Starting phenix.real_space_refine
on Thu Mar 13 11:06:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wzg_21972/03_2025/6wzg_21972.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wzg_21972/03_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_21972/03_2025/6wzg_21972.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wzg_21972/03_2025/6wzg_21972.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wzg_21972/03_2025/6wzg_21972.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wzg_21972/03_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.23, per 1000 atoms: 0.70
  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: 2.64
  Conformation dependent library (CDL) restraints added in 1.2 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: 0.93
  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: 2.38

  Time building geometry restraints manager: 3.08 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:             2.140
  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:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.190
  Find NCS groups from input model:        0.090
  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:             0.010
  Load rotamer database and sin/cos tables:11.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.640
-------------------------------------------------------------------------------
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   9112  Z= 0.796
  Angle     :  1.561  10.517  12339  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 

*********************** 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  : 1.032 
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: 1.5777
  time to fit residues: 295.8504
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  : 0.932 
-------------------------------------------------------------------------------
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   9112  Z= 0.200
  Angle     :  0.595   7.059  12339  Z= 0.332
  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 

*********************** 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  : 1.070 
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: 1.5908
  time to fit residues: 266.9495
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  : 0.947 
-------------------------------------------------------------------------------
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:    0.7980
   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:    0.8382

-------------------------------------------------------------------------------
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 = 0.176347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.119477 restraints weight = 8245.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 1.41
r_work: 0.3181 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9112  Z= 0.176
  Angle     :  0.531   5.894  12339  Z= 0.300
  Chirality :  0.042   0.144   1387
  Planarity :  0.004   0.036   1589
  Dihedral  :  4.897  59.896   1267
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 14.08 %
    Favored  : 83.28 %
  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 (0.25), residues: 1151
  helix:  2.67 (0.23), residues: 462
  sheet:  0.61 (0.33), residues: 216
  loop : -0.14 (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   0.004   0.000   ARG B  96 

*********************** 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
  152 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 0.936 
Fit side-chains
REVERT: R  135 ARG cc_start: 0.5802 (ttt90) cc_final: 0.5191 (ttm-80)
REVERT: R  140 LEU cc_start: 0.7431 (mt) cc_final: 0.7171 (mm)
REVERT: R  169 ARG cc_start: 0.6419 (ttt180) cc_final: 0.6053 (ttm-80)
REVERT: R  297 ILE cc_start: 0.7610 (mt) cc_final: 0.7275 (mp)
REVERT: A   24 LYS cc_start: 0.7311 (mmtt) cc_final: 0.7080 (pptt)
REVERT: A   31 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7237 (tp40)
REVERT: A   53 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7980 (pttp)
REVERT: A   59 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6775 (mm110)
REVERT: A  240 ASP cc_start: 0.7782 (p0) cc_final: 0.7507 (p0)
REVERT: B    9 GLN cc_start: 0.6315 (OUTLIER) cc_final: 0.6006 (tm-30)
REVERT: B  261 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8510 (mp)
  outliers start: 24
  outliers final: 9
  residues processed: 142
  average time/residue: 1.4958
  time to fit residues: 223.8618
Evaluate side-chains
  138 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   45 CYS
Chi-restraints excluded: chain R residue  205 VAL
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  307 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:    6.9990
   chunk 80 optimal weight:    0.4980
   chunk 68 optimal weight:    0.0970
   chunk 28 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 104 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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
B  35 ASN
B 268 ASN
N 120 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.175987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.122128 restraints weight = 8150.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.65
r_work: 0.3141 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3026 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.2605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9112  Z= 0.173
  Angle     :  0.517   5.392  12339  Z= 0.291
  Chirality :  0.042   0.142   1387
  Planarity :  0.004   0.038   1589
  Dihedral  :  4.585  20.118   1266
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 14.08 %
    Favored  : 83.17 %
  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:  1.66 (0.25), residues: 1151
  helix:  2.75 (0.23), residues: 456
  sheet:  0.44 (0.33), residues: 220
  loop : -0.19 (0.28), residues: 475

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   0.024   0.002   TYR R 146 
 ARG   0.005   0.000   ARG A  20 

*********************** 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
  155 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.938 
Fit side-chains
REVERT: R  135 ARG cc_start: 0.5844 (ttt90) cc_final: 0.5170 (ttm-80)
REVERT: R  140 LEU cc_start: 0.7450 (mt) cc_final: 0.7199 (mm)
REVERT: R  169 ARG cc_start: 0.6437 (ttt180) cc_final: 0.6064 (ttm-80)
REVERT: R  221 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7288 (tp)
REVERT: R  297 ILE cc_start: 0.7625 (mt) cc_final: 0.7271 (mp)
REVERT: R  369 GLN cc_start: 0.7163 (tm-30) cc_final: 0.6499 (tm-30)
REVERT: A   24 LYS cc_start: 0.7339 (mmtt) cc_final: 0.7059 (pptt)
REVERT: A   31 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7254 (tp40)
REVERT: A   53 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.8000 (pttp)
REVERT: A  240 ASP cc_start: 0.7856 (p0) cc_final: 0.7601 (p0)
REVERT: B    9 GLN cc_start: 0.6334 (OUTLIER) cc_final: 0.6012 (tm-30)
REVERT: B  214 ARG cc_start: 0.7687 (mmt-90) cc_final: 0.7225 (mtt180)
REVERT: B  261 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8588 (mp)
REVERT: B  325 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.7992 (tpp)
  outliers start: 25
  outliers final: 10
  residues processed: 146
  average time/residue: 1.5198
  time to fit residues: 233.7921
Evaluate side-chains
  142 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
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  221 LEU
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  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 B residue  325 MET
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:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 10 optimal weight:   40.0000
   chunk 49 optimal weight:    8.9990
   chunk 77 optimal weight:    0.0570
   chunk 12 optimal weight:    9.9990
   chunk 44 optimal weight:    6.9990
   chunk 57 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.7302

-------------------------------------------------------------------------------
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 = 0.3985 r_free = 0.3985 target = 0.176476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.119375 restraints weight = 8130.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 1.42
r_work: 0.3182 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.2732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   9112  Z= 0.157
  Angle     :  0.493   5.850  12339  Z= 0.278
  Chirality :  0.041   0.143   1387
  Planarity :  0.003   0.039   1589
  Dihedral  :  4.453  19.396   1266
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 14.52 %
    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:  1.71 (0.25), residues: 1151
  helix:  2.90 (0.23), residues: 450
  sheet:  0.36 (0.33), residues: 220
  loop : -0.19 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 234 
 HIS   0.003   0.001   HIS A  41 
 PHE   0.017   0.002   PHE R 313 
 TYR   0.023   0.001   TYR R 146 
 ARG   0.006   0.000   ARG A  20 

*********************** 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
  150 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.987 
Fit side-chains
REVERT: R  135 ARG cc_start: 0.5643 (ttt90) cc_final: 0.4869 (ttm-80)
REVERT: R  140 LEU cc_start: 0.7423 (mt) cc_final: 0.7175 (mm)
REVERT: R  169 ARG cc_start: 0.6452 (ttt180) cc_final: 0.6080 (ttm-80)
REVERT: R  221 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7317 (tp)
REVERT: R  297 ILE cc_start: 0.7686 (mt) cc_final: 0.7328 (mp)
REVERT: R  369 GLN cc_start: 0.7304 (tm-30) cc_final: 0.6667 (tm-30)
REVERT: A   24 LYS cc_start: 0.7322 (mmtt) cc_final: 0.7073 (pptt)
REVERT: A   31 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7241 (tp40)
REVERT: A   53 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7993 (pttp)
REVERT: A   59 GLN cc_start: 0.7074 (mm-40) cc_final: 0.5818 (pt0)
REVERT: A  240 ASP cc_start: 0.7834 (p0) cc_final: 0.7626 (p0)
REVERT: A  307 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7161 (mptt)
REVERT: B    9 GLN cc_start: 0.6391 (OUTLIER) cc_final: 0.6077 (tm-30)
REVERT: B   96 ARG cc_start: 0.8005 (mtm110) cc_final: 0.7723 (mtt180)
REVERT: B  195 ASP cc_start: 0.7216 (p0) cc_final: 0.6856 (p0)
REVERT: B  261 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8548 (mp)
REVERT: B  325 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.7988 (tpp)
  outliers start: 23
  outliers final: 10
  residues processed: 143
  average time/residue: 1.5753
  time to fit residues: 237.0281
Evaluate side-chains
  142 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  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  221 LEU
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  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 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:    7.9990
   chunk 44 optimal weight:    6.9990
   chunk 82 optimal weight:    0.0370
   chunk 17 optimal weight:    5.9990
   chunk 98 optimal weight:    3.9990
   chunk 97 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.3662

-------------------------------------------------------------------------------
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
N 120 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.174232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.116643 restraints weight = 8056.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 1.40
r_work: 0.3146 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   9112  Z= 0.226
  Angle     :  0.557   5.647  12339  Z= 0.313
  Chirality :  0.043   0.143   1387
  Planarity :  0.004   0.041   1589
  Dihedral  :  4.751  23.058   1266
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 14.85 %
    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:  1.47 (0.24), residues: 1151
  helix:  2.66 (0.23), residues: 450
  sheet:  0.20 (0.33), residues: 214
  loop : -0.25 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 234 
 HIS   0.006   0.001   HIS R 241 
 PHE   0.019   0.002   PHE R 313 
 TYR   0.024   0.002   TYR R 146 
 ARG   0.005   0.001   ARG A  20 

*********************** 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
  150 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.935 
Fit side-chains
REVERT: R  135 ARG cc_start: 0.5754 (ttt90) cc_final: 0.4955 (ttm-80)
REVERT: R  140 LEU cc_start: 0.7448 (mt) cc_final: 0.7187 (mm)
REVERT: R  169 ARG cc_start: 0.6528 (ttt180) cc_final: 0.6148 (ttm-80)
REVERT: R  221 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7279 (tp)
REVERT: R  325 ARG cc_start: 0.6450 (OUTLIER) cc_final: 0.5721 (mpt-90)
REVERT: R  369 GLN cc_start: 0.7319 (tm-30) cc_final: 0.6577 (tm-30)
REVERT: A   24 LYS cc_start: 0.7334 (mmtt) cc_final: 0.7098 (pptt)
REVERT: A   31 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7254 (tp40)
REVERT: A   53 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8043 (pttp)
REVERT: A   59 GLN cc_start: 0.7136 (mm-40) cc_final: 0.5904 (pt0)
REVERT: B    9 GLN cc_start: 0.6428 (OUTLIER) cc_final: 0.6077 (tm-30)
REVERT: B   96 ARG cc_start: 0.8000 (mtm110) cc_final: 0.7721 (mtt180)
REVERT: B  195 ASP cc_start: 0.7360 (p0) cc_final: 0.6999 (p0)
REVERT: B  261 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8531 (mp)
REVERT: B  325 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7987 (tpp)
  outliers start: 23
  outliers final: 12
  residues processed: 142
  average time/residue: 1.7572
  time to fit residues: 262.3783
Evaluate side-chains
  143 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    2 SER
Chi-restraints excluded: chain R residue  156 MET
Chi-restraints excluded: chain R residue  205 VAL
Chi-restraints excluded: chain R residue  206 THR
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   31 GLN
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue  265 ARG
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   59 TYR
Chi-restraints excluded: chain B residue  178 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 107 optimal weight:    0.5980
   chunk 69 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 100 optimal weight:    0.7980
   chunk 108 optimal weight:    0.7980
   chunk 106 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3979 r_free = 0.3979 target = 0.175761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.118439 restraints weight = 8257.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 1.44
r_work: 0.3172 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   9112  Z= 0.160
  Angle     :  0.499   5.503  12339  Z= 0.281
  Chirality :  0.041   0.143   1387
  Planarity :  0.003   0.040   1589
  Dihedral  :  4.514  21.081   1266
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.40 %
    Favored  : 82.18 %
  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 (0.24), residues: 1151
  helix:  2.84 (0.23), residues: 450
  sheet:  0.25 (0.33), residues: 212
  loop : -0.24 (0.27), residues: 489

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   0.017   0.002   PHE R 313 
 TYR   0.023   0.001   TYR R 146 
 ARG   0.006   0.000   ARG A  20 

*********************** 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
  152 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.933 
Fit side-chains
REVERT: R  135 ARG cc_start: 0.5702 (ttt90) cc_final: 0.4866 (ttm-80)
REVERT: R  140 LEU cc_start: 0.7415 (mt) cc_final: 0.7162 (mm)
REVERT: R  169 ARG cc_start: 0.6514 (ttt180) cc_final: 0.6151 (ttm-80)
REVERT: R  221 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7335 (tp)
REVERT: R  325 ARG cc_start: 0.6296 (OUTLIER) cc_final: 0.5728 (mpt-90)
REVERT: R  369 GLN cc_start: 0.7282 (tm-30) cc_final: 0.6619 (tm-30)
REVERT: A   24 LYS cc_start: 0.7289 (mmtt) cc_final: 0.7024 (pptt)
REVERT: A   31 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7228 (tp40)
REVERT: A   53 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.8031 (pttp)
REVERT: A   59 GLN cc_start: 0.7119 (mm-40) cc_final: 0.5888 (pt0)
REVERT: B    9 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.6067 (tm-30)
REVERT: B  325 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.7978 (tpp)
  outliers start: 22
  outliers final: 13
  residues processed: 143
  average time/residue: 1.5943
  time to fit residues: 239.9025
Evaluate side-chains
  143 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    2 SER
Chi-restraints excluded: chain R residue  156 MET
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   31 GLN
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  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   59 TYR
Chi-restraints excluded: chain B residue  178 THR
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:   10.0000
   chunk 105 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 27 optimal weight:    8.9990
   chunk 2 optimal weight:    0.6980
   chunk 94 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0060
   chunk 3 optimal weight:   50.0000
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.5000

-------------------------------------------------------------------------------
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 = 0.3959 r_free = 0.3959 target = 0.173806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.115974 restraints weight = 8226.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 1.44
r_work: 0.3137 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   9112  Z= 0.239
  Angle     :  0.568   5.773  12339  Z= 0.319
  Chirality :  0.044   0.144   1387
  Planarity :  0.004   0.042   1589
  Dihedral  :  4.808  24.158   1266
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.51 %
    Favored  : 82.07 %
  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:  1.44 (0.24), residues: 1151
  helix:  2.60 (0.23), residues: 450
  sheet:  0.23 (0.33), residues: 214
  loop : -0.25 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 234 
 HIS   0.006   0.001   HIS R 241 
 PHE   0.020   0.002   PHE R 313 
 TYR   0.023   0.002   TYR R 146 
 ARG   0.007   0.001   ARG A  20 

*********************** 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
  148 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.970 
Fit side-chains
REVERT: R  140 LEU cc_start: 0.7490 (mt) cc_final: 0.7221 (mm)
REVERT: R  169 ARG cc_start: 0.6558 (ttt180) cc_final: 0.6179 (ttm-80)
REVERT: R  221 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7315 (tp)
REVERT: R  325 ARG cc_start: 0.6367 (OUTLIER) cc_final: 0.5755 (mpt-90)
REVERT: R  369 GLN cc_start: 0.7343 (tm-30) cc_final: 0.6611 (tm-30)
REVERT: A   24 LYS cc_start: 0.7308 (mmtt) cc_final: 0.7091 (pptt)
REVERT: A   31 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7274 (tp40)
REVERT: A   53 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8059 (pttp)
REVERT: B    9 GLN cc_start: 0.6498 (OUTLIER) cc_final: 0.6124 (tm-30)
REVERT: B  325 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8023 (tpp)
  outliers start: 22
  outliers final: 13
  residues processed: 140
  average time/residue: 1.5580
  time to fit residues: 229.5297
Evaluate side-chains
  142 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    2 SER
Chi-restraints excluded: chain R residue   45 CYS
Chi-restraints excluded: chain R residue  156 MET
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   31 GLN
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  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  325 MET
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:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 67 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 109 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 112 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3968 r_free = 0.3968 target = 0.174705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.117548 restraints weight = 8132.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 1.40
r_work: 0.3156 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9112  Z= 0.190
  Angle     :  0.527   5.523  12339  Z= 0.297
  Chirality :  0.042   0.145   1387
  Planarity :  0.004   0.042   1589
  Dihedral  :  4.650  22.875   1266
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.84 %
    Favored  : 81.74 %
  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:  1.53 (0.24), residues: 1151
  helix:  2.71 (0.24), residues: 450
  sheet:  0.28 (0.33), residues: 213
  loop : -0.26 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 234 
 HIS   0.005   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 

*********************** 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
  147 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 1.054 
Fit side-chains
REVERT: R  140 LEU cc_start: 0.7471 (mt) cc_final: 0.7209 (mm)
REVERT: R  169 ARG cc_start: 0.6529 (ttt180) cc_final: 0.6160 (ttm-80)
REVERT: R  221 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7288 (tp)
REVERT: R  272 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6517 (mp)
REVERT: R  325 ARG cc_start: 0.6297 (OUTLIER) cc_final: 0.5687 (mpt-90)
REVERT: R  369 GLN cc_start: 0.7304 (tm-30) cc_final: 0.6635 (tm-30)
REVERT: A   24 LYS cc_start: 0.7333 (mmtt) cc_final: 0.7085 (pptt)
REVERT: A   31 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7245 (tp40)
REVERT: A   53 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8041 (pttp)
REVERT: A   59 GLN cc_start: 0.7103 (mm-40) cc_final: 0.5839 (pt0)
REVERT: B    9 GLN cc_start: 0.6455 (OUTLIER) cc_final: 0.6098 (tm-30)
REVERT: B  325 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8025 (tpp)
REVERT: N  105 ARG cc_start: 0.7649 (mtm110) cc_final: 0.7429 (mtm110)
  outliers start: 22
  outliers final: 12
  residues processed: 138
  average time/residue: 1.7383
  time to fit residues: 252.1927
Evaluate side-chains
  142 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    2 SER
Chi-restraints excluded: chain R residue  156 MET
Chi-restraints excluded: chain R residue  205 VAL
Chi-restraints excluded: chain R residue  221 LEU
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  325 ARG
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  296 LEU
Chi-restraints excluded: chain A residue  307 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  325 MET
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:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3974 r_free = 0.3974 target = 0.175196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.117868 restraints weight = 8208.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.42
r_work: 0.3164 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.2965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9112  Z= 0.174
  Angle     :  0.516   5.499  12339  Z= 0.290
  Chirality :  0.042   0.145   1387
  Planarity :  0.004   0.042   1589
  Dihedral  :  4.563  22.226   1266
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 16.28 %
    Favored  : 81.63 %
  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: 1151
  helix:  2.77 (0.24), residues: 450
  sheet:  0.17 (0.33), residues: 224
  loop : -0.22 (0.28), residues: 477

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   0.017   0.002   PHE R 313 
 TYR   0.023   0.002   TYR R 146 
 ARG   0.007   0.000   ARG A  20 

********************** 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
  144 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 2.570 
Fit side-chains
REVERT: R  140 LEU cc_start: 0.7427 (mt) cc_final: 0.7172 (mm)
REVERT: R  169 ARG cc_start: 0.6545 (ttt180) cc_final: 0.6178 (ttm-80)
REVERT: R  221 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7320 (tp)
REVERT: R  325 ARG cc_start: 0.6200 (OUTLIER) cc_final: 0.5566 (mpt-90)
REVERT: R  369 GLN cc_start: 0.7309 (tm-30) cc_final: 0.6674 (tm-30)
REVERT: A   24 LYS cc_start: 0.7230 (mmtt) cc_final: 0.7015 (pptt)
REVERT: A   31 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7231 (tp40)
REVERT: A   59 GLN cc_start: 0.7104 (mm-40) cc_final: 0.5828 (pt0)
REVERT: B    9 GLN cc_start: 0.6465 (OUTLIER) cc_final: 0.6101 (tm-30)
REVERT: B  325 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8012 (tpp)
  outliers start: 19
  outliers final: 12
  residues processed: 135
  average time/residue: 1.7867
  time to fit residues: 255.2979
Evaluate side-chains
  141 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    2 SER
Chi-restraints excluded: chain R residue  156 MET
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   31 GLN
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  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  325 MET
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:    0.0040
   chunk 106 optimal weight:    0.7980
   chunk 75 optimal weight:    0.8980
   chunk 108 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9980
   overall best weight:    0.6992

-------------------------------------------------------------------------------
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 = 0.3983 r_free = 0.3983 target = 0.176027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.120769 restraints weight = 8212.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.72
r_work: 0.3161 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   9112  Z= 0.155
  Angle     :  0.497   5.491  12339  Z= 0.280
  Chirality :  0.041   0.142   1387
  Planarity :  0.003   0.042   1589
  Dihedral  :  4.432  20.411   1266
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.39 %
    Favored  : 81.74 %
  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: 1151
  helix:  2.86 (0.24), residues: 450
  sheet:  0.24 (0.33), residues: 222
  loop : -0.21 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 234 
 HIS   0.003   0.001   HIS R 241 
 PHE   0.016   0.002   PHE R 313 
 TYR   0.023   0.002   TYR R 146 
 ARG   0.007   0.000   ARG A  20 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10395.76 seconds
wall clock time: 179 minutes 47.19 seconds (10787.19 seconds total)