Starting phenix.real_space_refine
on Fri Mar 14 02:59:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j6q_36011/03_2025/8j6q_36011.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j6q_36011/03_2025/8j6q_36011.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j6q_36011/03_2025/8j6q_36011.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j6q_36011/03_2025/8j6q_36011.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j6q_36011/03_2025/8j6q_36011.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j6q_36011/03_2025/8j6q_36011.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.007
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      69      5.16       5
     C    5876      2.51       5
     N    1554      2.21       5
     O    1688      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9187
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1811
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "S"
      Number of atoms: 1795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1795
          Classifications: {'peptide': 234}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2420
          Classifications: {'peptide': 295}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 284}
    Chain: "R"
      Number of atoms: 110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 110
          Unusual residues: {'3HR': 1, 'CLR': 2, 'IX8': 1, 'NAG': 1}
          Classifications: {'undetermined': 5, 'water': 1}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.65, per 1000 atoms: 0.61
  Number of scatterers: 9187
  At special positions: 0
  Unit cell: (106.02, 119.04, 113.46, 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      69     16.00
     O    1688      8.00
     N    1554      7.00
     C    5876      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  18 " - pdb=" SG  CYS R 183 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  19 " - pdb=" SG  CYS R 266 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 100 " - pdb=" SG  CYS R 177 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG R 405 " - " ASN R  17 "
  Time building additional restraints: 2.29
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2156

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 14 sheets defined
      38.3% alpha, 23.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.616A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.335A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.666A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.034A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.607A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.526A  pdb=" N   GLN G  11 " --> pdb=" O   ALA G   7 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.098A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
    Processing helix  chain 'S' and resid 220 through 224
    Processing helix  chain 'R' and resid 23 through 54
      removed outlier: 3.877A  pdb=" N   VAL R  27 " --> pdb=" O   ASP R  23 " (cutoff:3.500A)
      Proline residue:  R  31  - end of helix
    Processing helix  chain 'R' and resid 60 through 78
    Processing helix  chain 'R' and resid 79 through 89
      removed outlier: 3.671A  pdb=" N   LEU R  83 " --> pdb=" O   CYS R  79 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ARG R  89 " --> pdb=" O   ASP R  85 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 96 through 130
      removed outlier: 3.728A  pdb=" N   CYS R 100 " --> pdb=" O   GLY R  96 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 134 through 139
      removed outlier: 3.661A  pdb=" N   ILE R 139 " --> pdb=" O   LEU R 136 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 160
    Processing helix  chain 'R' and resid 161 through 165
      removed outlier: 3.672A  pdb=" N   LYS R 164 " --> pdb=" O   HIS R 161 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LYS R 165 " --> pdb=" O   LEU R 162 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 161 through 165'
    Processing helix  chain 'R' and resid 170 through 174
      removed outlier: 4.031A  pdb=" N   GLY R 173 " --> pdb=" O   GLN R 170 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 187 through 218
      removed outlier: 3.523A  pdb=" N   ALA R 191 " --> pdb=" O   GLN R 187 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   PHE R 197 " --> pdb=" O   PHE R 193 " (cutoff:3.500A)
      Proline residue:  R 200  - end of helix
    Processing helix  chain 'R' and resid 219 through 222
      removed outlier: 3.644A  pdb=" N   ARG R 222 " --> pdb=" O   GLN R 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 219 through 222'
    Processing helix  chain 'R' and resid 223 through 261
      Proline residue:  R 246  - end of helix
    Processing helix  chain 'R' and resid 265 through 267
      No H-bonds generated for 'chain 'R' and resid 265 through 267'
    Processing helix  chain 'R' and resid 268 through 295
      removed outlier: 4.461A  pdb=" N   VAL R 272 " --> pdb=" O   VAL R 268 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   THR R 283 " --> pdb=" O   THR R 279 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   TYR R 284 " --> pdb=" O   LEU R 280 " (cutoff:3.500A)
      Proline residue:  R 291  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 5.945A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.276A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.455A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.787A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.836A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.518A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.256A  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: 6.657A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.672A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.547A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12
      removed outlier: 5.958A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.048A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   ALA S  40 " --> pdb=" O   LEU S  45 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   LEU S  45 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 3.860A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148
      removed outlier: 6.525A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 10 through 12

    448 hydrogen bonds defined for protein.
    1242 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.78

  Time building geometry restraints manager: 2.72 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1985
        1.33 -     1.46: 2469
        1.46 -     1.58: 4837
        1.58 -     1.71: 1
        1.71 -     1.83: 100
  Bond restraints: 9392
  Sorted by residual:
  bond pdb=" C2  IX8 R 401 "
       pdb=" C25 IX8 R 401 "
    ideal  model  delta    sigma   weight residual
    1.522  1.649 -0.127 2.00e-02 2.50e+03 4.01e+01
  bond pdb=" C4  IX8 R 401 "
       pdb=" N3  IX8 R 401 "
    ideal  model  delta    sigma   weight residual
    1.341  1.442 -0.101 2.00e-02 2.50e+03 2.54e+01
  bond pdb=" C2  IX8 R 401 "
       pdb=" N3  IX8 R 401 "
    ideal  model  delta    sigma   weight residual
    1.451  1.538 -0.087 2.00e-02 2.50e+03 1.87e+01
  bond pdb=" C15 IX8 R 401 "
       pdb=" C16 IX8 R 401 "
    ideal  model  delta    sigma   weight residual
    1.460  1.545 -0.085 2.00e-02 2.50e+03 1.82e+01
  bond pdb=" C11 IX8 R 401 "
       pdb=" N10 IX8 R 401 "
    ideal  model  delta    sigma   weight residual
    1.359  1.442 -0.083 2.00e-02 2.50e+03 1.74e+01
  ... (remaining 9387 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 12443
        2.00 -     4.00: 207
        4.00 -     6.00: 53
        6.00 -     8.01: 12
        8.01 -    10.01: 4
  Bond angle restraints: 12719
  Sorted by residual:
  angle pdb=" N   CYS R  18 "
        pdb=" CA  CYS R  18 "
        pdb=" C   CYS R  18 "
      ideal   model   delta    sigma   weight residual
     108.24  113.37   -5.13 1.32e+00 5.74e-01 1.51e+01
  angle pdb=" N   VAL S  64 "
        pdb=" CA  VAL S  64 "
        pdb=" C   VAL S  64 "
      ideal   model   delta    sigma   weight residual
     113.20  109.70    3.50 9.60e-01 1.09e+00 1.33e+01
  angle pdb=" C   ASP S  73 "
        pdb=" N   ASP S  74 "
        pdb=" CA  ASP S  74 "
      ideal   model   delta    sigma   weight residual
     120.06  124.17   -4.11 1.19e+00 7.06e-01 1.19e+01
  angle pdb=" CA  GLN R 170 "
        pdb=" CB  GLN R 170 "
        pdb=" CG  GLN R 170 "
      ideal   model   delta    sigma   weight residual
     114.10  120.97   -6.87 2.00e+00 2.50e-01 1.18e+01
  angle pdb=" N   GLU A  25 "
        pdb=" CA  GLU A  25 "
        pdb=" CB  GLU A  25 "
      ideal   model   delta    sigma   weight residual
     110.28  115.52   -5.24 1.55e+00 4.16e-01 1.14e+01
  ... (remaining 12714 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 5174
       17.82 -    35.64: 422
       35.64 -    53.46: 55
       53.46 -    71.28: 21
       71.28 -    89.10: 6
  Dihedral angle restraints: 5678
    sinusoidal: 2343
      harmonic: 3335
  Sorted by residual:
  dihedral pdb=" CB  CYS R  18 "
           pdb=" SG  CYS R  18 "
           pdb=" SG  CYS R 183 "
           pdb=" CB  CYS R 183 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   52.96   40.04     1      1.00e+01 1.00e-02 2.25e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.71   18.29     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.88   18.12     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 5675 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 1322
       0.089 -    0.179: 101
       0.179 -    0.268: 6
       0.268 -    0.357: 0
       0.357 -    0.446: 1
  Chirality restraints: 1430
  Sorted by residual:
  chirality pdb=" C2  IX8 R 401 "
            pdb=" C1  IX8 R 401 "
            pdb=" C25 IX8 R 401 "
            pdb=" N3  IX8 R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.86   -0.45 2.00e-01 2.50e+01 4.98e+00
  chirality pdb=" C3  3HR R 403 "
            pdb=" C2  3HR R 403 "
            pdb=" C4  3HR R 403 "
            pdb=" O2  3HR R 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.58    0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" C13 CLR R 402 "
            pdb=" C12 CLR R 402 "
            pdb=" C14 CLR R 402 "
            pdb=" C17 CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.73   -0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 1427 not shown)

  Planarity restraints: 1596
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "   -0.049 5.00e-02 4.00e+02   7.45e-02 8.87e+00
        pdb=" N   PRO S  75 "    0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.032 5.00e-02 4.00e+02   4.80e-02 3.69e+00
        pdb=" N   PRO B 236 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R  38 "    0.006 2.00e-02 2.50e+03   1.36e-02 3.23e+00
        pdb=" CG  PHE R  38 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE R  38 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE R  38 "    0.018 2.00e-02 2.50e+03
        pdb=" CE1 PHE R  38 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE R  38 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE R  38 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1593 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 534
        2.73 -     3.27: 8950
        3.27 -     3.82: 16278
        3.82 -     4.36: 20262
        4.36 -     4.90: 34023
  Nonbonded interactions: 80047
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 175 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OD1 ASN A 269 "
            pdb=" OG1 THR A 324 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASP B 154 "
     model   vdw
     2.266 3.040
  ... (remaining 80042 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     23.960
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.070
  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:             0.020
  Load rotamer database and sin/cos tables:14.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
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   0.127   9392  Z= 0.281
  Angle     :  0.695  10.008  12719  Z= 0.355
  Chirality :  0.048   0.446   1430
  Planarity :  0.004   0.074   1595
  Dihedral  : 13.239  89.104   3507
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.25), residues: 1137
  helix:  1.12 (0.26), residues: 384
  sheet:  0.12 (0.30), residues: 283
  loop : -0.23 (0.30), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.028   0.002   PHE R  38 
 TYR   0.025   0.002   TYR S 190 
 ARG   0.005   0.000   ARG A  21 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 1.027 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 1.3647
  time to fit residues: 230.5742
Evaluate side-chains
  142 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 57 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 87 optimal weight:    6.9990
   chunk 33 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 101 optimal weight:    3.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 269 ASN
A 331 ASN
B 268 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.160503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.120342 restraints weight = 9174.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 2.07
r_work: 0.3067 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.1177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9392  Z= 0.218
  Angle     :  0.544   8.350  12719  Z= 0.294
  Chirality :  0.042   0.190   1430
  Planarity :  0.004   0.066   1595
  Dihedral  :  7.049  89.157   1415
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  8.74 %
    Favored  : 89.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.25), residues: 1137
  helix:  1.71 (0.27), residues: 381
  sheet:  0.04 (0.30), residues: 279
  loop : -0.20 (0.30), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 211 
 HIS   0.003   0.001   HIS R 189 
 PHE   0.013   0.001   PHE R  38 
 TYR   0.025   0.002   TYR S 190 
 ARG   0.004   0.000   ARG S  72 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 146
  time to evaluate  : 0.945 
Fit side-chains
REVERT: B   46 ARG cc_start: 0.7772 (mpp-170) cc_final: 0.7497 (mtm-85)
REVERT: B   96 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7971 (mtt-85)
REVERT: B  217 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7492 (pp-130)
REVERT: G   36 ASP cc_start: 0.8236 (m-30) cc_final: 0.7935 (m-30)
REVERT: S  160 ARG cc_start: 0.7596 (mtm110) cc_final: 0.6748 (mmm160)
REVERT: S  202 ARG cc_start: 0.8314 (ptt-90) cc_final: 0.8046 (ptt-90)
REVERT: R  102 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6971 (mm)
REVERT: R  110 ASN cc_start: 0.8600 (m110) cc_final: 0.8329 (m110)
  outliers start: 13
  outliers final: 2
  residues processed: 148
  average time/residue: 1.3818
  time to fit residues: 216.9110
Evaluate side-chains
  140 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 135
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain R residue  102 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 76 optimal weight:    0.7980
   chunk 108 optimal weight:    6.9990
   chunk 24 optimal weight:    9.9990
   chunk 79 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B 268 ASN
B 340 ASN
R 189 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.157639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.116150 restraints weight = 9173.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.03
r_work: 0.2996 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2864 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9392  Z= 0.317
  Angle     :  0.588   7.729  12719  Z= 0.316
  Chirality :  0.044   0.209   1430
  Planarity :  0.004   0.066   1595
  Dihedral  :  6.748  82.355   1415
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 11.76 %
    Favored  : 86.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.25), residues: 1137
  helix:  1.73 (0.27), residues: 381
  sheet: -0.06 (0.29), residues: 290
  loop : -0.23 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.006   0.001   HIS R 189 
 PHE   0.013   0.002   PHE R 277 
 TYR   0.026   0.002   TYR S 190 
 ARG   0.003   0.000   ARG B 251 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.992 
Fit side-chains
REVERT: A  186 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7032 (mp0)
REVERT: A  240 MET cc_start: 0.6165 (tpp) cc_final: 0.5800 (tpt)
REVERT: A  306 GLN cc_start: 0.8144 (mm110) cc_final: 0.7821 (mm-40)
REVERT: B   46 ARG cc_start: 0.7843 (mpp-170) cc_final: 0.7545 (mtm-85)
REVERT: B  172 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7323 (tm-30)
REVERT: G   36 ASP cc_start: 0.8359 (m-30) cc_final: 0.7950 (m-30)
REVERT: S  160 ARG cc_start: 0.7648 (mtm110) cc_final: 0.6850 (mmm160)
REVERT: S  202 ARG cc_start: 0.8331 (ptt-90) cc_final: 0.8097 (ptt-90)
REVERT: R  102 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7240 (mm)
REVERT: R  253 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7032 (tpm170)
  outliers start: 16
  outliers final: 4
  residues processed: 149
  average time/residue: 1.3624
  time to fit residues: 215.3250
Evaluate side-chains
  139 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 133
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain R residue  102 LEU
Chi-restraints excluded: chain R residue  159 THR
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  271 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 102 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 111 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 108 optimal weight:   10.0000
   chunk 83 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
B 268 ASN
B 340 ASN
S 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.158981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.119572 restraints weight = 9085.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 1.89
r_work: 0.3046 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9392  Z= 0.216
  Angle     :  0.527   7.166  12719  Z= 0.285
  Chirality :  0.042   0.190   1430
  Planarity :  0.004   0.064   1595
  Dihedral  :  6.354  76.732   1415
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.37 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.26), residues: 1137
  helix:  1.88 (0.27), residues: 380
  sheet: -0.12 (0.29), residues: 290
  loop : -0.20 (0.31), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.023   0.001   PHE R  38 
 TYR   0.025   0.001   TYR S 190 
 ARG   0.005   0.000   ARG G  62 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 1.036 
Fit side-chains
REVERT: A  240 MET cc_start: 0.6137 (tpp) cc_final: 0.5791 (tpt)
REVERT: B   46 ARG cc_start: 0.7885 (mpp-170) cc_final: 0.7601 (mtm-85)
REVERT: B  172 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7371 (tm-30)
REVERT: G   36 ASP cc_start: 0.8378 (m-30) cc_final: 0.7991 (m-30)
REVERT: S  160 ARG cc_start: 0.7601 (mtm110) cc_final: 0.7398 (mtm110)
REVERT: S  202 ARG cc_start: 0.8390 (ptt-90) cc_final: 0.8181 (ptt-90)
REVERT: R  102 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7294 (mm)
REVERT: R  110 ASN cc_start: 0.8604 (m110) cc_final: 0.8385 (m110)
REVERT: R  253 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7035 (tpm170)
  outliers start: 15
  outliers final: 8
  residues processed: 144
  average time/residue: 1.3528
  time to fit residues: 206.8268
Evaluate side-chains
  140 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue  117 LEU
Chi-restraints excluded: chain R residue  102 LEU
Chi-restraints excluded: chain R residue  159 THR
Chi-restraints excluded: chain R residue  222 ARG
Chi-restraints excluded: chain R residue  253 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 93 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 72 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 71 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 88 optimal weight:    0.4980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
B 268 ASN
B 340 ASN
S 186 GLN
R 219 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.159198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.120317 restraints weight = 9094.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 1.85
r_work: 0.3046 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9392  Z= 0.222
  Angle     :  0.523   7.148  12719  Z= 0.282
  Chirality :  0.042   0.192   1430
  Planarity :  0.004   0.062   1595
  Dihedral  :  6.178  70.833   1415
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.27 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.26), residues: 1137
  helix:  1.93 (0.27), residues: 379
  sheet: -0.28 (0.29), residues: 286
  loop : -0.09 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.017   0.001   PHE R  38 
 TYR   0.026   0.001   TYR S 190 
 ARG   0.006   0.000   ARG G  62 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 2.496 
Fit side-chains
REVERT: A  186 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7137 (tt0)
REVERT: A  240 MET cc_start: 0.6071 (tpp) cc_final: 0.5792 (tpt)
REVERT: A  306 GLN cc_start: 0.8043 (mm110) cc_final: 0.7619 (mp10)
REVERT: B   46 ARG cc_start: 0.7857 (mpp-170) cc_final: 0.7562 (mtm-85)
REVERT: G   36 ASP cc_start: 0.8366 (m-30) cc_final: 0.7955 (m-30)
REVERT: S   89 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7472 (pp20)
REVERT: S  160 ARG cc_start: 0.7609 (mtm110) cc_final: 0.7404 (mtm110)
REVERT: S  202 ARG cc_start: 0.8426 (ptt-90) cc_final: 0.8186 (ptt-90)
REVERT: R   42 LEU cc_start: 0.7977 (tp) cc_final: 0.7756 (tp)
REVERT: R  102 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7271 (mm)
REVERT: R  110 ASN cc_start: 0.8604 (m110) cc_final: 0.8387 (m110)
REVERT: R  253 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7021 (tpm170)
  outliers start: 22
  outliers final: 10
  residues processed: 144
  average time/residue: 1.9110
  time to fit residues: 293.9204
Evaluate side-chains
  144 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain S residue  117 LEU
Chi-restraints excluded: chain R residue  102 LEU
Chi-restraints excluded: chain R residue  159 THR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  253 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 88 optimal weight:    1.9990
   chunk 98 optimal weight:    0.1980
   chunk 101 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0470
   chunk 11 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    1.2484

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
B 340 ASN
S 186 GLN
R 219 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.158407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.116851 restraints weight = 9052.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 1.93
r_work: 0.3022 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9392  Z= 0.256
  Angle     :  0.545   7.132  12719  Z= 0.293
  Chirality :  0.043   0.198   1430
  Planarity :  0.004   0.063   1595
  Dihedral  :  6.151  65.840   1415
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 14.37 %
    Favored  : 83.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.26), residues: 1137
  helix:  1.92 (0.27), residues: 380
  sheet: -0.23 (0.29), residues: 282
  loop : -0.09 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.025   0.001   PHE R  38 
 TYR   0.026   0.002   TYR S 190 
 ARG   0.006   0.000   ARG B 197 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 0.992 
Fit side-chains
REVERT: A  240 MET cc_start: 0.5978 (tpp) cc_final: 0.5716 (tpt)
REVERT: A  306 GLN cc_start: 0.8062 (mm110) cc_final: 0.7625 (mp10)
REVERT: B   46 ARG cc_start: 0.7892 (mpp-170) cc_final: 0.7585 (mtm-85)
REVERT: G   36 ASP cc_start: 0.8387 (m-30) cc_final: 0.7992 (m-30)
REVERT: G   38 MET cc_start: 0.8258 (mtp) cc_final: 0.7921 (mtp)
REVERT: S   89 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7468 (pp20)
REVERT: S  160 ARG cc_start: 0.7642 (mtm110) cc_final: 0.7432 (mtm110)
REVERT: S  202 ARG cc_start: 0.8438 (ptt-90) cc_final: 0.8175 (ptt-90)
REVERT: R  102 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7328 (mm)
REVERT: R  110 ASN cc_start: 0.8648 (m110) cc_final: 0.8419 (m110)
REVERT: R  253 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.6786 (tpm170)
  outliers start: 23
  outliers final: 10
  residues processed: 151
  average time/residue: 1.4156
  time to fit residues: 226.9886
Evaluate side-chains
  147 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 134
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain S residue  117 LEU
Chi-restraints excluded: chain R residue  102 LEU
Chi-restraints excluded: chain R residue  159 THR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  271 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 110 optimal weight:    0.6980
   chunk 97 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
B 340 ASN
S 186 GLN
R 219 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.159840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.120668 restraints weight = 9275.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.88
r_work: 0.3060 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9392  Z= 0.199
  Angle     :  0.518   7.118  12719  Z= 0.281
  Chirality :  0.042   0.182   1430
  Planarity :  0.004   0.063   1595
  Dihedral  :  6.136  61.591   1415
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.58 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.26), residues: 1137
  helix:  2.08 (0.27), residues: 378
  sheet: -0.26 (0.30), residues: 285
  loop : -0.04 (0.31), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.002   0.001   HIS B  91 
 PHE   0.021   0.001   PHE R  38 
 TYR   0.025   0.001   TYR S 190 
 ARG   0.007   0.000   ARG B 197 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 1.765 
Fit side-chains
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.7914 (tt0) cc_final: 0.7422 (tt0)
REVERT: A  240 MET cc_start: 0.6119 (tpp) cc_final: 0.5879 (tpt)
REVERT: A  306 GLN cc_start: 0.7936 (mm110) cc_final: 0.7501 (mp10)
REVERT: B   46 ARG cc_start: 0.7890 (mpp-170) cc_final: 0.7573 (mtm-85)
REVERT: G   21 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.5859 (ttt)
REVERT: G   36 ASP cc_start: 0.8349 (m-30) cc_final: 0.8020 (m-30)
REVERT: S   89 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7471 (pp20)
REVERT: S  160 ARG cc_start: 0.7612 (mtm110) cc_final: 0.6930 (mtp-110)
REVERT: S  202 ARG cc_start: 0.8441 (ptt-90) cc_final: 0.8172 (ptt-90)
REVERT: R  102 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7291 (mm)
REVERT: R  253 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7009 (tpm170)
  outliers start: 17
  outliers final: 7
  residues processed: 151
  average time/residue: 1.9223
  time to fit residues: 306.2850
Evaluate side-chains
  148 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 137
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain R residue  102 LEU
Chi-restraints excluded: chain R residue  159 THR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  271 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 24 optimal weight:    8.9990
   chunk 75 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
B 268 ASN
B 340 ASN
** S 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 219 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.158607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.117617 restraints weight = 9235.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 2.04
r_work: 0.3025 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9392  Z= 0.251
  Angle     :  0.551   7.124  12719  Z= 0.297
  Chirality :  0.043   0.197   1430
  Planarity :  0.004   0.063   1595
  Dihedral  :  6.136  59.766   1415
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 14.77 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.26), residues: 1137
  helix:  2.04 (0.27), residues: 379
  sheet: -0.28 (0.29), residues: 285
  loop : -0.07 (0.31), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.027   0.001   PHE R  38 
 TYR   0.026   0.002   TYR S 190 
 ARG   0.007   0.000   ARG B 197 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
REVERT: A    4 THR cc_start: 0.7039 (OUTLIER) cc_final: 0.6756 (m)
REVERT: A  240 MET cc_start: 0.6078 (tpp) cc_final: 0.5817 (tpt)
REVERT: A  306 GLN cc_start: 0.7920 (mm110) cc_final: 0.7471 (mp10)
REVERT: B   46 ARG cc_start: 0.7881 (mpp-170) cc_final: 0.7541 (mtm-85)
REVERT: B  259 GLN cc_start: 0.7978 (tt0) cc_final: 0.7705 (tt0)
REVERT: G   36 ASP cc_start: 0.8367 (m-30) cc_final: 0.8021 (m-30)
REVERT: S   89 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7497 (pp20)
REVERT: S  160 ARG cc_start: 0.7636 (mtm110) cc_final: 0.7422 (mtm110)
REVERT: S  202 ARG cc_start: 0.8445 (ptt-90) cc_final: 0.8150 (ptt-90)
REVERT: R  102 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7235 (mm)
REVERT: R  253 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.6768 (tpm170)
  outliers start: 20
  outliers final: 10
  residues processed: 144
  average time/residue: 1.4051
  time to fit residues: 214.3940
Evaluate side-chains
  149 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain R residue  102 LEU
Chi-restraints excluded: chain R residue  159 THR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  222 ARG
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  271 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 19 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 53 optimal weight:    0.5980
   chunk 96 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 91 optimal weight:    0.1980
   chunk 77 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
B 340 ASN
** S 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 219 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.160571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.121598 restraints weight = 9201.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 1.88
r_work: 0.3074 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9392  Z= 0.175
  Angle     :  0.511  10.496  12719  Z= 0.275
  Chirality :  0.041   0.179   1430
  Planarity :  0.004   0.061   1595
  Dihedral  :  5.816  59.374   1415
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 15.68 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.26), residues: 1137
  helix:  2.20 (0.27), residues: 379
  sheet: -0.21 (0.30), residues: 286
  loop : -0.00 (0.31), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 211 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.025   0.001   PHE R  38 
 TYR   0.025   0.001   TYR S 190 
 ARG   0.007   0.000   ARG B 197 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
REVERT: A    4 THR cc_start: 0.7096 (t) cc_final: 0.6817 (m)
REVERT: A  240 MET cc_start: 0.6128 (tpp) cc_final: 0.5920 (tpt)
REVERT: B   46 ARG cc_start: 0.7920 (mpp-170) cc_final: 0.7615 (mtm-85)
REVERT: B  259 GLN cc_start: 0.7974 (tt0) cc_final: 0.7692 (tt0)
REVERT: G   36 ASP cc_start: 0.8275 (m-30) cc_final: 0.7964 (m-30)
REVERT: S   89 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7536 (pp20)
REVERT: S  202 ARG cc_start: 0.8507 (ptt-90) cc_final: 0.8238 (ptt-90)
REVERT: R   42 LEU cc_start: 0.7990 (tp) cc_final: 0.7788 (tp)
REVERT: R  102 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7306 (mm)
REVERT: R  216 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7539 (mtt-85)
REVERT: R  253 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7047 (tpm170)
  outliers start: 15
  outliers final: 10
  residues processed: 149
  average time/residue: 1.3425
  time to fit residues: 213.1713
Evaluate side-chains
  149 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain R residue  102 LEU
Chi-restraints excluded: chain R residue  159 THR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  235 VAL
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  271 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 5 optimal weight:    7.9990
   chunk 10 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0670
   chunk 110 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0870
   chunk 88 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.4096

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.163122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.124570 restraints weight = 9335.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.90
r_work: 0.3106 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   9392  Z= 0.158
  Angle     :  0.501   9.251  12719  Z= 0.269
  Chirality :  0.041   0.182   1430
  Planarity :  0.004   0.060   1595
  Dihedral  :  5.631  59.535   1415
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 16.18 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.26), residues: 1137
  helix:  2.23 (0.27), residues: 380
  sheet: -0.19 (0.30), residues: 287
  loop :  0.05 (0.31), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.022   0.001   PHE R  38 
 TYR   0.024   0.001   TYR S 190 
 ARG   0.007   0.000   ARG B 197 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 149
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
REVERT: A    4 THR cc_start: 0.7100 (OUTLIER) cc_final: 0.6816 (m)
REVERT: A  318 GLU cc_start: 0.6332 (tm-30) cc_final: 0.5981 (tt0)
REVERT: A  334 PHE cc_start: 0.8759 (t80) cc_final: 0.8556 (t80)
REVERT: B   46 ARG cc_start: 0.7870 (mpp-170) cc_final: 0.7556 (mtm-85)
REVERT: B  259 GLN cc_start: 0.7783 (tt0) cc_final: 0.7506 (tt0)
REVERT: G   36 ASP cc_start: 0.8171 (m-30) cc_final: 0.7899 (m-30)
REVERT: S   89 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7506 (pp20)
REVERT: S  192 MET cc_start: 0.8200 (ttp) cc_final: 0.7923 (tmm)
REVERT: S  202 ARG cc_start: 0.8384 (ptt-90) cc_final: 0.8109 (ptt-90)
REVERT: R  216 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7493 (mtt-85)
REVERT: R  253 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7078 (tpm170)
REVERT: R  293 VAL cc_start: 0.8784 (m) cc_final: 0.8483 (p)
  outliers start: 13
  outliers final: 8
  residues processed: 154
  average time/residue: 1.2672
  time to fit residues: 208.0909
Evaluate side-chains
  149 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain R residue  159 THR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  235 VAL
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  271 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 111 optimal weight:    0.6980
   chunk 52 optimal weight:    5.9990
   chunk 86 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 59 optimal weight:    0.0470
   chunk 102 optimal weight:    1.9990
   chunk 108 optimal weight:    4.9990
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B  75 GLN
B 268 ASN
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.161357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.122508 restraints weight = 9247.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 1.89
r_work: 0.3081 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   9392  Z= 0.188
  Angle     :  0.517   8.883  12719  Z= 0.277
  Chirality :  0.042   0.181   1430
  Planarity :  0.004   0.059   1595
  Dihedral  :  5.684  59.849   1415
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 16.78 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.26), residues: 1137
  helix:  2.18 (0.27), residues: 381
  sheet: -0.27 (0.30), residues: 292
  loop :  0.08 (0.31), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.022   0.001   PHE R  38 
 TYR   0.024   0.001   TYR S 190 
 ARG   0.007   0.000   ARG B 197 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8608.02 seconds
wall clock time: 151 minutes 59.72 seconds (9119.72 seconds total)