0.5521 (OUTLIER) cc_final: 0.4829 (m-10)
REVERT: R  469 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6993 (mm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 128
  average time/residue: 0.2368
  time to fit residues: 41.1943
Evaluate side-chains
  128 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain R residue  363 ILE
Chi-restraints excluded: chain R residue  430 THR
Chi-restraints excluded: chain R residue  447 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0770
   chunk 102 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 85 optimal weight:   20.0000
   chunk 28 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   chunk 109 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
** R 374 ASN ** 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 = 0.4096 r_free = 0.4096 target = 0.190335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.153986 restraints weight = 9719.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3711 rms_B_bonded: 1.61
r_work: 0.3578 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3447 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9047  Z= 0.116
  Angle     :  0.478   6.693  12291  Z= 0.256
  Chirality :  0.040   0.261   1379
  Planarity :  0.003   0.052   1563
  Dihedral  :  4.165  46.495   1246
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.21 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.26), residues: 1119
  helix:  2.98 (0.25), residues: 425
  sheet: -0.54 (0.32), residues: 225
  loop :  0.18 (0.31), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 211 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.028   0.001   PHE R 335 
 TYR   0.026   0.001   TYR R 191 
 ARG   0.004   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03613 (  472)
  hydrogen bonds       : angle       4.29300 ( 1341)
  SS BOND              : bond        0.00351 (    6)
  SS BOND              : angle       1.02526 (   12)
  covalent geometry    : bond        0.00256 ( 9041)
  covalent geometry    : angle       0.47730 (12279)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.891 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.7668 (mtpt) cc_final: 0.7338 (ttpp)
REVERT: A  278 ASN cc_start: 0.8409 (m110) cc_final: 0.8118 (m110)
REVERT: N  105 ARG cc_start: 0.8000 (ttt90) cc_final: 0.6872 (tmt170)
REVERT: R  335 PHE cc_start: 0.6222 (p90) cc_final: 0.5874 (p90)
REVERT: R  447 PHE cc_start: 0.5594 (OUTLIER) cc_final: 0.4878 (m-10)
  outliers start: 13
  outliers final: 9
  residues processed: 132
  average time/residue: 0.2382
  time to fit residues: 42.5996
Evaluate side-chains
  129 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain R residue  363 ILE
Chi-restraints excluded: chain R residue  430 THR
Chi-restraints excluded: chain R residue  447 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 83 optimal weight:   50.0000
   chunk 28 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 98 optimal weight:    0.5980
   chunk 104 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
R 225 HIS
** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.187606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.150446 restraints weight = 9734.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 1.63
r_work: 0.3557 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3429 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9047  Z= 0.166
  Angle     :  0.530   7.194  12291  Z= 0.283
  Chirality :  0.042   0.275   1379
  Planarity :  0.004   0.056   1563
  Dihedral  :  4.223  23.633   1244
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.21 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.26), residues: 1119
  helix:  2.80 (0.25), residues: 424
  sheet: -0.58 (0.32), residues: 225
  loop :  0.15 (0.31), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 211 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.027   0.002   PHE R 335 
 TYR   0.027   0.002   TYR R 191 
 ARG   0.004   0.000   ARG R 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03994 (  472)
  hydrogen bonds       : angle       4.50110 ( 1341)
  SS BOND              : bond        0.00476 (    6)
  SS BOND              : angle       1.09339 (   12)
  covalent geometry    : bond        0.00384 ( 9041)
  covalent geometry    : angle       0.52927 (12279)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.7623 (mtpt) cc_final: 0.7293 (ttpp)
REVERT: N  105 ARG cc_start: 0.8045 (ttt90) cc_final: 0.6942 (tmt170)
REVERT: R  335 PHE cc_start: 0.6350 (p90) cc_final: 0.5951 (p90)
REVERT: R  447 PHE cc_start: 0.5645 (OUTLIER) cc_final: 0.5033 (m-10)
  outliers start: 15
  outliers final: 14
  residues processed: 124
  average time/residue: 0.2524
  time to fit residues: 41.9570
Evaluate side-chains
  124 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain R residue  203 THR
Chi-restraints excluded: chain R residue  349 THR
Chi-restraints excluded: chain R residue  363 ILE
Chi-restraints excluded: chain R residue  430 THR
Chi-restraints excluded: chain R residue  447 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 110 optimal weight:    0.7980
   chunk 77 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 105 optimal weight:    0.2980
   chunk 61 optimal weight:    8.9990
   chunk 81 optimal weight:    0.4980
   chunk 109 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** R 374 ASN ** 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 = 0.4107 r_free = 0.4107 target = 0.191127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.152976 restraints weight = 9605.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 1.83
r_work: 0.3569 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3435 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9047  Z= 0.111
  Angle     :  0.480   6.859  12291  Z= 0.258
  Chirality :  0.040   0.263   1379
  Planarity :  0.004   0.053   1563
  Dihedral  :  3.993  21.617   1244
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 14.65 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.26), residues: 1119
  helix:  2.94 (0.25), residues: 425
  sheet: -0.50 (0.32), residues: 221
  loop :  0.17 (0.31), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 298 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.027   0.001   PHE R 335 
 TYR   0.025   0.001   TYR R 191 
 ARG   0.004   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03606 (  472)
  hydrogen bonds       : angle       4.31055 ( 1341)
  SS BOND              : bond        0.00328 (    6)
  SS BOND              : angle       0.85280 (   12)
  covalent geometry    : bond        0.00242 ( 9041)
  covalent geometry    : angle       0.47925 (12279)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.887 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.7554 (mtpt) cc_final: 0.7222 (ttpp)
REVERT: N  105 ARG cc_start: 0.8057 (ttt90) cc_final: 0.6871 (tmt170)
REVERT: R  317 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7394 (tm-30)
REVERT: R  335 PHE cc_start: 0.6211 (p90) cc_final: 0.5851 (p90)
REVERT: R  447 PHE cc_start: 0.5610 (OUTLIER) cc_final: 0.4845 (m-10)
  outliers start: 12
  outliers final: 10
  residues processed: 124
  average time/residue: 0.2302
  time to fit residues: 38.7027
Evaluate side-chains
  124 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain R residue  363 ILE
Chi-restraints excluded: chain R residue  430 THR
Chi-restraints excluded: chain R residue  447 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 81 optimal weight:    8.9990
   chunk 63 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 92 optimal weight:    0.0020
   chunk 12 optimal weight:    3.9990
   chunk 23 optimal weight:    8.9990
   overall best weight:    1.1192

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

Flipped N/Q/H residues before XYZ refinement:
** R 374 ASN ** 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 = 0.4077 r_free = 0.4077 target = 0.188156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.149205 restraints weight = 9669.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 1.86
r_work: 0.3542 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9047  Z= 0.151
  Angle     :  0.517   6.764  12291  Z= 0.276
  Chirality :  0.042   0.267   1379
  Planarity :  0.004   0.056   1563
  Dihedral  :  4.158  23.153   1244
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 14.65 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.26), residues: 1119
  helix:  2.81 (0.25), residues: 426
  sheet: -0.58 (0.32), residues: 223
  loop :  0.17 (0.31), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 234 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.027   0.002   PHE R 335 
 TYR   0.026   0.002   TYR R 191 
 ARG   0.004   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03887 (  472)
  hydrogen bonds       : angle       4.43987 ( 1341)
  SS BOND              : bond        0.00441 (    6)
  SS BOND              : angle       1.00778 (   12)
  covalent geometry    : bond        0.00347 ( 9041)
  covalent geometry    : angle       0.51671 (12279)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4950.42 seconds
wall clock time: 86 minutes 22.97 seconds (5182.97 seconds total)