Starting phenix.real_space_refine
on Tue Mar  3 20:38:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7eja_31157/03_2026/7eja_31157.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7eja_31157/03_2026/7eja_31157.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/7eja_31157/03_2026/7eja_31157.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7eja_31157/03_2026/7eja_31157.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7eja_31157/03_2026/7eja_31157.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7eja_31157/03_2026/7eja_31157.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=  -0.007 sd=   0.192
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      58      5.16       5
     C    5487      2.51       5
     N    1458      2.21       5
     O    1581      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8584
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1632
          Classifications: {'peptide': 210}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'CIS': 7, 'PTRANS': 4, 'TRANS': 198}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 30
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "B"
      Number of atoms: 2541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2541
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 324}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "G"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 418
          Classifications: {'peptide': 54}
          Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 48}
    Chain: "R"
      Number of atoms: 2193
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 2193
          Classifications: {'peptide': 269}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 256}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "H"
      Number of atoms: 1785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1785
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'CZX': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   LYS H 236 " occ=0.00
      ... (7 atoms not shown)
      pdb=" NZ  LYS H 236 " occ=0.00
  Time building chain proxies: 2.14, per 1000 atoms: 0.25
  Number of scatterers: 8584
  At special positions: 0
  Unit cell: (88.4, 120.7, 124.95, 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      58     16.00
     O    1581      8.00
     N    1458      7.00
     C    5487      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 121 " - pdb=" SG  CYS R 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 147 " - pdb=" SG  CYS H 217 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 456.9 milliseconds
  

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2052

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 12 sheets defined
      34.7% alpha, 18.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.682A  pdb=" N   ARG A  10 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 52
      removed outlier: 4.207A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 214
      removed outlier: 4.170A  pdb=" N   TRP A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 217
      No H-bonds generated for 'chain 'A' and resid 215 through 217'
    Processing helix  chain 'A' and resid 245 through 256
      removed outlier: 4.213A  pdb=" N   MET A 249 " --> pdb=" O   HIS A 245 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ASP A 252 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 281
      removed outlier: 4.100A  pdb=" N   LYS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 307
    Processing helix  chain 'A' and resid 329 through 350
      removed outlier: 4.482A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 25
      removed outlier: 3.591A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 24
      removed outlier: 3.802A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LYS G  20 " --> pdb=" O   VAL G  16 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLU G  22 " --> pdb=" O   GLN G  18 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'R' and resid 47 through 74
    Processing helix  chain 'R' and resid 83 through 108
      removed outlier: 4.473A  pdb=" N   LEU R  87 " --> pdb=" O   GLN R  83 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ILE R 102 " --> pdb=" O   ALA R  98 " (cutoff:3.500A)
      Proline residue:  R 103  - end of helix
    Processing helix  chain 'R' and resid 120 through 151
    Processing helix  chain 'R' and resid 152 through 157
    Processing helix  chain 'R' and resid 158 through 160
      No H-bonds generated for 'chain 'R' and resid 158 through 160'
    Processing helix  chain 'R' and resid 161 through 181
    Processing helix  chain 'R' and resid 208 through 242
      removed outlier: 3.683A  pdb=" N   ILE R 213 " --> pdb=" O   LYS R 209 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   SER R 214 " --> pdb=" O   TRP R 210 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   ALA R 222 " --> pdb=" O   GLY R 218 " (cutoff:3.500A)
      Proline residue:  R 223  - end of helix
    Processing helix  chain 'R' and resid 376 through 411
      removed outlier: 3.698A  pdb=" N   ASN R 382 " --> pdb=" O   ARG R 378 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   PHE R 398 " --> pdb=" O   VAL R 394 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL R 399 " --> pdb=" O   ILE R 395 " (cutoff:3.500A)
      Proline residue:  R 404  - end of helix
    Processing helix  chain 'R' and resid 422 through 443
      removed outlier: 3.775A  pdb=" N   GLY R 430 " --> pdb=" O   PHE R 426 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   TYR R 431 " --> pdb=" O   PHE R 427 " (cutoff:3.500A)
      Proline residue:  R 438  - end of helix
      removed outlier: 3.543A  pdb=" N   TYR R 441 " --> pdb=" O   ASN R 437 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 445 through 457
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.762A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 189
      removed outlier: 3.862A  pdb=" N   VAL A 186 " --> pdb=" O   ASP A 201 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASP A 201 " --> pdb=" O   VAL A 186 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ALA A 221 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.967A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY B 319 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLY B 330 " --> pdb=" O   CYS B 317 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.931A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   SER B  72 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.306A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.615A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.679A  pdb=" N   SER B 191 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.576A  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: 6.599A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.706A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 277
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6
      removed outlier: 3.804A  pdb=" N   THR H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   THR H  69 " --> pdb=" O   GLN H  82 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 58 through 60
      removed outlier: 5.464A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 134 through 136
      removed outlier: 3.847A  pdb=" N   GLU H 234 " --> pdb=" O   VAL H 135 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   LEU H 162 " --> pdb=" O   TYR H 178 " (cutoff:3.500A)
      removed outlier: 5.239A  pdb=" N   TYR H 178 " --> pdb=" O   LEU H 162 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   TRP H 164 " --> pdb=" O   LEU H 176 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LEU H 176 " --> pdb=" O   TRP H 164 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 143 through 148
      removed outlier: 3.952A  pdb=" N   PHE H 200 " --> pdb=" O   CYS H 147 " (cutoff:3.500A)

    361 hydrogen bonds defined for protein.
    1035 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.19

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1385
        1.31 -     1.44: 2457
        1.44 -     1.56: 4847
        1.56 -     1.69: 0
        1.69 -     1.81: 79
  Bond restraints: 8768
  Sorted by residual:
  bond pdb=" N   ILE R 123 "
       pdb=" CA  ILE R 123 "
    ideal  model  delta    sigma   weight residual
    1.461  1.396  0.065 1.17e-02 7.31e+03 3.07e+01
  bond pdb=" N   ASN A 346 "
       pdb=" CA  ASN A 346 "
    ideal  model  delta    sigma   weight residual
    1.459  1.400  0.060 1.20e-02 6.94e+03 2.47e+01
  bond pdb=" CA  TYR R 156 "
       pdb=" C   TYR R 156 "
    ideal  model  delta    sigma   weight residual
    1.524  1.460  0.064 1.29e-02 6.01e+03 2.45e+01
  bond pdb=" CA  ASN A 346 "
       pdb=" C   ASN A 346 "
    ideal  model  delta    sigma   weight residual
    1.524  1.463  0.060 1.26e-02 6.30e+03 2.30e+01
  bond pdb=" N   PRO R 438 "
       pdb=" CD  PRO R 438 "
    ideal  model  delta    sigma   weight residual
    1.473  1.539 -0.066 1.40e-02 5.10e+03 2.22e+01
  ... (remaining 8763 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.88: 11697
        2.88 -     5.76: 148
        5.76 -     8.64: 27
        8.64 -    11.53: 6
       11.53 -    14.41: 3
  Bond angle restraints: 11881
  Sorted by residual:
  angle pdb=" N   ARG R 378 "
        pdb=" CA  ARG R 378 "
        pdb=" C   ARG R 378 "
      ideal   model   delta    sigma   weight residual
     111.28  121.19   -9.91 1.09e+00 8.42e-01 8.27e+01
  angle pdb=" N   LYS A 211 "
        pdb=" CA  LYS A 211 "
        pdb=" C   LYS A 211 "
      ideal   model   delta    sigma   weight residual
     111.14  119.75   -8.61 1.08e+00 8.57e-01 6.36e+01
  angle pdb=" N   HIS A 214 "
        pdb=" CA  HIS A 214 "
        pdb=" C   HIS A 214 "
      ideal   model   delta    sigma   weight residual
     111.28  119.83   -8.55 1.09e+00 8.42e-01 6.16e+01
  angle pdb=" N   LYS R 159 "
        pdb=" CA  LYS R 159 "
        pdb=" C   LYS R 159 "
      ideal   model   delta    sigma   weight residual
     113.15  122.41   -9.26 1.19e+00 7.06e-01 6.06e+01
  angle pdb=" N   CYS R 121 "
        pdb=" CA  CYS R 121 "
        pdb=" C   CYS R 121 "
      ideal   model   delta    sigma   weight residual
     112.90  103.56    9.34 1.31e+00 5.83e-01 5.08e+01
  ... (remaining 11876 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.99: 5081
       33.99 -    67.98: 90
       67.98 -   101.97: 9
      101.97 -   135.95: 0
      135.95 -   169.94: 2
  Dihedral angle restraints: 5182
    sinusoidal: 2004
      harmonic: 3178
  Sorted by residual:
  dihedral pdb=" N   ILE R 123 "
           pdb=" C   ILE R 123 "
           pdb=" CA  ILE R 123 "
           pdb=" CB  ILE R 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  109.48   13.92     0      2.50e+00 1.60e-01 3.10e+01
  dihedral pdb=" C   PHE A 216 "
           pdb=" N   PHE A 216 "
           pdb=" CA  PHE A 216 "
           pdb=" CB  PHE A 216 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.35   13.75     0      2.50e+00 1.60e-01 3.02e+01
  dihedral pdb=" CA  ILE G  25 "
           pdb=" C   ILE G  25 "
           pdb=" N   ASP G  26 "
           pdb=" CA  ASP G  26 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.22  -23.78     0      5.00e+00 4.00e-02 2.26e+01
  ... (remaining 5179 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 1292
       0.110 -    0.219: 39
       0.219 -    0.329: 12
       0.329 -    0.438: 4
       0.438 -    0.548: 2
  Chirality restraints: 1349
  Sorted by residual:
  chirality pdb=" CA  PHE A 216 "
            pdb=" N   PHE A 216 "
            pdb=" C   PHE A 216 "
            pdb=" CB  PHE A 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.55 2.00e-01 2.50e+01 7.51e+00
  chirality pdb=" CA  GLU A 217 "
            pdb=" N   GLU A 217 "
            pdb=" C   GLU A 217 "
            pdb=" CB  GLU A 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.46e+00
  chirality pdb=" CA  LYS R 159 "
            pdb=" N   LYS R 159 "
            pdb=" C   LYS R 159 "
            pdb=" CB  LYS R 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.04e+00
  ... (remaining 1346 not shown)

  Planarity restraints: 1496
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 161 "    0.036 5.00e-02 4.00e+02   5.51e-02 4.86e+00
        pdb=" N   PRO R 162 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO R 162 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO R 162 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 183 "    0.010 2.00e-02 2.50e+03   1.97e-02 3.90e+00
        pdb=" C   THR A 183 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   THR A 183 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLY A 184 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 282 "   -0.031 5.00e-02 4.00e+02   4.65e-02 3.45e+00
        pdb=" N   PRO A 283 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 283 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 283 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1493 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 68
        2.49 -     3.10: 6396
        3.10 -     3.70: 13194
        3.70 -     4.30: 17548
        4.30 -     4.90: 28824
  Nonbonded interactions: 66030
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN R  83 "
            pdb=" NH2 ARG R 160 "
     model   vdw
     1.893 3.120
  nonbonded pdb=" O   PHE A 224 "
            pdb=" N   PHE A 268 "
     model   vdw
     1.959 3.120
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASN B 110 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" OG  SER H 192 "
            pdb=" OG1 THR H 203 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.224 3.040
  ... (remaining 66025 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 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:             1.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     9.390
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.103   8772  Z= 0.305
  Angle     :  0.850  14.408  11887  Z= 0.537
  Chirality :  0.059   0.548   1349
  Planarity :  0.004   0.055   1496
  Dihedral  : 13.816 169.942   3121
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 17.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.75 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.26), residues: 1075
  helix:  1.20 (0.28), residues: 341
  sheet: -0.37 (0.33), residues: 263
  loop : -1.32 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 202 
 TYR   0.013   0.001   TYR R 156 
 PHE   0.022   0.001   PHE R 398 
 TRP   0.008   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 8768)
  covalent geometry    : angle       0.84981 (11881)
  SS BOND              : bond        0.00262 (    3)
  SS BOND              : angle       0.57853 (    6)
  hydrogen bonds       : bond        0.17853 (  361)
  hydrogen bonds       : angle       7.31004 ( 1035)
  Misc. bond           : bond        0.10299 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 231
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 ARG cc_start: 0.8918 (mmm160) cc_final: 0.8705 (mmm-85)
REVERT: B   36 ASN cc_start: 0.8672 (m-40) cc_final: 0.8362 (p0)
REVERT: B  255 LEU cc_start: 0.9382 (pt) cc_final: 0.9117 (mm)
REVERT: B  261 LEU cc_start: 0.9371 (mt) cc_final: 0.9168 (mt)
REVERT: B  280 LYS cc_start: 0.9349 (tptp) cc_final: 0.9026 (tptp)
REVERT: B  292 PHE cc_start: 0.7801 (m-10) cc_final: 0.7482 (m-10)
REVERT: G   21 MET cc_start: 0.8107 (mmp) cc_final: 0.7294 (mtm)
REVERT: G   32 LYS cc_start: 0.9511 (ptpp) cc_final: 0.9293 (ptmm)
REVERT: G   42 GLU cc_start: 0.8135 (tp30) cc_final: 0.7530 (mt-10)
REVERT: G   58 GLU cc_start: 0.8998 (mp0) cc_final: 0.8428 (mp0)
REVERT: R   53 CYS cc_start: 0.9179 (m) cc_final: 0.8880 (p)
REVERT: R   57 LEU cc_start: 0.9416 (tp) cc_final: 0.9184 (tp)
REVERT: R  109 GLU cc_start: 0.8887 (tp30) cc_final: 0.8314 (tm-30)
REVERT: R  450 ARG cc_start: 0.9489 (mtm110) cc_final: 0.9217 (mtm-85)
REVERT: H   46 GLU cc_start: 0.8579 (pt0) cc_final: 0.8189 (pm20)
REVERT: H   90 ASP cc_start: 0.8059 (m-30) cc_final: 0.7532 (m-30)
REVERT: H  137 VAL cc_start: 0.7359 (m) cc_final: 0.7129 (m)
REVERT: H  180 MET cc_start: 0.8772 (ppp) cc_final: 0.8274 (ppp)
REVERT: H  210 GLU cc_start: 0.8971 (mp0) cc_final: 0.8577 (mp0)
REVERT: H  211 ASP cc_start: 0.7848 (m-30) cc_final: 0.7330 (m-30)
REVERT: H  218 MET cc_start: 0.8712 (tmm) cc_final: 0.8146 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 231
  average time/residue: 0.1016
  time to fit residues: 31.1461
Evaluate side-chains
  152 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:   30.0000
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 256 ASN
A 333 GLN
B 176 GLN
B 266 HIS
** R 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 433 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.091218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.066902 restraints weight = 31828.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.068946 restraints weight = 17282.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.070313 restraints weight = 11823.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.071165 restraints weight = 9288.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.071642 restraints weight = 8007.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8772  Z= 0.206
  Angle     :  0.733  10.496  11887  Z= 0.382
  Chirality :  0.046   0.187   1349
  Planarity :  0.004   0.053   1496
  Dihedral  :  8.111 162.391   1193
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.58 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.26), residues: 1075
  helix:  1.36 (0.28), residues: 341
  sheet: -0.34 (0.32), residues: 273
  loop : -1.33 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H 168 
 TYR   0.028   0.002   TYR R 156 
 PHE   0.029   0.002   PHE R 387 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.009   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 8768)
  covalent geometry    : angle       0.73262 (11881)
  SS BOND              : bond        0.00533 (    3)
  SS BOND              : angle       0.59544 (    6)
  hydrogen bonds       : bond        0.04743 (  361)
  hydrogen bonds       : angle       5.15121 ( 1035)
  Misc. bond           : bond        0.00092 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 177
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8589 (tm-30)
REVERT: A  354 TYR cc_start: 0.8672 (p90) cc_final: 0.8372 (p90)
REVERT: B   12 GLU cc_start: 0.9307 (pt0) cc_final: 0.8980 (pm20)
REVERT: B   36 ASN cc_start: 0.8618 (m-40) cc_final: 0.8317 (p0)
REVERT: B  292 PHE cc_start: 0.8132 (m-10) cc_final: 0.7699 (m-10)
REVERT: G   17 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8449 (pm20)
REVERT: G   42 GLU cc_start: 0.8187 (tp30) cc_final: 0.7573 (mt-10)
REVERT: G   58 GLU cc_start: 0.9086 (mp0) cc_final: 0.8498 (mp0)
REVERT: R   53 CYS cc_start: 0.9082 (m) cc_final: 0.8858 (m)
REVERT: R   94 ASP cc_start: 0.8252 (t70) cc_final: 0.7458 (t70)
REVERT: R   95 ILE cc_start: 0.9703 (mm) cc_final: 0.9494 (mm)
REVERT: R  109 GLU cc_start: 0.8831 (tp30) cc_final: 0.8201 (tm-30)
REVERT: R  381 GLN cc_start: 0.9012 (pt0) cc_final: 0.8511 (pt0)
REVERT: R  446 HIS cc_start: 0.9010 (OUTLIER) cc_final: 0.8649 (t70)
REVERT: R  447 ASP cc_start: 0.9333 (p0) cc_final: 0.9111 (p0)
REVERT: H  180 MET cc_start: 0.8840 (ppp) cc_final: 0.8389 (ppp)
REVERT: H  218 MET cc_start: 0.8637 (tmm) cc_final: 0.8327 (tmm)
  outliers start: 20
  outliers final: 13
  residues processed: 190
  average time/residue: 0.0908
  time to fit residues: 23.6232
Evaluate side-chains
  159 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain R residue  127 LEU
Chi-restraints excluded: chain R residue  128 ASP
Chi-restraints excluded: chain R residue  140 CYS
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  382 ASN
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain R residue  433 ASN
Chi-restraints excluded: chain R residue  446 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 22 optimal weight:   10.0000
   chunk 97 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0870
   chunk 26 optimal weight:    7.9990
   overall best weight:    2.3964

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
** R 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.091896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.067962 restraints weight = 31322.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.070001 restraints weight = 16911.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.071405 restraints weight = 11536.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.072308 restraints weight = 9038.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.072900 restraints weight = 7750.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8772  Z= 0.159
  Angle     :  0.723  12.079  11887  Z= 0.366
  Chirality :  0.044   0.145   1349
  Planarity :  0.004   0.051   1496
  Dihedral  :  8.062 162.004   1193
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 16.24 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.26), residues: 1075
  helix:  1.46 (0.28), residues: 340
  sheet: -0.28 (0.32), residues: 270
  loop : -1.34 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 378 
 TYR   0.025   0.002   TYR R 409 
 PHE   0.021   0.001   PHE R 387 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.007   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 8768)
  covalent geometry    : angle       0.72324 (11881)
  SS BOND              : bond        0.00374 (    3)
  SS BOND              : angle       0.59830 (    6)
  hydrogen bonds       : bond        0.04285 (  361)
  hydrogen bonds       : angle       4.75057 ( 1035)
  Misc. bond           : bond        0.00067 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 161
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8619 (tm-30)
REVERT: A  320 TYR cc_start: 0.8556 (m-80) cc_final: 0.7700 (m-80)
REVERT: A  354 TYR cc_start: 0.8679 (p90) cc_final: 0.8278 (p90)
REVERT: B   12 GLU cc_start: 0.9308 (pt0) cc_final: 0.8965 (pm20)
REVERT: B   36 ASN cc_start: 0.8554 (m-40) cc_final: 0.8249 (p0)
REVERT: B  232 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8459 (tt)
REVERT: B  292 PHE cc_start: 0.8130 (m-10) cc_final: 0.7743 (m-10)
REVERT: G   21 MET cc_start: 0.8441 (mmm) cc_final: 0.7403 (mtm)
REVERT: G   38 MET cc_start: 0.6537 (ptp) cc_final: 0.6178 (ptt)
REVERT: G   42 GLU cc_start: 0.8158 (tp30) cc_final: 0.7672 (mt-10)
REVERT: G   58 GLU cc_start: 0.9131 (mp0) cc_final: 0.8556 (mp0)
REVERT: R   49 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7192 (pt)
REVERT: R   53 CYS cc_start: 0.9065 (m) cc_final: 0.8856 (m)
REVERT: R   94 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7354 (t70)
REVERT: R  109 GLU cc_start: 0.8668 (tp30) cc_final: 0.8113 (tm-30)
REVERT: R  446 HIS cc_start: 0.8966 (OUTLIER) cc_final: 0.8673 (t70)
REVERT: H  180 MET cc_start: 0.8828 (ppp) cc_final: 0.8386 (ppp)
REVERT: H  218 MET cc_start: 0.8634 (tmm) cc_final: 0.8419 (tmm)
  outliers start: 28
  outliers final: 19
  residues processed: 179
  average time/residue: 0.0863
  time to fit residues: 21.5748
Evaluate side-chains
  164 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue   58 LEU
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue   96 LEU
Chi-restraints excluded: chain R residue  127 LEU
Chi-restraints excluded: chain R residue  128 ASP
Chi-restraints excluded: chain R residue  140 CYS
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  382 ASN
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain R residue  435 SER
Chi-restraints excluded: chain R residue  446 HIS
Chi-restraints excluded: chain R residue  454 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 84 optimal weight:    0.0570
   chunk 29 optimal weight:    6.9990
   chunk 107 optimal weight:    4.9990
   chunk 24 optimal weight:    8.9990
   chunk 81 optimal weight:    0.1980
   chunk 56 optimal weight:    0.4980
   chunk 37 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.5500

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
R 381 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.094428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.070081 restraints weight = 31375.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.072232 restraints weight = 16780.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.073650 restraints weight = 11371.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.074570 restraints weight = 8889.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.075106 restraints weight = 7634.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8772  Z= 0.125
  Angle     :  0.702  12.334  11887  Z= 0.350
  Chirality :  0.043   0.154   1349
  Planarity :  0.004   0.052   1496
  Dihedral  :  7.967 162.988   1193
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 16.34 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.26), residues: 1075
  helix:  1.63 (0.28), residues: 337
  sheet:  0.03 (0.35), residues: 243
  loop : -1.36 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 168 
 TYR   0.024   0.001   TYR R 409 
 PHE   0.021   0.001   PHE R 387 
 TRP   0.010   0.001   TRP B 169 
 HIS   0.006   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8768)
  covalent geometry    : angle       0.70182 (11881)
  SS BOND              : bond        0.00296 (    3)
  SS BOND              : angle       0.54931 (    6)
  hydrogen bonds       : bond        0.03687 (  361)
  hydrogen bonds       : angle       4.46168 ( 1035)
  Misc. bond           : bond        0.00017 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 168
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 TYR cc_start: 0.8713 (p90) cc_final: 0.8269 (p90)
REVERT: B   12 GLU cc_start: 0.9308 (pt0) cc_final: 0.8978 (pm20)
REVERT: B   17 GLN cc_start: 0.7419 (tm-30) cc_final: 0.7119 (pp30)
REVERT: B   36 ASN cc_start: 0.8587 (m-40) cc_final: 0.8223 (p0)
REVERT: B   59 TYR cc_start: 0.8407 (m-80) cc_final: 0.8136 (m-80)
REVERT: B  175 GLN cc_start: 0.8213 (mp10) cc_final: 0.7970 (mp10)
REVERT: B  220 GLN cc_start: 0.8678 (mp10) cc_final: 0.8439 (mp10)
REVERT: B  283 ARG cc_start: 0.7207 (ttt180) cc_final: 0.6833 (ttt180)
REVERT: B  292 PHE cc_start: 0.8000 (m-10) cc_final: 0.7615 (m-10)
REVERT: G   21 MET cc_start: 0.8555 (mmm) cc_final: 0.7690 (mtm)
REVERT: G   38 MET cc_start: 0.6640 (ptp) cc_final: 0.5950 (ptt)
REVERT: G   42 GLU cc_start: 0.8096 (tp30) cc_final: 0.7504 (mt-10)
REVERT: G   58 GLU cc_start: 0.9106 (mp0) cc_final: 0.8547 (mp0)
REVERT: R   53 CYS cc_start: 0.9044 (m) cc_final: 0.8730 (p)
REVERT: R   94 ASP cc_start: 0.8179 (t70) cc_final: 0.7319 (t70)
REVERT: R   95 ILE cc_start: 0.9691 (mm) cc_final: 0.9462 (mm)
REVERT: R  109 GLU cc_start: 0.8684 (tp30) cc_final: 0.8212 (tm-30)
REVERT: R  204 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8688 (tm-30)
REVERT: R  446 HIS cc_start: 0.8941 (OUTLIER) cc_final: 0.8725 (t70)
REVERT: R  450 ARG cc_start: 0.9476 (mtm110) cc_final: 0.9264 (mtm110)
REVERT: H   34 MET cc_start: 0.8600 (tpp) cc_final: 0.8317 (tpp)
REVERT: H  218 MET cc_start: 0.8689 (tmm) cc_final: 0.8483 (tmm)
REVERT: H  232 LYS cc_start: 0.8141 (mppt) cc_final: 0.7854 (pptt)
  outliers start: 28
  outliers final: 15
  residues processed: 188
  average time/residue: 0.0902
  time to fit residues: 23.3957
Evaluate side-chains
  164 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain R residue   47 VAL
Chi-restraints excluded: chain R residue   96 LEU
Chi-restraints excluded: chain R residue  127 LEU
Chi-restraints excluded: chain R residue  140 CYS
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  230 VAL
Chi-restraints excluded: chain R residue  382 ASN
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain R residue  446 HIS
Chi-restraints excluded: chain R residue  454 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0570
   chunk 48 optimal weight:    9.9990
   chunk 73 optimal weight:   30.0000
   chunk 29 optimal weight:    0.2980
   chunk 52 optimal weight:    5.9990
   chunk 100 optimal weight:   10.0000
   chunk 66 optimal weight:    0.4980
   chunk 10 optimal weight:    0.0980
   chunk 7 optimal weight:    9.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.5900

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

Flipped N/Q/H residues before XYZ refinement:
R 138 HIS
R 433 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.095045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.070776 restraints weight = 31285.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.072947 restraints weight = 16713.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.074364 restraints weight = 11287.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.075318 restraints weight = 8829.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.075807 restraints weight = 7558.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8772  Z= 0.119
  Angle     :  0.699  13.097  11887  Z= 0.344
  Chirality :  0.043   0.223   1349
  Planarity :  0.004   0.052   1496
  Dihedral  :  7.866 161.807   1193
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.85 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.26), residues: 1075
  helix:  1.61 (0.28), residues: 342
  sheet:  0.05 (0.35), residues: 241
  loop : -1.33 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  87 
 TYR   0.016   0.001   TYR R 156 
 PHE   0.018   0.001   PHE R 387 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8768)
  covalent geometry    : angle       0.69915 (11881)
  SS BOND              : bond        0.00233 (    3)
  SS BOND              : angle       0.45764 (    6)
  hydrogen bonds       : bond        0.03393 (  361)
  hydrogen bonds       : angle       4.32766 ( 1035)
  Misc. bond           : bond        0.00021 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 169
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8665 (tm-30)
REVERT: A  354 TYR cc_start: 0.8711 (p90) cc_final: 0.8232 (p90)
REVERT: B   12 GLU cc_start: 0.9301 (pt0) cc_final: 0.8975 (pm20)
REVERT: B   17 GLN cc_start: 0.7361 (tm-30) cc_final: 0.7121 (pp30)
REVERT: B  292 PHE cc_start: 0.7960 (m-10) cc_final: 0.7592 (m-10)
REVERT: G   21 MET cc_start: 0.8565 (mmm) cc_final: 0.7702 (mtm)
REVERT: G   38 MET cc_start: 0.6607 (ptp) cc_final: 0.5949 (ptt)
REVERT: G   42 GLU cc_start: 0.8072 (tp30) cc_final: 0.7475 (mt-10)
REVERT: G   58 GLU cc_start: 0.9063 (mp0) cc_final: 0.8517 (mp0)
REVERT: R   53 CYS cc_start: 0.9021 (m) cc_final: 0.8741 (p)
REVERT: R  109 GLU cc_start: 0.8640 (tp30) cc_final: 0.8249 (tm-30)
REVERT: R  111 MET cc_start: 0.8563 (mtm) cc_final: 0.8279 (ptp)
REVERT: R  448 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8635 (t80)
REVERT: H  190 ARG cc_start: 0.5944 (OUTLIER) cc_final: 0.5292 (ptm160)
  outliers start: 25
  outliers final: 19
  residues processed: 184
  average time/residue: 0.0932
  time to fit residues: 23.2623
Evaluate side-chains
  171 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain R residue   47 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue   96 LEU
Chi-restraints excluded: chain R residue  138 HIS
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  230 VAL
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain R residue  448 PHE
Chi-restraints excluded: chain R residue  454 LYS
Chi-restraints excluded: chain H residue  190 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 56 optimal weight:    0.6980
   chunk 98 optimal weight:   40.0000
   chunk 40 optimal weight:    8.9990
   chunk 18 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 91 optimal weight:   20.0000
   chunk 44 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
R 138 HIS
** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.093881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.069690 restraints weight = 31247.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.071822 restraints weight = 16768.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.073222 restraints weight = 11379.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.074108 restraints weight = 8904.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.074717 restraints weight = 7652.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.3048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8772  Z= 0.144
  Angle     :  0.737  13.165  11887  Z= 0.364
  Chirality :  0.043   0.175   1349
  Planarity :  0.004   0.051   1496
  Dihedral  :  7.867 161.150   1193
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.11 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.26), residues: 1075
  helix:  1.63 (0.29), residues: 340
  sheet: -0.09 (0.35), residues: 244
  loop : -1.35 (0.27), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H 190 
 TYR   0.015   0.001   TYR R 156 
 PHE   0.021   0.001   PHE R 387 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.016   0.001   HIS R 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8768)
  covalent geometry    : angle       0.73692 (11881)
  SS BOND              : bond        0.00293 (    3)
  SS BOND              : angle       0.54187 (    6)
  hydrogen bonds       : bond        0.03557 (  361)
  hydrogen bonds       : angle       4.38430 ( 1035)
  Misc. bond           : bond        0.00052 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 152
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 TYR cc_start: 0.8709 (p90) cc_final: 0.8145 (p90)
REVERT: B   12 GLU cc_start: 0.9291 (pt0) cc_final: 0.8960 (pm20)
REVERT: B  130 GLU cc_start: 0.8960 (mp0) cc_final: 0.8718 (mp0)
REVERT: B  283 ARG cc_start: 0.7252 (ttt180) cc_final: 0.6954 (ttt180)
REVERT: B  292 PHE cc_start: 0.8097 (m-10) cc_final: 0.7709 (m-10)
REVERT: G   21 MET cc_start: 0.8580 (mmm) cc_final: 0.7710 (mtm)
REVERT: G   38 MET cc_start: 0.6641 (ptp) cc_final: 0.5990 (ptt)
REVERT: G   42 GLU cc_start: 0.8088 (tp30) cc_final: 0.7492 (mt-10)
REVERT: G   58 GLU cc_start: 0.9077 (mp0) cc_final: 0.8526 (mp0)
REVERT: R   94 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7444 (t70)
REVERT: R  109 GLU cc_start: 0.8650 (tp30) cc_final: 0.8265 (tm-30)
REVERT: R  111 MET cc_start: 0.8601 (mtm) cc_final: 0.8315 (ptp)
REVERT: H  218 MET cc_start: 0.8660 (tmm) cc_final: 0.8362 (ppp)
  outliers start: 27
  outliers final: 19
  residues processed: 171
  average time/residue: 0.0909
  time to fit residues: 21.3820
Evaluate side-chains
  161 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  138 HIS
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  230 VAL
Chi-restraints excluded: chain R residue  382 ASN
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain R residue  435 SER
Chi-restraints excluded: chain R residue  454 LYS
Chi-restraints excluded: chain H residue  190 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 92 optimal weight:    8.9990
   chunk 76 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 54 optimal weight:   20.0000
   chunk 99 optimal weight:   20.0000
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
R 138 HIS
R 433 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.093442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.069189 restraints weight = 31931.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.071310 restraints weight = 17081.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.072711 restraints weight = 11581.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.073644 restraints weight = 9062.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.074212 restraints weight = 7771.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.3141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8772  Z= 0.148
  Angle     :  0.764  15.296  11887  Z= 0.373
  Chirality :  0.044   0.352   1349
  Planarity :  0.004   0.050   1496
  Dihedral  :  7.831 160.048   1193
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 20.22 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.26), residues: 1075
  helix:  1.60 (0.29), residues: 340
  sheet: -0.20 (0.34), residues: 246
  loop : -1.32 (0.28), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H 190 
 TYR   0.015   0.001   TYR R 156 
 PHE   0.021   0.001   PHE R 387 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 8768)
  covalent geometry    : angle       0.76380 (11881)
  SS BOND              : bond        0.00330 (    3)
  SS BOND              : angle       0.56075 (    6)
  hydrogen bonds       : bond        0.03663 (  361)
  hydrogen bonds       : angle       4.38472 ( 1035)
  Misc. bond           : bond        0.00054 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 148
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 TYR cc_start: 0.8711 (p90) cc_final: 0.8119 (p90)
REVERT: B   12 GLU cc_start: 0.9289 (pt0) cc_final: 0.8958 (pm20)
REVERT: B  130 GLU cc_start: 0.8959 (mp0) cc_final: 0.8715 (mp0)
REVERT: B  283 ARG cc_start: 0.7363 (ttt180) cc_final: 0.7074 (ttt180)
REVERT: B  292 PHE cc_start: 0.8115 (m-10) cc_final: 0.7698 (m-10)
REVERT: G   21 MET cc_start: 0.8559 (mmm) cc_final: 0.7692 (mtm)
REVERT: G   38 MET cc_start: 0.6695 (ptp) cc_final: 0.6050 (ptt)
REVERT: G   42 GLU cc_start: 0.8086 (tp30) cc_final: 0.7514 (mt-10)
REVERT: G   58 GLU cc_start: 0.9085 (mp0) cc_final: 0.8540 (mp0)
REVERT: R   79 LEU cc_start: 0.8809 (tp) cc_final: 0.8589 (tp)
REVERT: R   94 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7435 (t70)
REVERT: R  109 GLU cc_start: 0.8658 (tp30) cc_final: 0.8261 (tm-30)
REVERT: R  111 MET cc_start: 0.8622 (mtm) cc_final: 0.8331 (ptp)
REVERT: H  160 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8139 (p)
  outliers start: 32
  outliers final: 22
  residues processed: 171
  average time/residue: 0.0952
  time to fit residues: 22.0456
Evaluate side-chains
  164 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  138 HIS
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  230 VAL
Chi-restraints excluded: chain R residue  382 ASN
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain R residue  433 ASN
Chi-restraints excluded: chain R residue  435 SER
Chi-restraints excluded: chain R residue  439 VAL
Chi-restraints excluded: chain R residue  454 LYS
Chi-restraints excluded: chain H residue   90 ASP
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  190 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 100 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 31 optimal weight:    8.9990
   chunk 60 optimal weight:    5.9990
   chunk 105 optimal weight:   30.0000
   chunk 39 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 87 optimal weight:    8.9990
   overall best weight:    3.9386

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
R 138 HIS
** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.090530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.066533 restraints weight = 31794.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.068521 restraints weight = 17518.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.069867 restraints weight = 12066.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.070737 restraints weight = 9519.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.071214 restraints weight = 8220.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.3241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8772  Z= 0.223
  Angle     :  0.813  14.794  11887  Z= 0.404
  Chirality :  0.045   0.205   1349
  Planarity :  0.004   0.047   1496
  Dihedral  :  7.934 159.210   1193
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 21.29 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.26), residues: 1075
  helix:  1.46 (0.28), residues: 344
  sheet: -0.40 (0.33), residues: 250
  loop : -1.33 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H 190 
 TYR   0.023   0.002   TYR H 161 
 PHE   0.033   0.002   PHE R 387 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.018   0.002   HIS R 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 8768)
  covalent geometry    : angle       0.81289 (11881)
  SS BOND              : bond        0.00401 (    3)
  SS BOND              : angle       0.53278 (    6)
  hydrogen bonds       : bond        0.04210 (  361)
  hydrogen bonds       : angle       4.55208 ( 1035)
  Misc. bond           : bond        0.00085 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 146
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 TYR cc_start: 0.8720 (p90) cc_final: 0.8509 (p90)
REVERT: B   12 GLU cc_start: 0.9276 (pt0) cc_final: 0.8957 (pm20)
REVERT: B   36 ASN cc_start: 0.8511 (m-40) cc_final: 0.8231 (p0)
REVERT: B  130 GLU cc_start: 0.8958 (mp0) cc_final: 0.8693 (mp0)
REVERT: B  175 GLN cc_start: 0.8327 (mp10) cc_final: 0.8056 (mp10)
REVERT: B  292 PHE cc_start: 0.8339 (m-10) cc_final: 0.8006 (m-80)
REVERT: G   24 ASN cc_start: 0.7795 (t0) cc_final: 0.7202 (m-40)
REVERT: G   38 MET cc_start: 0.6718 (ptp) cc_final: 0.6458 (ptt)
REVERT: G   42 GLU cc_start: 0.8095 (tp30) cc_final: 0.7628 (mt-10)
REVERT: G   58 GLU cc_start: 0.9126 (mp0) cc_final: 0.8451 (mp0)
REVERT: R   94 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7560 (t70)
REVERT: R  109 GLU cc_start: 0.8611 (tp30) cc_final: 0.8164 (tm-30)
  outliers start: 25
  outliers final: 23
  residues processed: 163
  average time/residue: 0.0890
  time to fit residues: 19.9740
Evaluate side-chains
  163 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 139
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  138 HIS
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  230 VAL
Chi-restraints excluded: chain R residue  382 ASN
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain R residue  435 SER
Chi-restraints excluded: chain R residue  439 VAL
Chi-restraints excluded: chain R residue  454 LYS
Chi-restraints excluded: chain H residue   90 ASP
Chi-restraints excluded: chain H residue  190 ARG
Chi-restraints excluded: chain H residue  212 VAL
Chi-restraints excluded: chain H residue  225 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 46 optimal weight:    8.9990
   chunk 92 optimal weight:    5.9990
   chunk 19 optimal weight:    0.5980
   chunk 76 optimal weight:    0.7980
   chunk 99 optimal weight:    7.9990
   chunk 49 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 94 optimal weight:   10.0000
   chunk 84 optimal weight:    0.0570
   chunk 65 optimal weight:    6.9990
   overall best weight:    2.2902

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
R 138 HIS
** R 433 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 = 0.3745 r_free = 0.3745 target = 0.091949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.067952 restraints weight = 31912.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.070023 restraints weight = 17358.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.071325 restraints weight = 11866.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.072275 restraints weight = 9385.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.072861 restraints weight = 8058.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8772  Z= 0.163
  Angle     :  0.823  14.245  11887  Z= 0.400
  Chirality :  0.044   0.195   1349
  Planarity :  0.004   0.047   1496
  Dihedral  :  7.858 157.134   1193
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 21.94 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.26), residues: 1075
  helix:  1.43 (0.29), residues: 340
  sheet: -0.42 (0.33), residues: 248
  loop : -1.38 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 450 
 TYR   0.017   0.001   TYR H 161 
 PHE   0.030   0.001   PHE R 387 
 TRP   0.010   0.001   TRP B 169 
 HIS   0.009   0.001   HIS R 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 8768)
  covalent geometry    : angle       0.82279 (11881)
  SS BOND              : bond        0.00333 (    3)
  SS BOND              : angle       0.60179 (    6)
  hydrogen bonds       : bond        0.03994 (  361)
  hydrogen bonds       : angle       4.45250 ( 1035)
  Misc. bond           : bond        0.00047 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LEU cc_start: 0.3486 (OUTLIER) cc_final: 0.3269 (pp)
REVERT: A  318 GLU cc_start: 0.7285 (tt0) cc_final: 0.7057 (tt0)
REVERT: A  354 TYR cc_start: 0.8695 (p90) cc_final: 0.8162 (p90)
REVERT: B   12 GLU cc_start: 0.9279 (pt0) cc_final: 0.8947 (pm20)
REVERT: B   36 ASN cc_start: 0.8566 (m-40) cc_final: 0.8226 (p0)
REVERT: B   59 TYR cc_start: 0.8621 (m-80) cc_final: 0.8092 (m-80)
REVERT: B  292 PHE cc_start: 0.8298 (m-10) cc_final: 0.7955 (m-80)
REVERT: G   21 MET cc_start: 0.8227 (mmm) cc_final: 0.7027 (mtm)
REVERT: G   38 MET cc_start: 0.6696 (ptp) cc_final: 0.6455 (ptt)
REVERT: G   42 GLU cc_start: 0.8073 (tp30) cc_final: 0.7619 (mt-10)
REVERT: G   58 GLU cc_start: 0.9118 (mp0) cc_final: 0.8427 (mp0)
REVERT: R   94 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7480 (t70)
REVERT: R  109 GLU cc_start: 0.8604 (tp30) cc_final: 0.8149 (tm-30)
REVERT: H  160 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8144 (p)
REVERT: H  232 LYS cc_start: 0.8080 (mppt) cc_final: 0.7663 (pptt)
  outliers start: 26
  outliers final: 22
  residues processed: 167
  average time/residue: 0.0883
  time to fit residues: 20.3741
Evaluate side-chains
  170 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 145
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  138 HIS
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  230 VAL
Chi-restraints excluded: chain R residue  382 ASN
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain R residue  435 SER
Chi-restraints excluded: chain R residue  439 VAL
Chi-restraints excluded: chain R residue  454 LYS
Chi-restraints excluded: chain H residue   90 ASP
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  190 ARG
Chi-restraints excluded: chain H residue  212 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 103 optimal weight:    5.9990
   chunk 16 optimal weight:    8.9990
   chunk 28 optimal weight:    9.9990
   chunk 97 optimal weight:    6.9990
   chunk 83 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0980
   chunk 98 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0020
   chunk 66 optimal weight:    5.9990
   chunk 93 optimal weight:    6.9990
   overall best weight:    2.2194

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
R 138 HIS
R 433 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.092139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.068182 restraints weight = 31877.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.070276 restraints weight = 17291.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.071658 restraints weight = 11793.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.072449 restraints weight = 9264.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.073112 restraints weight = 8035.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.3385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8772  Z= 0.161
  Angle     :  0.838  17.169  11887  Z= 0.404
  Chirality :  0.044   0.193   1349
  Planarity :  0.004   0.048   1496
  Dihedral  :  7.798 155.135   1193
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 21.72 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.26), residues: 1075
  helix:  1.36 (0.29), residues: 340
  sheet: -0.39 (0.34), residues: 246
  loop : -1.37 (0.28), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 450 
 TYR   0.017   0.001   TYR R 156 
 PHE   0.035   0.001   PHE R 387 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.013   0.001   HIS R 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 8768)
  covalent geometry    : angle       0.83859 (11881)
  SS BOND              : bond        0.00316 (    3)
  SS BOND              : angle       0.59875 (    6)
  hydrogen bonds       : bond        0.03928 (  361)
  hydrogen bonds       : angle       4.46875 ( 1035)
  Misc. bond           : bond        0.00039 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LEU cc_start: 0.3680 (OUTLIER) cc_final: 0.3413 (pp)
REVERT: A  354 TYR cc_start: 0.8685 (p90) cc_final: 0.8162 (p90)
REVERT: B   12 GLU cc_start: 0.9267 (pt0) cc_final: 0.8933 (pm20)
REVERT: B   36 ASN cc_start: 0.8564 (m-40) cc_final: 0.8232 (p0)
REVERT: B   59 TYR cc_start: 0.8627 (m-80) cc_final: 0.8087 (m-80)
REVERT: B  283 ARG cc_start: 0.7598 (ttt180) cc_final: 0.6877 (ttt90)
REVERT: B  292 PHE cc_start: 0.8302 (m-10) cc_final: 0.7945 (m-80)
REVERT: G   21 MET cc_start: 0.8209 (mmm) cc_final: 0.7149 (mtm)
REVERT: G   24 ASN cc_start: 0.7707 (t0) cc_final: 0.7254 (m-40)
REVERT: G   38 MET cc_start: 0.6716 (ptp) cc_final: 0.6425 (ptt)
REVERT: G   42 GLU cc_start: 0.8061 (tp30) cc_final: 0.7603 (mt-10)
REVERT: G   58 GLU cc_start: 0.9123 (mp0) cc_final: 0.8434 (mp0)
REVERT: R   94 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7501 (t70)
REVERT: R  109 GLU cc_start: 0.8604 (tp30) cc_final: 0.8176 (tm-30)
REVERT: H  160 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8075 (p)
REVERT: H  211 ASP cc_start: 0.8032 (m-30) cc_final: 0.7770 (m-30)
REVERT: H  234 GLU cc_start: 0.6875 (pm20) cc_final: 0.6063 (pp20)
  outliers start: 28
  outliers final: 23
  residues processed: 168
  average time/residue: 0.0851
  time to fit residues: 19.8990
Evaluate side-chains
  168 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 142
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  127 LEU
Chi-restraints excluded: chain R residue  138 HIS
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  230 VAL
Chi-restraints excluded: chain R residue  382 ASN
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain R residue  433 ASN
Chi-restraints excluded: chain R residue  435 SER
Chi-restraints excluded: chain R residue  439 VAL
Chi-restraints excluded: chain R residue  454 LYS
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  190 ARG
Chi-restraints excluded: chain H residue  212 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 58 optimal weight:    8.9990
   chunk 16 optimal weight:    0.0570
   chunk 54 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 103 optimal weight:    0.0270
   chunk 22 optimal weight:   20.0000
   chunk 78 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    1.4162

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
R 138 HIS
** R 433 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 = 0.3757 r_free = 0.3757 target = 0.092814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.068843 restraints weight = 31267.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.070947 restraints weight = 16915.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.072334 restraints weight = 11503.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.073205 restraints weight = 9021.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.073830 restraints weight = 7753.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.3419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8772  Z= 0.142
  Angle     :  0.827  17.037  11887  Z= 0.397
  Chirality :  0.044   0.194   1349
  Planarity :  0.004   0.048   1496
  Dihedral  :  7.730 153.296   1193
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 22.37 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.26), residues: 1075
  helix:  1.37 (0.29), residues: 340
  sheet: -0.29 (0.34), residues: 244
  loop : -1.38 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 190 
 TYR   0.016   0.001   TYR R 156 
 PHE   0.030   0.001   PHE R 387 
 TRP   0.009   0.001   TRP B  99 
 HIS   0.008   0.001   HIS R 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8768)
  covalent geometry    : angle       0.82736 (11881)
  SS BOND              : bond        0.00284 (    3)
  SS BOND              : angle       0.56176 (    6)
  hydrogen bonds       : bond        0.03812 (  361)
  hydrogen bonds       : angle       4.41263 ( 1035)
  Misc. bond           : bond        0.00025 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1741.72 seconds
wall clock time: 30 minutes 41.33 seconds (1841.33 seconds total)