Starting phenix.real_space_refine
on Mon May 12 05:52:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8flr_29284/05_2025/8flr_29284.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8flr_29284/05_2025/8flr_29284.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8flr_29284/05_2025/8flr_29284.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8flr_29284/05_2025/8flr_29284.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8flr_29284/05_2025/8flr_29284.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8flr_29284/05_2025/8flr_29284.cif"
  }
  resolution = 2.94
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.112
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      56      5.16       5
     C    5688      2.51       5
     N    1552      2.21       5
     O    1632      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8928
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1897
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 6, 'TRANS': 226}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "B"
      Number of atoms: 2563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2563
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 30
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 25
    Chain: "G"
      Number of atoms: 403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 403
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "N"
      Number of atoms: 957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 957
          Classifications: {'peptide': 126}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "P"
      Number of atoms: 272
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 272
          Classifications: {'peptide': 32}
          Link IDs: {'TRANS': 31}
    Chain: "R"
      Number of atoms: 2826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2826
          Classifications: {'peptide': 363}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 11, 'TRANS': 351}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 168
          Unresolved non-hydrogen angles: 206
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 107
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "R"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 8
          Classifications: {'water': 8}
          Link IDs: {None: 7}
  Time building chain proxies: 5.03, per 1000 atoms: 0.56
  Number of scatterers: 8928
  At special positions: 0
  Unit cell: (73.1, 94.35, 173.4, 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      56     16.00
     O    1632      8.00
     N    1552      7.00
     C    5688      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  48 " - pdb=" SG  CYS R 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 108 " - pdb=" SG  CYS R 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 131 " - pdb=" SG  CYS R 170 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 281 " - pdb=" SG  CYS R 351 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.12
  Conformation dependent library (CDL) restraints added in 942.2 milliseconds
  

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2154

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      43.2% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 39
      removed outlier: 3.542A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 51
      No H-bonds generated for 'chain 'A' and resid 49 through 51'
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.535A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 279
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.757A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.492A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 317
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.639A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 9 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.590A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.537A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 2 through 32
    Processing helix  chain 'R' and resid 33 through 54
    Processing helix  chain 'R' and resid 177 through 212
      removed outlier: 4.336A  pdb=" N   ARG R 181 " --> pdb=" O   GLU R 177 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 245
    Processing helix  chain 'R' and resid 278 through 312
      removed outlier: 3.660A  pdb=" N   ALA R 284 " --> pdb=" O   GLY R 280 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLY R 303 " --> pdb=" O   ILE R 299 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 316 through 347
      removed outlier: 3.676A  pdb=" N   TRP R 322 " --> pdb=" O   LYS R 318 " (cutoff:3.500A)
      Proline residue:  R 332  - end of helix
    Processing helix  chain 'R' and resid 356 through 359
      removed outlier: 3.987A  pdb=" N   LYS R 359 " --> pdb=" O   SER R 356 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 356 through 359'
    Processing helix  chain 'R' and resid 360 through 391
      Proline residue:  R 366  - end of helix
    Processing helix  chain 'R' and resid 400 through 418
      Proline residue:  R 415  - end of helix
    Processing helix  chain 'R' and resid 419 through 423
      removed outlier: 3.524A  pdb=" N   VAL R 423 " --> pdb=" O   HIS R 420 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 434 through 460
      removed outlier: 4.293A  pdb=" N   GLY R 452 " --> pdb=" O   ASN R 448 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   PHE R 453 " --> pdb=" O   SER R 449 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 463 through 479
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.811A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.758A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.736A  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: 3.520A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.445A  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: 4.151A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.984A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.937A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.052A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.104A  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: 6.535A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.708A  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: 3.670A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.529A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112
      removed outlier: 3.705A  pdb=" N   GLU R 111 " --> pdb=" O   TRP R 118 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'R' and resid 126 through 130

    499 hydrogen bonds defined for protein.
    1440 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: 2.55

  Time building geometry restraints manager: 2.49 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2905
        1.34 -     1.46: 2048
        1.46 -     1.58: 4089
        1.58 -     1.70: 0
        1.70 -     1.81: 78
  Bond restraints: 9120
  Sorted by residual:
  bond pdb=" N   LEU R 321 "
       pdb=" CA  LEU R 321 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.035 1.23e-02 6.61e+03 8.29e+00
  bond pdb=" N   VAL R 432 "
       pdb=" CA  VAL R 432 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 8.03e+00
  bond pdb=" N   VAL R 171 "
       pdb=" CA  VAL R 171 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.72e+00
  bond pdb=" N   ILE P  28 "
       pdb=" CA  ILE P  28 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.17e-02 7.31e+03 7.36e+00
  bond pdb=" N   GLU R 317 "
       pdb=" CA  GLU R 317 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.28e-02 6.10e+03 7.20e+00
  ... (remaining 9115 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 12143
        1.96 -     3.91: 211
        3.91 -     5.87: 22
        5.87 -     7.82: 2
        7.82 -     9.78: 1
  Bond angle restraints: 12379
  Sorted by residual:
  angle pdb=" CA  CYS R 217 "
        pdb=" C   CYS R 217 "
        pdb=" O   CYS R 217 "
      ideal   model   delta    sigma   weight residual
     121.40  116.94    4.46 1.13e+00 7.83e-01 1.56e+01
  angle pdb=" N   ILE P  31 "
        pdb=" CA  ILE P  31 "
        pdb=" C   ILE P  31 "
      ideal   model   delta    sigma   weight residual
     112.80  108.57    4.23 1.15e+00 7.56e-01 1.35e+01
  angle pdb=" C   VAL R 334 "
        pdb=" N   PHE R 335 "
        pdb=" CA  PHE R 335 "
      ideal   model   delta    sigma   weight residual
     121.14  114.94    6.20 1.75e+00 3.27e-01 1.25e+01
  angle pdb=" CA  TYR R 191 "
        pdb=" CB  TYR R 191 "
        pdb=" CG  TYR R 191 "
      ideal   model   delta    sigma   weight residual
     113.90  119.99   -6.09 1.80e+00 3.09e-01 1.15e+01
  angle pdb=" CA  ARG R 219 "
        pdb=" C   ARG R 219 "
        pdb=" O   ARG R 219 "
      ideal   model   delta    sigma   weight residual
     120.82  117.50    3.32 1.05e+00 9.07e-01 9.99e+00
  ... (remaining 12374 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 4893
       17.93 -    35.86: 365
       35.86 -    53.79: 75
       53.79 -    71.72: 14
       71.72 -    89.65: 9
  Dihedral angle restraints: 5356
    sinusoidal: 2023
      harmonic: 3333
  Sorted by residual:
  dihedral pdb=" CB  CYS R 281 "
           pdb=" SG  CYS R 281 "
           pdb=" SG  CYS R 351 "
           pdb=" CB  CYS R 351 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.17  -43.17     1      1.00e+01 1.00e-02 2.60e+01
  dihedral pdb=" CA  CYS N  99 "
           pdb=" C   CYS N  99 "
           pdb=" N   PRO N 100 "
           pdb=" CA  PRO N 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.56  -25.44     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  LEU A 291 "
           pdb=" C   LEU A 291 "
           pdb=" N   ASN A 292 "
           pdb=" CA  ASN A 292 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.25  -23.75     0      5.00e+00 4.00e-02 2.26e+01
  ... (remaining 5353 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1092
       0.049 -    0.099: 235
       0.099 -    0.148: 52
       0.148 -    0.198: 7
       0.198 -    0.247: 1
  Chirality restraints: 1387
  Sorted by residual:
  chirality pdb=" CA  CYS R 217 "
            pdb=" N   CYS R 217 "
            pdb=" C   CYS R 217 "
            pdb=" CB  CYS R 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CA  ILE P  31 "
            pdb=" N   ILE P  31 "
            pdb=" C   ILE P  31 "
            pdb=" CB  ILE P  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.37e-01
  chirality pdb=" CA  PHE R 335 "
            pdb=" N   PHE R 335 "
            pdb=" C   PHE R 335 "
            pdb=" CB  PHE R 335 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.18e-01
  ... (remaining 1384 not shown)

  Planarity restraints: 1575
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS R 216 "   -0.011 2.00e-02 2.50e+03   2.23e-02 4.99e+00
        pdb=" C   HIS R 216 "    0.039 2.00e-02 2.50e+03
        pdb=" O   HIS R 216 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   CYS R 217 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 376 "   -0.009 2.00e-02 2.50e+03   1.73e-02 3.00e+00
        pdb=" C   ILE R 376 "    0.030 2.00e-02 2.50e+03
        pdb=" O   ILE R 376 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU R 377 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.028 5.00e-02 4.00e+02   4.22e-02 2.85e+00
        pdb=" N   PRO B 236 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1572 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 701
        2.74 -     3.28: 8964
        3.28 -     3.82: 15715
        3.82 -     4.36: 19096
        4.36 -     4.90: 32751
  Nonbonded interactions: 77227
  Sorted by model distance:
  nonbonded pdb=" O   ARG N  98 "
            pdb=" OH  TYR N 115 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   MET B 325 "
            pdb=" ND2 ASN B 340 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   ALA R 242 "
            pdb=" OG  SER R 246 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.221 3.040
  ... (remaining 77222 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     22.040
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:9.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6987
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9126  Z= 0.213
  Angle     :  0.591   9.776  12391  Z= 0.365
  Chirality :  0.044   0.247   1387
  Planarity :  0.004   0.042   1575
  Dihedral  : 13.800  89.652   3184
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.65 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.25), residues: 1125
  helix:  2.06 (0.25), residues: 442
  sheet: -0.27 (0.32), residues: 226
  loop :  0.28 (0.31), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.020   0.001   TYR N  60 
 ARG   0.009   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13207 (  499)
  hydrogen bonds       : angle       5.91908 ( 1440)
  SS BOND              : bond        0.00126 (    6)
  SS BOND              : angle       1.50256 (   12)
  covalent geometry    : bond        0.00347 ( 9120)
  covalent geometry    : angle       0.58900 (12379)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 ASP cc_start: 0.6587 (p0) cc_final: 0.6264 (p0)
REVERT: B  153 ASP cc_start: 0.7840 (p0) cc_final: 0.7570 (p0)
REVERT: R  189 MET cc_start: 0.7184 (tmm) cc_final: 0.6880 (tmt)
REVERT: R  390 ARG cc_start: 0.7504 (ttp-110) cc_final: 0.7294 (ttm170)
  outliers start: 1
  outliers final: 0
  residues processed: 140
  average time/residue: 1.1082
  time to fit residues: 167.0520
Evaluate side-chains
  113 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 84 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
B 125 ASN
** B 259 GLN ** 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 = 0.4182 r_free = 0.4182 target = 0.202103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.158608 restraints weight = 9032.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 1.91
r_work: 0.3541 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3402 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.1033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9126  Z= 0.152
  Angle     :  0.544  11.575  12391  Z= 0.290
  Chirality :  0.042   0.179   1387
  Planarity :  0.004   0.047   1575
  Dihedral  :  4.375  24.259   1244
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  5.99 %
    Favored  : 92.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.25), residues: 1125
  helix:  2.63 (0.24), residues: 435
  sheet: -0.12 (0.33), residues: 212
  loop :  0.13 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 298 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.034   0.002   PHE R 335 
 TYR   0.036   0.001   TYR R 191 
 ARG   0.006   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04496 (  499)
  hydrogen bonds       : angle       4.75759 ( 1440)
  SS BOND              : bond        0.00200 (    6)
  SS BOND              : angle       1.58067 (   12)
  covalent geometry    : bond        0.00338 ( 9120)
  covalent geometry    : angle       0.54229 (12379)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 ASP cc_start: 0.7329 (p0) cc_final: 0.6858 (p0)
REVERT: B  155 ASN cc_start: 0.7884 (t0) cc_final: 0.7584 (t0)
REVERT: G   47 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7585 (mt-10)
REVERT: N   95 TYR cc_start: 0.8682 (m-80) cc_final: 0.8480 (m-80)
REVERT: R  214 ARG cc_start: 0.7391 (ptm160) cc_final: 0.7044 (pmm150)
REVERT: R  390 ARG cc_start: 0.7916 (ttp-110) cc_final: 0.7573 (ttm170)
REVERT: R  411 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7727 (mp)
  outliers start: 15
  outliers final: 7
  residues processed: 128
  average time/residue: 1.1459
  time to fit residues: 157.2908
Evaluate side-chains
  114 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue  138 PHE
Chi-restraints excluded: chain R residue  409 SER
Chi-restraints excluded: chain R residue  411 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 101 optimal weight:    0.7980
   chunk 58 optimal weight:    7.9990
   chunk 88 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 61 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
B 125 ASN
B 176 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.201844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.158345 restraints weight = 9121.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 1.99
r_work: 0.3540 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3396 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.1226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9126  Z= 0.142
  Angle     :  0.528  13.070  12391  Z= 0.279
  Chirality :  0.041   0.176   1387
  Planarity :  0.004   0.048   1575
  Dihedral  :  4.290  22.530   1244
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  9.15 %
    Favored  : 89.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.64 (0.25), residues: 1125
  helix:  2.76 (0.24), residues: 435
  sheet: -0.15 (0.33), residues: 210
  loop :  0.17 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 298 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.016   0.001   PHE R 335 
 TYR   0.031   0.001   TYR R 191 
 ARG   0.008   0.000   ARG R 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04257 (  499)
  hydrogen bonds       : angle       4.63079 ( 1440)
  SS BOND              : bond        0.00163 (    6)
  SS BOND              : angle       1.42975 (   12)
  covalent geometry    : bond        0.00317 ( 9120)
  covalent geometry    : angle       0.52639 (12379)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 ASP cc_start: 0.7369 (p0) cc_final: 0.6898 (p0)
REVERT: B  155 ASN cc_start: 0.7873 (t0) cc_final: 0.7577 (t0)
REVERT: N   29 PHE cc_start: 0.7346 (t80) cc_final: 0.7047 (t80)
REVERT: N   59 SER cc_start: 0.8720 (m) cc_final: 0.8501 (t)
REVERT: N   95 TYR cc_start: 0.8693 (m-80) cc_final: 0.8489 (m-80)
REVERT: R  214 ARG cc_start: 0.7416 (ptm160) cc_final: 0.7056 (pmm150)
REVERT: R  390 ARG cc_start: 0.7951 (ttp-110) cc_final: 0.7565 (ttm170)
  outliers start: 17
  outliers final: 11
  residues processed: 127
  average time/residue: 1.0607
  time to fit residues: 144.6570
Evaluate side-chains
  116 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  138 PHE
Chi-restraints excluded: chain R residue  409 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 68 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 95 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 79 optimal weight:    8.9990
   chunk 52 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0980
   chunk 108 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.204395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.162985 restraints weight = 9051.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 1.77
r_work: 0.3564 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3421 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.1387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9126  Z= 0.119
  Angle     :  0.502  11.929  12391  Z= 0.267
  Chirality :  0.040   0.162   1387
  Planarity :  0.004   0.054   1575
  Dihedral  :  4.166  21.449   1244
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 10.24 %
    Favored  : 87.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.26), residues: 1125
  helix:  2.75 (0.24), residues: 443
  sheet: -0.28 (0.33), residues: 216
  loop :  0.18 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 298 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.016   0.001   PHE R 335 
 TYR   0.028   0.001   TYR R 191 
 ARG   0.009   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03952 (  499)
  hydrogen bonds       : angle       4.49047 ( 1440)
  SS BOND              : bond        0.00175 (    6)
  SS BOND              : angle       1.23464 (   12)
  covalent geometry    : bond        0.00259 ( 9120)
  covalent geometry    : angle       0.50079 (12379)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 ASP cc_start: 0.7427 (p0) cc_final: 0.6899 (p0)
REVERT: B  155 ASN cc_start: 0.7797 (t0) cc_final: 0.7568 (m-40)
REVERT: N   29 PHE cc_start: 0.7385 (t80) cc_final: 0.7109 (t80)
REVERT: R  214 ARG cc_start: 0.7433 (ptm160) cc_final: 0.7066 (pmm150)
REVERT: R  379 ILE cc_start: 0.7352 (pt) cc_final: 0.7119 (pt)
REVERT: R  390 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7556 (ttm170)
  outliers start: 21
  outliers final: 11
  residues processed: 133
  average time/residue: 1.0413
  time to fit residues: 149.6254
Evaluate side-chains
  122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  138 PHE
Chi-restraints excluded: chain R residue  409 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    0.0270
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 71 optimal weight:    0.2980
   chunk 53 optimal weight:    0.4980
   chunk 88 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.4438

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN
** B 259 GLN ** 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 = 0.4220 r_free = 0.4220 target = 0.205895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.162801 restraints weight = 9020.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 1.79
r_work: 0.3593 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3457 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9126  Z= 0.107
  Angle     :  0.486  10.718  12391  Z= 0.259
  Chirality :  0.040   0.204   1387
  Planarity :  0.004   0.053   1575
  Dihedral  :  4.087  26.131   1244
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 12.31 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.26), residues: 1125
  helix:  2.85 (0.24), residues: 443
  sheet: -0.21 (0.33), residues: 216
  loop :  0.23 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 298 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.032   0.001   PHE R 335 
 TYR   0.027   0.001   TYR R 191 
 ARG   0.010   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03748 (  499)
  hydrogen bonds       : angle       4.37908 ( 1440)
  SS BOND              : bond        0.00084 (    6)
  SS BOND              : angle       1.02518 (   12)
  covalent geometry    : bond        0.00226 ( 9120)
  covalent geometry    : angle       0.48483 (12379)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 ASP cc_start: 0.7362 (p0) cc_final: 0.6892 (p0)
REVERT: B  155 ASN cc_start: 0.7714 (t0) cc_final: 0.7466 (m-40)
REVERT: N   29 PHE cc_start: 0.7357 (t80) cc_final: 0.7080 (t80)
REVERT: R  214 ARG cc_start: 0.7381 (ptm160) cc_final: 0.7070 (pmm150)
REVERT: R  390 ARG cc_start: 0.7945 (ttp-110) cc_final: 0.7464 (ttm170)
  outliers start: 15
  outliers final: 9
  residues processed: 123
  average time/residue: 1.0899
  time to fit residues: 144.3442
Evaluate side-chains
  121 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  138 PHE
Chi-restraints excluded: chain R residue  409 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 51 optimal weight:    0.2980
   chunk 56 optimal weight:    7.9990
   chunk 110 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 25 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** 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 = 0.4178 r_free = 0.4178 target = 0.201259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.157839 restraints weight = 9045.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 1.95
r_work: 0.3515 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9126  Z= 0.175
  Angle     :  0.564  13.723  12391  Z= 0.295
  Chirality :  0.042   0.171   1387
  Planarity :  0.004   0.056   1575
  Dihedral  :  4.386  25.413   1244
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 13.07 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.26), residues: 1125
  helix:  2.67 (0.24), residues: 443
  sheet: -0.19 (0.33), residues: 216
  loop :  0.18 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.031   0.002   PHE R 335 
 TYR   0.027   0.002   TYR R 191 
 ARG   0.010   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04269 (  499)
  hydrogen bonds       : angle       4.59492 ( 1440)
  SS BOND              : bond        0.00163 (    6)
  SS BOND              : angle       1.69566 (   12)
  covalent geometry    : bond        0.00404 ( 9120)
  covalent geometry    : angle       0.56199 (12379)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7524 (mtt90)
REVERT: A  240 ASP cc_start: 0.7405 (p0) cc_final: 0.6956 (p0)
REVERT: A  370 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7145 (tt0)
REVERT: B  134 ARG cc_start: 0.6852 (ptm160) cc_final: 0.6229 (ptm160)
REVERT: B  155 ASN cc_start: 0.7991 (t0) cc_final: 0.7695 (m-40)
REVERT: B  173 THR cc_start: 0.8316 (p) cc_final: 0.8112 (p)
REVERT: R  214 ARG cc_start: 0.7379 (ptm160) cc_final: 0.6843 (pmm150)
REVERT: R  390 ARG cc_start: 0.7984 (ttp-110) cc_final: 0.7446 (ttm170)
REVERT: R  391 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7451 (mt-10)
  outliers start: 23
  outliers final: 10
  residues processed: 127
  average time/residue: 1.0871
  time to fit residues: 149.5050
Evaluate side-chains
  120 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  138 PHE
Chi-restraints excluded: chain R residue  409 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 39 optimal weight:    0.0370
   chunk 36 optimal weight:    0.8980
   chunk 104 optimal weight:    0.0050
   chunk 106 optimal weight:    2.9990
   chunk 92 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 95 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.4472

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.204760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.161583 restraints weight = 9071.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3761 rms_B_bonded: 1.86
r_work: 0.3578 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3438 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9126  Z= 0.108
  Angle     :  0.497  11.096  12391  Z= 0.263
  Chirality :  0.040   0.163   1387
  Planarity :  0.004   0.054   1575
  Dihedral  :  4.151  26.495   1244
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.38 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.26), residues: 1125
  helix:  2.86 (0.24), residues: 443
  sheet: -0.12 (0.32), residues: 216
  loop :  0.17 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 298 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.031   0.001   PHE R 335 
 TYR   0.024   0.001   TYR R 191 
 ARG   0.012   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03738 (  499)
  hydrogen bonds       : angle       4.38696 ( 1440)
  SS BOND              : bond        0.00148 (    6)
  SS BOND              : angle       1.00846 (   12)
  covalent geometry    : bond        0.00229 ( 9120)
  covalent geometry    : angle       0.49593 (12379)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7444 (mtt90)
REVERT: A  240 ASP cc_start: 0.7422 (p0) cc_final: 0.6937 (p0)
REVERT: A  370 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7161 (tt0)
REVERT: B  134 ARG cc_start: 0.6808 (ptm160) cc_final: 0.6202 (ptm160)
REVERT: B  155 ASN cc_start: 0.7839 (t0) cc_final: 0.7572 (m-40)
REVERT: N   29 PHE cc_start: 0.7210 (t80) cc_final: 0.6823 (t80)
REVERT: R  189 MET cc_start: 0.7688 (tmm) cc_final: 0.7436 (tmt)
REVERT: R  390 ARG cc_start: 0.7973 (ttp-110) cc_final: 0.7477 (ttm170)
  outliers start: 19
  outliers final: 11
  residues processed: 132
  average time/residue: 1.1227
  time to fit residues: 159.4969
Evaluate side-chains
  125 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  138 PHE
Chi-restraints excluded: chain R residue  409 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 95 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0870
   chunk 36 optimal weight:    0.0970
   chunk 45 optimal weight:    3.9990
   chunk 80 optimal weight:   50.0000
   overall best weight:    0.4956

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
** B 259 GLN ** 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 = 0.4215 r_free = 0.4215 target = 0.205235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.162466 restraints weight = 9121.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 1.90
r_work: 0.3579 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3445 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9126  Z= 0.112
  Angle     :  0.501  10.638  12391  Z= 0.266
  Chirality :  0.040   0.169   1387
  Planarity :  0.004   0.055   1575
  Dihedral  :  4.070  24.743   1244
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 15.47 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.26), residues: 1125
  helix:  2.89 (0.24), residues: 443
  sheet: -0.17 (0.32), residues: 218
  loop :  0.22 (0.31), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 211 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.012   0.001   PHE R 335 
 TYR   0.025   0.001   TYR N  60 
 ARG   0.013   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03704 (  499)
  hydrogen bonds       : angle       4.35637 ( 1440)
  SS BOND              : bond        0.00130 (    6)
  SS BOND              : angle       1.25731 (   12)
  covalent geometry    : bond        0.00242 ( 9120)
  covalent geometry    : angle       0.49931 (12379)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LYS cc_start: 0.8461 (ttpp) cc_final: 0.7999 (tttt)
REVERT: A  240 ASP cc_start: 0.7422 (p0) cc_final: 0.6945 (p0)
REVERT: A  370 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7176 (tt0)
REVERT: B  134 ARG cc_start: 0.6749 (ptm160) cc_final: 0.6186 (ptm160)
REVERT: B  155 ASN cc_start: 0.7842 (t0) cc_final: 0.7561 (m-40)
REVERT: N   29 PHE cc_start: 0.7268 (t80) cc_final: 0.6867 (t80)
REVERT: R  189 MET cc_start: 0.7617 (tmm) cc_final: 0.7413 (tmt)
REVERT: R  214 ARG cc_start: 0.7345 (ptm160) cc_final: 0.6885 (pmm150)
REVERT: R  390 ARG cc_start: 0.8010 (ttp-110) cc_final: 0.7503 (ttm170)
  outliers start: 13
  outliers final: 12
  residues processed: 121
  average time/residue: 1.0854
  time to fit residues: 141.6955
Evaluate side-chains
  122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  223 ASP
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  138 PHE
Chi-restraints excluded: chain R residue  409 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 101 optimal weight:    0.6980
   chunk 111 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 9 optimal weight:    0.3980
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.203585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.160661 restraints weight = 9057.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 1.76
r_work: 0.3568 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3430 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9126  Z= 0.135
  Angle     :  0.528  11.573  12391  Z= 0.278
  Chirality :  0.041   0.171   1387
  Planarity :  0.004   0.062   1575
  Dihedral  :  4.160  24.163   1244
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 14.71 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.26), residues: 1125
  helix:  2.82 (0.24), residues: 443
  sheet: -0.24 (0.31), residues: 231
  loop :  0.27 (0.31), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.026   0.002   TYR R 191 
 ARG   0.014   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03864 (  499)
  hydrogen bonds       : angle       4.39338 ( 1440)
  SS BOND              : bond        0.00174 (    6)
  SS BOND              : angle       1.61951 (   12)
  covalent geometry    : bond        0.00305 ( 9120)
  covalent geometry    : angle       0.52549 (12379)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LYS cc_start: 0.8467 (ttpp) cc_final: 0.7988 (tttt)
REVERT: A  240 ASP cc_start: 0.7361 (p0) cc_final: 0.6955 (p0)
REVERT: B  134 ARG cc_start: 0.6810 (ptm160) cc_final: 0.6208 (ptm160)
REVERT: B  155 ASN cc_start: 0.7888 (t0) cc_final: 0.7605 (m-40)
REVERT: N   29 PHE cc_start: 0.7298 (t80) cc_final: 0.6965 (t80)
REVERT: R  189 MET cc_start: 0.7641 (tmm) cc_final: 0.7411 (tmt)
REVERT: R  214 ARG cc_start: 0.7342 (ptm160) cc_final: 0.6883 (pmm150)
REVERT: R  390 ARG cc_start: 0.8015 (ttp-110) cc_final: 0.7500 (ttm170)
  outliers start: 17
  outliers final: 11
  residues processed: 124
  average time/residue: 1.0942
  time to fit residues: 146.1615
Evaluate side-chains
  123 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  138 PHE
Chi-restraints excluded: chain R residue  409 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 100 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 62 optimal weight:    0.0070
   chunk 35 optimal weight:    0.0770
   chunk 64 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.4956

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.205353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.162709 restraints weight = 9045.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 1.74
r_work: 0.3593 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3459 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9126  Z= 0.112
  Angle     :  0.508  10.482  12391  Z= 0.269
  Chirality :  0.040   0.168   1387
  Planarity :  0.004   0.063   1575
  Dihedral  :  4.058  23.751   1244
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 15.47 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.26), residues: 1125
  helix:  2.91 (0.24), residues: 443
  sheet: -0.20 (0.31), residues: 231
  loop :  0.27 (0.31), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.025   0.001   TYR R 191 
 ARG   0.015   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03672 (  499)
  hydrogen bonds       : angle       4.33091 ( 1440)
  SS BOND              : bond        0.00171 (    6)
  SS BOND              : angle       1.32965 (   12)
  covalent geometry    : bond        0.00242 ( 9120)
  covalent geometry    : angle       0.50628 (12379)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LYS cc_start: 0.8481 (ttpp) cc_final: 0.8035 (tttt)
REVERT: A  240 ASP cc_start: 0.7373 (p0) cc_final: 0.6925 (p0)
REVERT: B  134 ARG cc_start: 0.6769 (ptm160) cc_final: 0.6205 (ptm160)
REVERT: B  155 ASN cc_start: 0.7864 (t0) cc_final: 0.7577 (m-40)
REVERT: N   29 PHE cc_start: 0.7318 (t80) cc_final: 0.6984 (t80)
REVERT: R  214 ARG cc_start: 0.7334 (ptm160) cc_final: 0.6904 (pmm150)
REVERT: R  390 ARG cc_start: 0.8001 (ttp-110) cc_final: 0.7528 (ttm170)
  outliers start: 12
  outliers final: 11
  residues processed: 120
  average time/residue: 1.0841
  time to fit residues: 139.8299
Evaluate side-chains
  122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  138 PHE
Chi-restraints excluded: chain R residue  409 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 55 optimal weight:    6.9990
   chunk 84 optimal weight:   30.0000
   chunk 58 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 3 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 99 optimal weight:    4.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 357 HIS
** B 259 GLN ** 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 = 0.4170 r_free = 0.4170 target = 0.201698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.160035 restraints weight = 8983.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 1.63
r_work: 0.3514 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3370 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.1712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9126  Z= 0.139
  Angle     :  0.536  11.554  12391  Z= 0.282
  Chirality :  0.041   0.190   1387
  Planarity :  0.004   0.059   1575
  Dihedral  :  4.183  23.616   1244
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 15.25 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.26), residues: 1125
  helix:  2.83 (0.24), residues: 442
  sheet: -0.24 (0.31), residues: 231
  loop :  0.25 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B  62 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.026   0.002   TYR N  60 
 ARG   0.014   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03880 (  499)
  hydrogen bonds       : angle       4.40694 ( 1440)
  SS BOND              : bond        0.00153 (    6)
  SS BOND              : angle       1.59698 (   12)
  covalent geometry    : bond        0.00316 ( 9120)
  covalent geometry    : angle       0.53352 (12379)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6425.95 seconds
wall clock time: 111 minutes 30.22 seconds (6690.22 seconds total)