Starting phenix.real_space_refine
on Sat Jul 26 20:47:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wzg_21972/07_2025/6wzg_21972.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wzg_21972/07_2025/6wzg_21972.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wzg_21972/07_2025/6wzg_21972.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wzg_21972/07_2025/6wzg_21972.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wzg_21972/07_2025/6wzg_21972.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wzg_21972/07_2025/6wzg_21972.cif"
  }
  resolution = 2.3
  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=   0.004
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      57      5.16       5
     C    5643      2.51       5
     N    1592      2.21       5
     O    1647      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8939
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "P"
      Number of atoms: 213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 213
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "R"
      Number of atoms: 2781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 379, 2781
          Classifications: {'peptide': 379}
          Incomplete info: {'truncation_to_alanine': 86}
          Link IDs: {'PTRANS': 11, 'TRANS': 367}
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 311
          Unresolved non-hydrogen angles: 404
          Unresolved non-hydrogen dihedrals: 259
          Unresolved non-hydrogen chiralities: 24
          Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 194
    Chain: "A"
      Number of atoms: 1960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1960
          Classifications: {'peptide': 240}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 6, 'TRANS': 233}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
  Time building chain proxies: 5.60, per 1000 atoms: 0.63
  Number of scatterers: 8939
  At special positions: 0
  Unit cell: (94.62, 100.43, 161.02, 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      57     16.00
     O    1647      8.00
     N    1592      7.00
     C    5643      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  45 " - pdb=" SG  CYS R  75 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  66 " - pdb=" SG  CYS R 107 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  89 " - pdb=" SG  CYS R 123 " distance=2.05
    Simple disulfide: pdb=" SG  CYS R 215 " - pdb=" SG  CYS R 285 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.04

  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: 2.23
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2182

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 10 sheets defined
      42.2% alpha, 17.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'P' and resid 1 through 27
      removed outlier: 3.518A  pdb=" N   LEU P  22 " --> pdb=" O   ARG P  18 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 31 through 48
    Processing helix  chain 'R' and resid 90 through 95
      removed outlier: 3.934A  pdb=" N   MET R  95 " --> pdb=" O   ARG R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 132 through 167
      removed outlier: 3.587A  pdb=" N   ILE R 163 " --> pdb=" O   VAL R 159 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 201
      removed outlier: 3.601A  pdb=" N   SER R 201 " --> pdb=" O   ALA R 197 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 211 through 246
    Processing helix  chain 'R' and resid 254 through 280
      Proline residue:  R 266  - end of helix
    Processing helix  chain 'R' and resid 291 through 326
      removed outlier: 3.750A  pdb=" N   ILE R 297 " --> pdb=" O   SER R 293 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 332 through 352
      Proline residue:  R 349  - end of helix
    Processing helix  chain 'R' and resid 354 through 359
      removed outlier: 4.474A  pdb=" N   PHE R 358 " --> pdb=" O   HIS R 354 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 362 through 364
      No H-bonds generated for 'chain 'R' and resid 362 through 364'
    Processing helix  chain 'R' and resid 365 through 375
    Processing helix  chain 'R' and resid 376 through 378
      No H-bonds generated for 'chain 'R' and resid 376 through 378'
    Processing helix  chain 'R' and resid 379 through 389
    Processing helix  chain 'R' and resid 392 through 408
    Processing helix  chain 'A' and resid 13 through 40
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.611A  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 304
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.700A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 24
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 3.744A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 7.002A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.880A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.532A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 5.898A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.972A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.729A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.874A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.329A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.600A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.940A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.972A  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: 6.611A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.117A  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: 6.120A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.653A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.234A  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: 6.573A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    476 hydrogen bonds defined for protein.
    1347 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: 2.85

  Time building geometry restraints manager: 2.66 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1473
        1.29 -     1.43: 2428
        1.43 -     1.56: 5133
        1.56 -     1.69: 0
        1.69 -     1.82: 78
  Bond restraints: 9112
  Sorted by residual:
  bond pdb=" C   HIS R 178 "
       pdb=" O   HIS R 178 "
    ideal  model  delta    sigma   weight residual
    1.237  1.164  0.072 1.17e-02 7.31e+03 3.82e+01
  bond pdb=" N   ILE B  93 "
       pdb=" CA  ILE B  93 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.035 7.60e-03 1.73e+04 2.09e+01
  bond pdb=" C   ILE R 297 "
       pdb=" O   ILE R 297 "
    ideal  model  delta    sigma   weight residual
    1.237  1.181  0.056 1.23e-02 6.61e+03 2.07e+01
  bond pdb=" C   ARG R 174 "
       pdb=" O   ARG R 174 "
    ideal  model  delta    sigma   weight residual
    1.237  1.188  0.049 1.19e-02 7.06e+03 1.67e+01
  bond pdb=" C   ILE R 298 "
       pdb=" O   ILE R 298 "
    ideal  model  delta    sigma   weight residual
    1.231  1.187  0.044 1.07e-02 8.73e+03 1.66e+01
  ... (remaining 9107 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 10072
        2.10 -     4.21: 2115
        4.21 -     6.31: 125
        6.31 -     8.41: 23
        8.41 -    10.52: 4
  Bond angle restraints: 12339
  Sorted by residual:
  angle pdb=" N   SER R  74 "
        pdb=" CA  SER R  74 "
        pdb=" C   SER R  74 "
      ideal   model   delta    sigma   weight residual
     111.07  102.97    8.10 1.07e+00 8.73e-01 5.73e+01
  angle pdb=" N   ASP R 209 "
        pdb=" CA  ASP R 209 "
        pdb=" C   ASP R 209 "
      ideal   model   delta    sigma   weight residual
     114.39  103.87   10.52 1.45e+00 4.76e-01 5.26e+01
  angle pdb=" C   THR R 326 "
        pdb=" CA  THR R 326 "
        pdb=" CB  THR R 326 "
      ideal   model   delta    sigma   weight residual
     111.74  101.83    9.91 1.37e+00 5.33e-01 5.23e+01
  angle pdb=" N   ASP B 333 "
        pdb=" CA  ASP B 333 "
        pdb=" C   ASP B 333 "
      ideal   model   delta    sigma   weight residual
     113.02  105.22    7.80 1.20e+00 6.94e-01 4.23e+01
  angle pdb=" N   ASP B 163 "
        pdb=" CA  ASP B 163 "
        pdb=" C   ASP B 163 "
      ideal   model   delta    sigma   weight residual
     113.02  105.42    7.60 1.20e+00 6.94e-01 4.01e+01
  ... (remaining 12334 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 4919
       17.92 -    35.84: 406
       35.84 -    53.76: 70
       53.76 -    71.67: 22
       71.67 -    89.59: 7
  Dihedral angle restraints: 5424
    sinusoidal: 2048
      harmonic: 3376
  Sorted by residual:
  dihedral pdb=" CB  CYS R  89 "
           pdb=" SG  CYS R  89 "
           pdb=" SG  CYS R 123 "
           pdb=" CB  CYS R 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  169.26  -76.26     1      1.00e+01 1.00e-02 7.32e+01
  dihedral pdb=" C   TYR R 146 "
           pdb=" N   TYR R 146 "
           pdb=" CA  TYR R 146 "
           pdb=" CB  TYR R 146 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.79   16.19     0      2.50e+00 1.60e-01 4.19e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   40.19   52.81     1      1.00e+01 1.00e-02 3.80e+01
  ... (remaining 5421 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.108: 870
       0.108 -    0.216: 435
       0.216 -    0.324: 65
       0.324 -    0.432: 13
       0.432 -    0.540: 4
  Chirality restraints: 1387
  Sorted by residual:
  chirality pdb=" CA  TYR R 146 "
            pdb=" N   TYR R 146 "
            pdb=" C   TYR R 146 "
            pdb=" CB  TYR R 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.28e+00
  chirality pdb=" CA  ASN R 175 "
            pdb=" N   ASN R 175 "
            pdb=" C   ASN R 175 "
            pdb=" CB  ASN R 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.52 2.00e-01 2.50e+01 6.79e+00
  chirality pdb=" CA  TRP A 234 "
            pdb=" N   TRP A 234 "
            pdb=" C   TRP A 234 "
            pdb=" CB  TRP A 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.15e+00
  ... (remaining 1384 not shown)

  Planarity restraints: 1589
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 205 "    0.017 2.00e-02 2.50e+03   3.43e-02 1.18e+01
        pdb=" C   SER A 205 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   SER A 205 "    0.022 2.00e-02 2.50e+03
        pdb=" N   GLY A 206 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 277 "   -0.016 2.00e-02 2.50e+03   3.16e-02 9.98e+00
        pdb=" C   TRP A 277 "    0.055 2.00e-02 2.50e+03
        pdb=" O   TRP A 277 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ASN A 278 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 332 "   -0.015 2.00e-02 2.50e+03   2.93e-02 8.60e+00
        pdb=" C   TRP B 332 "    0.051 2.00e-02 2.50e+03
        pdb=" O   TRP B 332 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASP B 333 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1586 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1630
        2.80 -     3.32: 9004
        3.32 -     3.85: 14916
        3.85 -     4.37: 19498
        4.37 -     4.90: 30896
  Nonbonded interactions: 75944
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 205 "
            pdb=" O   ILE A 207 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" N   GLU R 251 "
            pdb=" OE1 GLU R 251 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" N   VAL R  85 "
            pdb=" O   LEU R 103 "
     model   vdw
     2.377 3.120
  nonbonded pdb=" NE2 GLN B 220 "
            pdb=" OD1 ASP B 258 "
     model   vdw
     2.392 3.120
  nonbonded pdb=" O   GLU B  12 "
            pdb=" ND2 ASN B  16 "
     model   vdw
     2.394 3.120
  ... (remaining 75939 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:             1.450
  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:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.800
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6793
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      :  0.012   0.072   9118  Z= 0.893
  Angle     :  1.563  10.517  12351  Z= 1.199
  Chirality :  0.121   0.540   1387
  Planarity :  0.007   0.034   1589
  Dihedral  : 14.021  89.594   3224
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  9.35 %
    Favored  : 89.00 %
  Cbeta Deviations :  1.65 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.24), residues: 1151
  helix:  1.41 (0.24), residues: 453
  sheet:  0.76 (0.34), residues: 208
  loop : -0.32 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP R 232 
 HIS   0.007   0.002   HIS A  41 
 PHE   0.022   0.002   PHE G  61 
 TYR   0.018   0.002   TYR R 146 
 ARG   0.005   0.001   ARG A 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20309 (  476)
  hydrogen bonds       : angle       6.92264 ( 1347)
  SS BOND              : bond        0.00911 (    6)
  SS BOND              : angle       2.81721 (   12)
  covalent geometry    : bond        0.01172 ( 9112)
  covalent geometry    : angle       1.56112 (12339)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 166
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
REVERT: R  321 MET cc_start: 0.6158 (tpt) cc_final: 0.5830 (mmm)
REVERT: A   17 LYS cc_start: 0.6608 (pttp) cc_final: 0.6228 (tppt)
REVERT: A  357 HIS cc_start: 0.8689 (OUTLIER) cc_final: 0.8263 (p90)
REVERT: B  124 TYR cc_start: 0.8512 (m-80) cc_final: 0.8310 (m-80)
  outliers start: 15
  outliers final: 3
  residues processed: 178
  average time/residue: 1.5124
  time to fit residues: 283.7675
Evaluate side-chains
  129 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 125
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  123 CYS
Chi-restraints excluded: chain R residue  146 TYR
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue  292 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 102 optimal weight:    0.8980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
R 132 ASN
R 178 HIS
R 180 HIS
R 229 ASN
R 327 GLN
R 396 GLN
R 404 GLN
A 220 HIS
A 362 HIS
B  35 ASN
B 259 GLN
B 340 ASN
N   1 GLN
N   3 GLN
N 120 GLN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.177848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.124108 restraints weight = 8144.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 1.64
r_work: 0.3177 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9118  Z= 0.150
  Angle     :  0.597   7.059  12351  Z= 0.333
  Chirality :  0.043   0.149   1387
  Planarity :  0.004   0.036   1589
  Dihedral  :  5.100  53.413   1273
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 13.97 %
    Favored  : 83.61 %
  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:  1.50 (0.24), residues: 1151
  helix:  2.28 (0.23), residues: 462
  sheet:  0.75 (0.33), residues: 217
  loop : -0.14 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  82 
 HIS   0.005   0.001   HIS R 407 
 PHE   0.021   0.002   PHE G  61 
 TYR   0.027   0.002   TYR R 146 
 ARG   0.004   0.001   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06052 (  476)
  hydrogen bonds       : angle       4.87364 ( 1347)
  SS BOND              : bond        0.00399 (    6)
  SS BOND              : angle       1.59937 (   12)
  covalent geometry    : bond        0.00303 ( 9112)
  covalent geometry    : angle       0.59522 (12339)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
REVERT: R  140 LEU cc_start: 0.7354 (mt) cc_final: 0.7081 (mm)
REVERT: R  169 ARG cc_start: 0.6320 (ttt180) cc_final: 0.5953 (ttm-80)
REVERT: R  297 ILE cc_start: 0.7620 (mt) cc_final: 0.7280 (mp)
REVERT: A   24 LYS cc_start: 0.7302 (mmtt) cc_final: 0.7070 (pptt)
REVERT: A   53 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7971 (pttp)
REVERT: A   59 GLN cc_start: 0.7042 (mm-40) cc_final: 0.6706 (mm110)
REVERT: A  240 ASP cc_start: 0.7740 (p0) cc_final: 0.7432 (p0)
REVERT: B    9 GLN cc_start: 0.6311 (OUTLIER) cc_final: 0.6031 (tm-30)
  outliers start: 22
  outliers final: 8
  residues processed: 159
  average time/residue: 1.5013
  time to fit residues: 252.4769
Evaluate side-chains
  139 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   45 CYS
Chi-restraints excluded: chain R residue  123 CYS
Chi-restraints excluded: chain R residue  206 THR
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 68 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 85 optimal weight:    3.9990
   chunk 89 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 94 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
R 354 HIS
B  35 ASN
B 259 GLN
N 120 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.176394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.119235 restraints weight = 8231.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.42
r_work: 0.3179 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9118  Z= 0.134
  Angle     :  0.535   5.928  12351  Z= 0.302
  Chirality :  0.042   0.144   1387
  Planarity :  0.004   0.036   1589
  Dihedral  :  4.911  59.578   1267
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 13.86 %
    Favored  : 83.39 %
  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:  1.70 (0.25), residues: 1151
  helix:  2.65 (0.23), residues: 462
  sheet:  0.61 (0.33), residues: 216
  loop : -0.15 (0.29), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 234 
 HIS   0.004   0.001   HIS R 241 
 PHE   0.018   0.002   PHE R 313 
 TYR   0.026   0.002   TYR R 146 
 ARG   0.005   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05563 (  476)
  hydrogen bonds       : angle       4.66192 ( 1347)
  SS BOND              : bond        0.00319 (    6)
  SS BOND              : angle       1.34931 (   12)
  covalent geometry    : bond        0.00271 ( 9112)
  covalent geometry    : angle       0.53320 (12339)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 1.103 
Fit side-chains
REVERT: R  135 ARG cc_start: 0.5813 (ttt90) cc_final: 0.5204 (ttm-80)
REVERT: R  140 LEU cc_start: 0.7454 (mt) cc_final: 0.7191 (mm)
REVERT: R  169 ARG cc_start: 0.6386 (ttt180) cc_final: 0.6016 (ttm-80)
REVERT: R  297 ILE cc_start: 0.7611 (mt) cc_final: 0.7277 (mp)
REVERT: A   24 LYS cc_start: 0.7312 (mmtt) cc_final: 0.7079 (pptt)
REVERT: A   31 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7249 (tp40)
REVERT: A   53 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7972 (pttp)
REVERT: A   59 GLN cc_start: 0.7067 (mm-40) cc_final: 0.6748 (mm110)
REVERT: A  240 ASP cc_start: 0.7779 (p0) cc_final: 0.7501 (p0)
REVERT: B    9 GLN cc_start: 0.6319 (OUTLIER) cc_final: 0.6009 (tm-30)
REVERT: B  214 ARG cc_start: 0.7579 (mmt180) cc_final: 0.7110 (mtt180)
REVERT: B  261 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8506 (mp)
  outliers start: 25
  outliers final: 8
  residues processed: 145
  average time/residue: 1.8767
  time to fit residues: 287.2581
Evaluate side-chains
  140 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  205 VAL
Chi-restraints excluded: chain R residue  206 THR
Chi-restraints excluded: chain R residue  339 ARG
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 80 optimal weight:    0.0870
   chunk 68 optimal weight:    0.0970
   chunk 28 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 104 optimal weight:    4.9990
   chunk 95 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 106 optimal weight:    0.2980
   overall best weight:    0.4556

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

Flipped N/Q/H residues before XYZ refinement:
R 136 HIS
A  54 ASN
A 387 HIS
B  35 ASN
B 268 ASN
N 120 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.178257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.124738 restraints weight = 8224.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 1.69
r_work: 0.3181 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9118  Z= 0.108
  Angle     :  0.478   5.343  12351  Z= 0.269
  Chirality :  0.041   0.141   1387
  Planarity :  0.003   0.038   1589
  Dihedral  :  4.338  18.059   1266
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.63 %
    Favored  : 82.95 %
  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:  1.85 (0.25), residues: 1151
  helix:  3.01 (0.23), residues: 450
  sheet:  0.43 (0.33), residues: 220
  loop : -0.10 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 234 
 HIS   0.003   0.001   HIS R 407 
 PHE   0.016   0.001   PHE R 313 
 TYR   0.023   0.001   TYR R 146 
 ARG   0.003   0.000   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04745 (  476)
  hydrogen bonds       : angle       4.43087 ( 1347)
  SS BOND              : bond        0.00279 (    6)
  SS BOND              : angle       1.01687 (   12)
  covalent geometry    : bond        0.00208 ( 9112)
  covalent geometry    : angle       0.47683 (12339)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.973 
Fit side-chains
REVERT: R  140 LEU cc_start: 0.7399 (mt) cc_final: 0.7152 (mm)
REVERT: R  169 ARG cc_start: 0.6417 (ttt180) cc_final: 0.6030 (ttm-80)
REVERT: R  221 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7270 (tp)
REVERT: R  297 ILE cc_start: 0.7602 (mt) cc_final: 0.7267 (mp)
REVERT: R  339 ARG cc_start: 0.6274 (OUTLIER) cc_final: 0.6069 (tpm-80)
REVERT: R  366 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6632 (tmt)
REVERT: R  369 GLN cc_start: 0.7142 (tm-30) cc_final: 0.6447 (tm-30)
REVERT: A   24 LYS cc_start: 0.7288 (mmtt) cc_final: 0.6979 (pptt)
REVERT: A   53 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7981 (pttp)
REVERT: A  240 ASP cc_start: 0.7764 (p0) cc_final: 0.7503 (p0)
REVERT: B    9 GLN cc_start: 0.6334 (OUTLIER) cc_final: 0.6057 (tm-30)
REVERT: B  214 ARG cc_start: 0.7703 (mmt180) cc_final: 0.7172 (mtt180)
REVERT: B  261 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8533 (mp)
  outliers start: 22
  outliers final: 6
  residues processed: 143
  average time/residue: 1.4821
  time to fit residues: 223.6836
Evaluate side-chains
  141 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    2 SER
Chi-restraints excluded: chain R residue  205 VAL
Chi-restraints excluded: chain R residue  221 LEU
Chi-restraints excluded: chain R residue  339 ARG
Chi-restraints excluded: chain R residue  366 MET
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0010
   chunk 75 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 49 optimal weight:   20.0000
   chunk 77 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 57 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    1.9992

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

Flipped N/Q/H residues before XYZ refinement:
R 327 GLN
B  35 ASN
B 268 ASN
N 120 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.173092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.115308 restraints weight = 8052.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 1.41
r_work: 0.3127 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077   9118  Z= 0.208
  Angle     :  0.626   6.407  12351  Z= 0.351
  Chirality :  0.046   0.151   1387
  Planarity :  0.005   0.039   1589
  Dihedral  :  5.005  25.298   1266
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 14.63 %
    Favored  : 82.73 %
  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:  1.35 (0.24), residues: 1151
  helix:  2.43 (0.23), residues: 456
  sheet:  0.25 (0.33), residues: 214
  loop : -0.27 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 234 
 HIS   0.007   0.002   HIS A  41 
 PHE   0.020   0.002   PHE R 313 
 TYR   0.025   0.002   TYR R 146 
 ARG   0.005   0.001   ARG P  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06352 (  476)
  hydrogen bonds       : angle       4.89775 ( 1347)
  SS BOND              : bond        0.00621 (    6)
  SS BOND              : angle       1.14680 (   12)
  covalent geometry    : bond        0.00453 ( 9112)
  covalent geometry    : angle       0.62563 (12339)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 1.047 
Fit side-chains
REVERT: R  135 ARG cc_start: 0.5734 (ttt90) cc_final: 0.5015 (ttm-80)
REVERT: R  140 LEU cc_start: 0.7512 (mt) cc_final: 0.7243 (mm)
REVERT: R  169 ARG cc_start: 0.6512 (ttt180) cc_final: 0.6128 (ttm-80)
REVERT: R  369 GLN cc_start: 0.7261 (tm-30) cc_final: 0.6472 (tm-30)
REVERT: A   24 LYS cc_start: 0.7322 (mmpt) cc_final: 0.7106 (pptt)
REVERT: A   31 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7240 (tp40)
REVERT: A   53 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8049 (ptpp)
REVERT: A  240 ASP cc_start: 0.7933 (p0) cc_final: 0.7711 (p0)
REVERT: A  314 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7237 (mp0)
REVERT: B    9 GLN cc_start: 0.6489 (OUTLIER) cc_final: 0.6130 (tm-30)
REVERT: B  195 ASP cc_start: 0.7371 (p0) cc_final: 0.7060 (p0)
REVERT: B  214 ARG cc_start: 0.7715 (mmt180) cc_final: 0.7226 (mtt180)
REVERT: B  261 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8551 (mp)
REVERT: B  325 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.7979 (tpp)
  outliers start: 24
  outliers final: 9
  residues processed: 139
  average time/residue: 1.5603
  time to fit residues: 228.3946
Evaluate side-chains
  138 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    2 SER
Chi-restraints excluded: chain R residue  205 VAL
Chi-restraints excluded: chain R residue  206 THR
Chi-restraints excluded: chain R residue  339 ARG
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 10 optimal weight:   40.0000
   chunk 44 optimal weight:    6.9990
   chunk 82 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 98 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 106 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
B  35 ASN
B 340 ASN
N 120 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.171859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.113865 restraints weight = 8008.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 1.40
r_work: 0.3102 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.094   9118  Z= 0.265
  Angle     :  0.695   7.008  12351  Z= 0.388
  Chirality :  0.049   0.170   1387
  Planarity :  0.006   0.047   1589
  Dihedral  :  5.359  27.748   1266
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 14.30 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.23), residues: 1151
  helix:  1.81 (0.23), residues: 456
  sheet:  0.24 (0.34), residues: 209
  loop : -0.48 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP A 234 
 HIS   0.009   0.002   HIS R 241 
 PHE   0.021   0.003   PHE R 313 
 TYR   0.027   0.003   TYR A 339 
 ARG   0.006   0.001   ARG P  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06988 (  476)
  hydrogen bonds       : angle       5.10714 ( 1347)
  SS BOND              : bond        0.00876 (    6)
  SS BOND              : angle       1.12787 (   12)
  covalent geometry    : bond        0.00589 ( 9112)
  covalent geometry    : angle       0.69479 (12339)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 127
  time to evaluate  : 0.967 
Fit side-chains
REVERT: R  140 LEU cc_start: 0.7617 (mt) cc_final: 0.7326 (mm)
REVERT: R  169 ARG cc_start: 0.6606 (ttt180) cc_final: 0.6165 (ttm-80)
REVERT: R  369 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6464 (tm-30)
REVERT: R  392 ASN cc_start: 0.7316 (t0) cc_final: 0.7095 (t0)
REVERT: A   24 LYS cc_start: 0.7360 (mmtt) cc_final: 0.7130 (ptmm)
REVERT: A   53 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8063 (ptpp)
REVERT: A  314 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7329 (mp0)
REVERT: B   38 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7986 (m-30)
REVERT: B  261 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8568 (mp)
REVERT: B  266 HIS cc_start: 0.7884 (t-90) cc_final: 0.7665 (t70)
REVERT: B  325 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8029 (tpp)
  outliers start: 27
  outliers final: 15
  residues processed: 144
  average time/residue: 1.5661
  time to fit residues: 237.2744
Evaluate side-chains
  143 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    2 SER
Chi-restraints excluded: chain R residue  205 VAL
Chi-restraints excluded: chain R residue  206 THR
Chi-restraints excluded: chain R residue  339 ARG
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 107 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 100 optimal weight:    0.5980
   chunk 108 optimal weight:    0.2980
   chunk 106 optimal weight:    0.9990
   chunk 5 optimal weight:   50.0000
   chunk 61 optimal weight:    0.9980
   chunk 91 optimal weight:    0.5980
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN
B 268 ASN
N 120 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.175828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.119009 restraints weight = 8304.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 1.41
r_work: 0.3178 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   9118  Z= 0.121
  Angle     :  0.506   5.624  12351  Z= 0.288
  Chirality :  0.041   0.145   1387
  Planarity :  0.004   0.041   1589
  Dihedral  :  4.677  22.321   1266
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 15.29 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.24), residues: 1151
  helix:  2.58 (0.24), residues: 450
  sheet:  0.33 (0.34), residues: 209
  loop : -0.37 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 234 
 HIS   0.003   0.001   HIS R 241 
 PHE   0.017   0.002   PHE B 253 
 TYR   0.024   0.001   TYR R 146 
 ARG   0.008   0.000   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05138 (  476)
  hydrogen bonds       : angle       4.59192 ( 1347)
  SS BOND              : bond        0.00240 (    6)
  SS BOND              : angle       0.90410 (   12)
  covalent geometry    : bond        0.00244 ( 9112)
  covalent geometry    : angle       0.50530 (12339)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 1.070 
Fit side-chains
REVERT: R  140 LEU cc_start: 0.7446 (mt) cc_final: 0.7200 (mm)
REVERT: R  169 ARG cc_start: 0.6487 (ttt180) cc_final: 0.6113 (ttm-80)
REVERT: R  221 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7272 (tp)
REVERT: R  325 ARG cc_start: 0.6259 (OUTLIER) cc_final: 0.5716 (mpt-90)
REVERT: R  369 GLN cc_start: 0.7249 (tm-30) cc_final: 0.6647 (tm-30)
REVERT: A   59 GLN cc_start: 0.7116 (mm-40) cc_final: 0.5800 (pt0)
REVERT: B    9 GLN cc_start: 0.6517 (OUTLIER) cc_final: 0.6129 (tm-30)
REVERT: B  325 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7633 (tpp)
  outliers start: 19
  outliers final: 10
  residues processed: 137
  average time/residue: 1.6839
  time to fit residues: 242.6281
Evaluate side-chains
  137 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    2 SER
Chi-restraints excluded: chain R residue  205 VAL
Chi-restraints excluded: chain R residue  221 LEU
Chi-restraints excluded: chain R residue  325 ARG
Chi-restraints excluded: chain R residue  339 ARG
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 5 optimal weight:   30.0000
   chunk 105 optimal weight:    0.0970
   chunk 31 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 2 optimal weight:   30.0000
   chunk 94 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 3 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   overall best weight:    2.1784

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN
N 120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.172671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.114699 restraints weight = 8213.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 1.42
r_work: 0.3114 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080   9118  Z= 0.219
  Angle     :  0.633   6.666  12351  Z= 0.355
  Chirality :  0.046   0.153   1387
  Planarity :  0.005   0.046   1589
  Dihedral  :  5.125  27.400   1266
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.29 %
    Favored  : 82.29 %
  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:  1.07 (0.24), residues: 1151
  helix:  2.13 (0.23), residues: 456
  sheet:  0.27 (0.34), residues: 209
  loop : -0.43 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 234 
 HIS   0.008   0.002   HIS R 241 
 PHE   0.021   0.003   PHE R 313 
 TYR   0.026   0.002   TYR A 339 
 ARG   0.007   0.001   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06437 (  476)
  hydrogen bonds       : angle       4.93864 ( 1347)
  SS BOND              : bond        0.00659 (    6)
  SS BOND              : angle       0.95816 (   12)
  covalent geometry    : bond        0.00482 ( 9112)
  covalent geometry    : angle       0.63269 (12339)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
REVERT: R  140 LEU cc_start: 0.7536 (mt) cc_final: 0.7266 (mm)
REVERT: R  369 GLN cc_start: 0.7421 (tm-30) cc_final: 0.6633 (tm-30)
REVERT: R  392 ASN cc_start: 0.7247 (t0) cc_final: 0.6991 (t0)
REVERT: A   59 GLN cc_start: 0.7059 (mm-40) cc_final: 0.6724 (mm110)
REVERT: A  314 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7224 (mt-10)
REVERT: G   52 THR cc_start: 0.6304 (OUTLIER) cc_final: 0.6025 (p)
  outliers start: 22
  outliers final: 13
  residues processed: 134
  average time/residue: 1.6428
  time to fit residues: 231.1969
Evaluate side-chains
  134 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    2 SER
Chi-restraints excluded: chain R residue  107 CYS
Chi-restraints excluded: chain R residue  205 VAL
Chi-restraints excluded: chain R residue  221 LEU
Chi-restraints excluded: chain R residue  339 ARG
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 109 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 112 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN
N 120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.174614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.117383 restraints weight = 8164.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 1.41
r_work: 0.3154 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9118  Z= 0.136
  Angle     :  0.533   5.624  12351  Z= 0.301
  Chirality :  0.042   0.147   1387
  Planarity :  0.004   0.041   1589
  Dihedral  :  4.770  24.322   1266
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.84 %
    Favored  : 82.29 %
  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:  1.32 (0.24), residues: 1151
  helix:  2.51 (0.24), residues: 450
  sheet:  0.27 (0.34), residues: 211
  loop : -0.37 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 234 
 HIS   0.004   0.001   HIS R 241 
 PHE   0.018   0.002   PHE R 313 
 TYR   0.023   0.002   TYR R 146 
 ARG   0.007   0.000   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05375 (  476)
  hydrogen bonds       : angle       4.65685 ( 1347)
  SS BOND              : bond        0.00356 (    6)
  SS BOND              : angle       1.78014 (   12)
  covalent geometry    : bond        0.00283 ( 9112)
  covalent geometry    : angle       0.53073 (12339)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.974 
Fit side-chains
REVERT: R  140 LEU cc_start: 0.7434 (mt) cc_final: 0.7181 (mm)
REVERT: R  325 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5750 (mpt-90)
REVERT: R  369 GLN cc_start: 0.7302 (tm-30) cc_final: 0.6641 (tm-30)
REVERT: A  314 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7169 (mt-10)
REVERT: B    9 GLN cc_start: 0.6526 (OUTLIER) cc_final: 0.6138 (tm-30)
  outliers start: 17
  outliers final: 11
  residues processed: 129
  average time/residue: 1.6310
  time to fit residues: 221.1044
Evaluate side-chains
  132 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    2 SER
Chi-restraints excluded: chain R residue  205 VAL
Chi-restraints excluded: chain R residue  325 ARG
Chi-restraints excluded: chain R residue  339 ARG
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 94 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
R 327 GLN
B  35 ASN
N 120 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.175320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.123386 restraints weight = 8247.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 1.67
r_work: 0.3136 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   9118  Z= 0.121
  Angle     :  0.508   5.537  12351  Z= 0.286
  Chirality :  0.041   0.145   1387
  Planarity :  0.004   0.042   1589
  Dihedral  :  4.570  22.223   1266
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.95 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.45 (0.25), residues: 1151
  helix:  2.70 (0.24), residues: 450
  sheet:  0.21 (0.33), residues: 220
  loop : -0.35 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 234 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.017   0.002   PHE R 313 
 TYR   0.023   0.001   TYR R 146 
 ARG   0.007   0.000   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04999 (  476)
  hydrogen bonds       : angle       4.52636 ( 1347)
  SS BOND              : bond        0.00300 (    6)
  SS BOND              : angle       1.66432 (   12)
  covalent geometry    : bond        0.00245 ( 9112)
  covalent geometry    : angle       0.50605 (12339)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.968 
Fit side-chains
REVERT: R  140 LEU cc_start: 0.7424 (mt) cc_final: 0.7173 (mm)
REVERT: R  221 LEU cc_start: 0.7571 (tp) cc_final: 0.7363 (tp)
REVERT: R  325 ARG cc_start: 0.6260 (OUTLIER) cc_final: 0.5716 (mpt-90)
REVERT: R  369 GLN cc_start: 0.7234 (tm-30) cc_final: 0.6599 (tm-30)
REVERT: A   59 GLN cc_start: 0.7091 (mm-40) cc_final: 0.6767 (mm110)
REVERT: A  314 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7132 (mt-10)
REVERT: B    9 GLN cc_start: 0.6493 (OUTLIER) cc_final: 0.6117 (tm-30)
REVERT: B  175 GLN cc_start: 0.8538 (mm110) cc_final: 0.8335 (mm110)
  outliers start: 15
  outliers final: 9
  residues processed: 130
  average time/residue: 1.7184
  time to fit residues: 234.2685
Evaluate side-chains
  132 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    2 SER
Chi-restraints excluded: chain R residue  205 VAL
Chi-restraints excluded: chain R residue  325 ARG
Chi-restraints excluded: chain R residue  339 ARG
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 97 optimal weight:    0.6980
   chunk 106 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   chunk 108 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 76 optimal weight:    4.9990
   chunk 96 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 105 optimal weight:    0.6980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN
B 340 ASN
N 120 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.174375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.119605 restraints weight = 8196.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 1.71
r_work: 0.3120 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3005 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.3019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9118  Z= 0.143
  Angle     :  0.539   6.009  12351  Z= 0.303
  Chirality :  0.042   0.149   1387
  Planarity :  0.004   0.042   1589
  Dihedral  :  4.706  23.799   1266
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.51 %
    Favored  : 82.62 %
  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:  1.36 (0.24), residues: 1151
  helix:  2.63 (0.24), residues: 450
  sheet:  0.11 (0.33), residues: 214
  loop : -0.37 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 234 
 HIS   0.004   0.001   HIS R 241 
 PHE   0.018   0.002   PHE R 313 
 TYR   0.023   0.002   TYR R 146 
 ARG   0.008   0.001   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05355 (  476)
  hydrogen bonds       : angle       4.61573 ( 1347)
  SS BOND              : bond        0.00382 (    6)
  SS BOND              : angle       1.51612 (   12)
  covalent geometry    : bond        0.00302 ( 9112)
  covalent geometry    : angle       0.53709 (12339)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10821.88 seconds
wall clock time: 189 minutes 36.16 seconds (11376.16 seconds total)