Starting phenix.real_space_refine
on Wed Mar  4 00:57:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vla_32022/03_2026/7vla_32022.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vla_32022/03_2026/7vla_32022.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vla_32022/03_2026/7vla_32022.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vla_32022/03_2026/7vla_32022.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vla_32022/03_2026/7vla_32022.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vla_32022/03_2026/7vla_32022.map"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
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      68      5.16       5
     C    6192      2.51       5
     N    1625      2.21       5
     O    1790      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9675
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1811
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "L"
      Number of atoms: 485
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 485
          Classifications: {'peptide': 64}
          Link IDs: {'PTRANS': 5, 'TRANS': 58}
    Chain: "R"
      Number of atoms: 2505
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 302, 2493
          Classifications: {'peptide': 302}
          Link IDs: {'PTRANS': 10, 'TRANS': 291}
      Conformer: "B"
        Number of residues, atoms: 302, 2493
          Classifications: {'peptide': 302}
          Link IDs: {'PTRANS': 10, 'TRANS': 291}
          bond proxies already assigned to first conformer: 2550
    Chain: "S"
      Number of atoms: 1795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1795
          Classifications: {'peptide': 234}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR R 291 " occ=0.50
      ... (22 atoms not shown)
      pdb=" OH BTYR R 291 " occ=0.50
  Time building chain proxies: 2.72, per 1000 atoms: 0.28
  Number of scatterers: 9675
  At special positions: 0
  Unit cell: (109.512, 135.876, 131.82, 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      68     16.00
     O    1790      8.00
     N    1625      7.00
     C    6192      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  32 " - pdb=" SG  CYS L  56 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  33 " - pdb=" SG  CYS L  72 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  43 " - pdb=" SG  CYS L  83 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  24 " - pdb=" SG  CYS R 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 594.2 milliseconds
  

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2292

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 15 sheets defined
      39.1% alpha, 23.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.760A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.859A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.558A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.870A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.515A  pdb=" N   LYS A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.531A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 6 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.607A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'L' and resid 42 through 46
      removed outlier: 3.831A  pdb=" N   MET L  46 " --> pdb=" O   CYS L  43 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 84
    Processing helix  chain 'L' and resid 85 through 87
      No H-bonds generated for 'chain 'L' and resid 85 through 87'
    Processing helix  chain 'R' and resid 26 through 62
      removed outlier: 3.598A  pdb=" N   GLN R  35 " --> pdb=" O   ALA R  31 " (cutoff:3.500A)
      Proline residue:  R  38  - end of helix
      removed outlier: 4.187A  pdb=" N   LEU R  43 " --> pdb=" O   PRO R  39 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   GLN R  61 " --> pdb=" O   LEU R  57 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   TYR R  62 " --> pdb=" O   VAL R  58 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 97
      removed outlier: 3.531A  pdb=" N   LEU R  87 " --> pdb=" O   PHE R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 140 through 145
      removed outlier: 3.613A  pdb=" N   ALA R 144 " --> pdb=" O   PHE R 140 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 165
    Processing helix  chain 'R' and resid 165 through 172
      removed outlier: 3.503A  pdb=" N   LEU R 169 " --> pdb=" O   SER R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 191 through 208
    Processing helix  chain 'R' and resid 208 through 227
    Processing helix  chain 'R' and resid 231 through 264
      Proline residue:  R 254  - end of helix
      removed outlier: 3.719A  pdb=" N   PHE R 264 " --> pdb=" O   LEU R 260 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 264 through 269
      removed outlier: 3.571A  pdb=" N   PHE R 269 " --> pdb=" O   GLN R 265 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 275 through 292
    Processing helix  chain 'R' and resid 292 through 302
      Proline residue:  R 298  - end of helix
    Processing helix  chain 'R' and resid 305 through 318
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.260A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
    Processing helix  chain 'S' and resid 220 through 224
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.504A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.638A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.711A  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: 5.809A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.542A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.962A  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: 6.913A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.926A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.164A  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: 6.410A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.694A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 48 through 51
      removed outlier: 3.609A  pdb=" N   SER L  48 " --> pdb=" O   LEU L  64 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA L  73 " --> pdb=" O   VAL L  61 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'R' and resid 173 through 177
    Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12
      removed outlier: 6.692A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 11 through 12
      removed outlier: 4.310A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141
    Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148
      removed outlier: 5.009A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   ARG S 191 " --> pdb=" O   ASN S 194 " (cutoff:3.500A)

    507 hydrogen bonds defined for protein.
    1399 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.76

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2529
        1.33 -     1.45: 1942
        1.45 -     1.57: 5320
        1.57 -     1.70: 2
        1.70 -     1.82: 96
  Bond restraints: 9889
  Sorted by residual:
  bond pdb=" N   CYS R 273 "
       pdb=" CA  CYS R 273 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.23e-02 6.61e+03 7.37e+00
  bond pdb=" C   TYR R 170 "
       pdb=" N   PHE R 171 "
    ideal  model  delta    sigma   weight residual
    1.332  1.369 -0.036 1.36e-02 5.41e+03 7.17e+00
  bond pdb=" C16 CLR R 401 "
       pdb=" C17 CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.554  1.603 -0.049 2.00e-02 2.50e+03 6.10e+00
  bond pdb=" C   LEU R  87 "
       pdb=" O   LEU R  87 "
    ideal  model  delta    sigma   weight residual
    1.244  1.221  0.023 9.80e-03 1.04e+04 5.42e+00
  bond pdb=" C23 CLR R 401 "
       pdb=" C24 CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.525  1.571 -0.046 2.00e-02 2.50e+03 5.40e+00
  ... (remaining 9884 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 12909
        2.05 -     4.11: 412
        4.11 -     6.16: 53
        6.16 -     8.22: 15
        8.22 -    10.27: 3
  Bond angle restraints: 13392
  Sorted by residual:
  angle pdb=" N   GLU R 274 "
        pdb=" CA  GLU R 274 "
        pdb=" C   GLU R 274 "
      ideal   model   delta    sigma   weight residual
     114.12  104.40    9.72 1.39e+00 5.18e-01 4.89e+01
  angle pdb=" N   SER B 245 "
        pdb=" CA  SER B 245 "
        pdb=" C   SER B 245 "
      ideal   model   delta    sigma   weight residual
     109.14  119.41  -10.27 1.49e+00 4.50e-01 4.75e+01
  angle pdb=" N   LYS S  43 "
        pdb=" CA  LYS S  43 "
        pdb=" C   LYS S  43 "
      ideal   model   delta    sigma   weight residual
     111.74  118.64   -6.90 1.35e+00 5.49e-01 2.61e+01
  angle pdb=" N   CYS B 250 "
        pdb=" CA  CYS B 250 "
        pdb=" C   CYS B 250 "
      ideal   model   delta    sigma   weight residual
     110.17  102.28    7.89 1.61e+00 3.86e-01 2.40e+01
  angle pdb=" N   LYS B 209 "
        pdb=" CA  LYS B 209 "
        pdb=" C   LYS B 209 "
      ideal   model   delta    sigma   weight residual
     108.34  115.74   -7.40 1.64e+00 3.72e-01 2.04e+01
  ... (remaining 13387 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.67: 5436
       16.67 -    33.34: 399
       33.34 -    50.01: 64
       50.01 -    66.67: 23
       66.67 -    83.34: 10
  Dihedral angle restraints: 5932
    sinusoidal: 2376
      harmonic: 3556
  Sorted by residual:
  dihedral pdb=" CB  CYS L  43 "
           pdb=" SG  CYS L  43 "
           pdb=" SG  CYS L  83 "
           pdb=" CB  CYS L  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -35.13  -50.87     1      1.00e+01 1.00e-02 3.54e+01
  dihedral pdb=" CA  GLU R 177 "
           pdb=" C   GLU R 177 "
           pdb=" N   PHE R 178 "
           pdb=" CA  PHE R 178 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.94   29.06     0      5.00e+00 4.00e-02 3.38e+01
  dihedral pdb=" CA  PHE B 199 "
           pdb=" C   PHE B 199 "
           pdb=" N   VAL B 200 "
           pdb=" CA  VAL B 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.45   28.55     0      5.00e+00 4.00e-02 3.26e+01
  ... (remaining 5929 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1334
       0.082 -    0.165: 158
       0.165 -    0.247: 13
       0.247 -    0.330: 6
       0.330 -    0.412: 1
  Chirality restraints: 1512
  Sorted by residual:
  chirality pdb=" CA  LYS S  43 "
            pdb=" N   LYS S  43 "
            pdb=" C   LYS S  43 "
            pdb=" CB  LYS S  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.25e+00
  chirality pdb=" C17 CLR R 401 "
            pdb=" C13 CLR R 401 "
            pdb=" C16 CLR R 401 "
            pdb=" C20 CLR R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.88   -0.32 2.00e-01 2.50e+01 2.61e+00
  chirality pdb=" CA  ALA B 248 "
            pdb=" N   ALA B 248 "
            pdb=" C   ALA B 248 "
            pdb=" CB  ALA B 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.17    0.32 2.00e-01 2.50e+01 2.49e+00
  ... (remaining 1509 not shown)

  Planarity restraints: 1683
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 176 "    0.029 2.00e-02 2.50e+03   2.52e-02 1.59e+01
        pdb=" CG  TRP R 176 "   -0.067 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 176 "    0.030 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 176 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 176 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 176 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 176 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 176 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 176 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 176 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA S  40 "   -0.036 5.00e-02 4.00e+02   5.48e-02 4.81e+00
        pdb=" N   PRO S  41 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO S  41 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO S  41 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG G  13 "    0.010 2.00e-02 2.50e+03   1.98e-02 3.93e+00
        pdb=" C   ARG G  13 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ARG G  13 "    0.013 2.00e-02 2.50e+03
        pdb=" N   LYS G  14 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1680 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.29: 10
        2.29 -     2.94: 4237
        2.94 -     3.59: 13606
        3.59 -     4.25: 22577
        4.25 -     4.90: 38946
  Nonbonded interactions: 79376
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU R 287 "
            pdb=" OH BTYR R 291 "
     model   vdw
     1.634 3.040
  nonbonded pdb=" O   ASP B 163 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.131 3.040
  nonbonded pdb=" O   ASP R 280 "
            pdb=" NE2 GLN R 284 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" O   MET S 192 "
            pdb=" OG  SER S 193 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG  SER B  67 "
            pdb=" OD1 ASP B 323 "
     model   vdw
     2.241 3.040
  ... (remaining 79371 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=0.50 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:             1.060
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.510
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
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      :  0.006   0.049   9896  Z= 0.282
  Angle     :  0.870  10.269  13406  Z= 0.509
  Chirality :  0.057   0.412   1512
  Planarity :  0.005   0.055   1683
  Dihedral  : 12.463  83.343   3619
  Min Nonbonded Distance : 1.634

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.66 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.24), residues: 1209
  helix:  1.81 (0.26), residues: 405
  sheet:  1.12 (0.29), residues: 314
  loop : -0.47 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  68 
 TYR   0.022   0.002   TYR S 103 
 PHE   0.023   0.003   PHE R 316 
 TRP   0.067   0.003   TRP R 176 
 HIS   0.007   0.002   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00565 ( 9889)
  covalent geometry    : angle       0.86631 (13392)
  SS BOND              : bond        0.00458 (    7)
  SS BOND              : angle       2.65347 (   14)
  hydrogen bonds       : bond        0.14244 (  502)
  hydrogen bonds       : angle       6.32154 ( 1399)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  195 ASP cc_start: 0.6883 (p0) cc_final: 0.6630 (p0)
REVERT: B  262 MET cc_start: 0.7591 (tpp) cc_final: 0.7347 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.7438
  time to fit residues: 137.7221
Evaluate side-chains
  139 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0770
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9990
   overall best weight:    1.3944

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
B  32 GLN
B 176 GLN
** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.184620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.151308 restraints weight = 23245.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 4.63
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3708
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3708 r_free = 0.3708    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3708 r_free = 0.3708    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3708
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9896  Z= 0.171
  Angle     :  0.641   9.296  13406  Z= 0.344
  Chirality :  0.045   0.184   1512
  Planarity :  0.005   0.048   1683
  Dihedral  :  6.047  57.867   1389
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  8.41 %
    Favored  : 90.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.24), residues: 1209
  helix:  2.08 (0.25), residues: 415
  sheet:  0.99 (0.30), residues: 297
  loop : -0.49 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  68 
 TYR   0.021   0.002   TYR R  62 
 PHE   0.024   0.002   PHE R  85 
 TRP   0.030   0.002   TRP R 176 
 HIS   0.004   0.001   HIS R 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 9889)
  covalent geometry    : angle       0.63774 (13392)
  SS BOND              : bond        0.00520 (    7)
  SS BOND              : angle       2.20919 (   14)
  hydrogen bonds       : bond        0.05007 (  502)
  hydrogen bonds       : angle       5.12919 ( 1399)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  262 MET cc_start: 0.7696 (tpp) cc_final: 0.7471 (tpp)
REVERT: B  280 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8061 (mttt)
REVERT: S  234 GLU cc_start: 0.8100 (pt0) cc_final: 0.7837 (pt0)
  outliers start: 16
  outliers final: 5
  residues processed: 144
  average time/residue: 0.7573
  time to fit residues: 115.0013
Evaluate side-chains
  136 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 130
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain R residue  261 ILE
Chi-restraints excluded: chain S residue   62 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 112 optimal weight:    0.5980
   chunk 87 optimal weight:    0.0010
   chunk 34 optimal weight:    4.9990
   chunk 110 optimal weight:    9.9990
   overall best weight:    1.1188

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 195 HIS
A 244 HIS
B  32 GLN
B 176 GLN
B 340 ASN
** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.184812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.152378 restraints weight = 19439.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 4.04
r_work: 0.2843 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2814
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2814 r_free = 0.2814    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2814 r_free = 0.2814    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2814
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9896  Z= 0.146
  Angle     :  0.576   7.156  13406  Z= 0.312
  Chirality :  0.043   0.182   1512
  Planarity :  0.004   0.045   1683
  Dihedral  :  5.636  51.103   1389
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  9.26 %
    Favored  : 89.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.24), residues: 1209
  helix:  2.38 (0.25), residues: 410
  sheet:  0.94 (0.29), residues: 301
  loop : -0.52 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  46 
 TYR   0.025   0.002   TYR A 296 
 PHE   0.018   0.002   PHE R 101 
 TRP   0.019   0.002   TRP R 176 
 HIS   0.004   0.001   HIS R 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9889)
  covalent geometry    : angle       0.57297 (13392)
  SS BOND              : bond        0.00476 (    7)
  SS BOND              : angle       1.92900 (   14)
  hydrogen bonds       : bond        0.04566 (  502)
  hydrogen bonds       : angle       4.90295 ( 1399)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7663 (tt0)
REVERT: A   51 LYS cc_start: 0.7816 (mttp) cc_final: 0.7497 (pptt)
REVERT: B   65 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8233 (p)
REVERT: B   75 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7677 (mm110)
REVERT: B   96 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8378 (mtt-85)
REVERT: B  176 GLN cc_start: 0.9211 (tt0) cc_final: 0.8990 (tt0)
REVERT: B  197 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7777 (mtt90)
REVERT: S  160 ARG cc_start: 0.8185 (ttm110) cc_final: 0.7572 (ttp80)
  outliers start: 18
  outliers final: 4
  residues processed: 149
  average time/residue: 0.7014
  time to fit residues: 110.6057
Evaluate side-chains
  143 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 134
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain R residue  257 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 103 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 74 optimal weight:    9.9990
   chunk 14 optimal weight:    0.7980
   chunk 100 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
B 340 ASN
** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.184827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.151211 restraints weight = 23268.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 4.40
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3615
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3615
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9896  Z= 0.139
  Angle     :  0.558   7.177  13406  Z= 0.300
  Chirality :  0.043   0.179   1512
  Planarity :  0.004   0.046   1683
  Dihedral  :  5.420  47.124   1389
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 10.30 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.24), residues: 1209
  helix:  2.45 (0.25), residues: 412
  sheet:  0.91 (0.29), residues: 301
  loop : -0.57 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  68 
 TYR   0.024   0.001   TYR A 296 
 PHE   0.014   0.001   PHE R  85 
 TRP   0.014   0.002   TRP B  82 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9889)
  covalent geometry    : angle       0.55566 (13392)
  SS BOND              : bond        0.00465 (    7)
  SS BOND              : angle       1.78823 (   14)
  hydrogen bonds       : bond        0.04333 (  502)
  hydrogen bonds       : angle       4.77397 ( 1399)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7091 (tt0)
REVERT: B   75 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7086 (mm110)
REVERT: B   96 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7589 (mtt-85)
REVERT: B  214 ARG cc_start: 0.7312 (mmt-90) cc_final: 0.6955 (mmt180)
REVERT: R  239 ARG cc_start: 0.7399 (ttm170) cc_final: 0.7051 (ptp-110)
  outliers start: 22
  outliers final: 5
  residues processed: 147
  average time/residue: 0.6877
  time to fit residues: 106.9672
Evaluate side-chains
  140 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 132
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain R residue  250 LEU
Chi-restraints excluded: chain R residue  257 LEU
Chi-restraints excluded: chain R residue  287 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 64 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 90 optimal weight:    8.9990
   chunk 28 optimal weight:    0.0870
   chunk 114 optimal weight:    0.0570
   chunk 31 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0470
   chunk 3 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.3576

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
B 176 GLN
B 340 ASN
** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.188355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.138696 restraints weight = 17236.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.40
r_work: 0.3141 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.2273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9896  Z= 0.101
  Angle     :  0.512   8.043  13406  Z= 0.273
  Chirality :  0.041   0.171   1512
  Planarity :  0.004   0.045   1683
  Dihedral  :  5.052  44.317   1389
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 11.06 %
    Favored  : 87.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.24), residues: 1209
  helix:  2.56 (0.25), residues: 413
  sheet:  0.86 (0.29), residues: 305
  loop : -0.53 (0.26), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  46 
 TYR   0.023   0.001   TYR A 296 
 PHE   0.018   0.001   PHE R 101 
 TRP   0.019   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 9889)
  covalent geometry    : angle       0.50920 (13392)
  SS BOND              : bond        0.00354 (    7)
  SS BOND              : angle       1.58974 (   14)
  hydrogen bonds       : bond        0.03581 (  502)
  hydrogen bonds       : angle       4.54828 ( 1399)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7378 (m-10)
REVERT: B  172 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8201 (tp30)
REVERT: S  160 ARG cc_start: 0.8137 (ttm110) cc_final: 0.7670 (mtp85)
REVERT: S  234 GLU cc_start: 0.8888 (pt0) cc_final: 0.8565 (pt0)
  outliers start: 19
  outliers final: 5
  residues processed: 153
  average time/residue: 0.6727
  time to fit residues: 109.3608
Evaluate side-chains
  137 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 131
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain R residue  250 LEU
Chi-restraints excluded: chain R residue  311 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 87 optimal weight:    0.0980
   chunk 92 optimal weight:    1.9990
   chunk 115 optimal weight:    4.9990
   chunk 79 optimal weight:    6.9990
   chunk 37 optimal weight:    0.6980
   chunk 118 optimal weight:    4.9990
   chunk 99 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 101 optimal weight:    0.7980
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.186611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.154044 restraints weight = 20286.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 4.26
r_work: 0.2867 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2844
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2844 r_free = 0.2844    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2844 r_free = 0.2844    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2844
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9896  Z= 0.115
  Angle     :  0.523   7.232  13406  Z= 0.279
  Chirality :  0.041   0.168   1512
  Planarity :  0.004   0.043   1683
  Dihedral  :  5.041  42.792   1389
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.91 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.24), residues: 1209
  helix:  2.62 (0.25), residues: 414
  sheet:  0.84 (0.29), residues: 306
  loop : -0.51 (0.26), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 219 
 TYR   0.023   0.001   TYR A 296 
 PHE   0.012   0.001   PHE A 189 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 9889)
  covalent geometry    : angle       0.52051 (13392)
  SS BOND              : bond        0.00434 (    7)
  SS BOND              : angle       1.68120 (   14)
  hydrogen bonds       : bond        0.03808 (  502)
  hydrogen bonds       : angle       4.55065 ( 1399)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7663 (tt0)
REVERT: B  172 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8177 (tp30)
REVERT: S  160 ARG cc_start: 0.8111 (ttm110) cc_final: 0.7501 (mtp85)
REVERT: S  234 GLU cc_start: 0.8914 (pt0) cc_final: 0.8504 (pt0)
  outliers start: 20
  outliers final: 10
  residues processed: 141
  average time/residue: 0.6502
  time to fit residues: 97.2995
Evaluate side-chains
  141 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain R residue   68 MET
Chi-restraints excluded: chain R residue  250 LEU
Chi-restraints excluded: chain R residue  257 LEU
Chi-restraints excluded: chain R residue  287 GLU
Chi-restraints excluded: chain R residue  311 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 88 optimal weight:    0.8980
   chunk 117 optimal weight:    4.9990
   chunk 114 optimal weight:    4.9990
   chunk 55 optimal weight:    0.6980
   chunk 104 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 78 optimal weight:    0.0980
   chunk 96 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
B 340 ASN
** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.183284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.137835 restraints weight = 20615.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.67
r_work: 0.3072 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2989
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2989 r_free = 0.2989    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2989 r_free = 0.2989    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2989
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9896  Z= 0.112
  Angle     :  0.524  10.321  13406  Z= 0.277
  Chirality :  0.041   0.164   1512
  Planarity :  0.004   0.044   1683
  Dihedral  :  4.977  41.870   1389
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 12.57 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.24), residues: 1209
  helix:  2.63 (0.25), residues: 415
  sheet:  0.85 (0.29), residues: 306
  loop : -0.48 (0.26), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 219 
 TYR   0.023   0.001   TYR A 296 
 PHE   0.018   0.001   PHE R 101 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 9889)
  covalent geometry    : angle       0.52115 (13392)
  SS BOND              : bond        0.00432 (    7)
  SS BOND              : angle       1.67650 (   14)
  hydrogen bonds       : bond        0.03717 (  502)
  hydrogen bonds       : angle       4.50802 ( 1399)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7496 (tt0)
REVERT: S  160 ARG cc_start: 0.7849 (ttm110) cc_final: 0.7484 (mtp85)
REVERT: S  234 GLU cc_start: 0.8752 (pt0) cc_final: 0.8416 (pt0)
  outliers start: 19
  outliers final: 9
  residues processed: 141
  average time/residue: 0.6803
  time to fit residues: 101.5199
Evaluate side-chains
  138 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain R residue   68 MET
Chi-restraints excluded: chain R residue  257 LEU
Chi-restraints excluded: chain R residue  287 GLU
Chi-restraints excluded: chain S residue   62 ASP
Chi-restraints excluded: chain S residue  162 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 110 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 64 optimal weight:    7.9990
   chunk 68 optimal weight:    0.9980
   chunk 117 optimal weight:    2.9990
   chunk 60 optimal weight:   30.0000
   chunk 83 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.180347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.127031 restraints weight = 14068.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 1.89
r_work: 0.3093 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2944
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2944
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9896  Z= 0.168
  Angle     :  0.588   9.377  13406  Z= 0.310
  Chirality :  0.043   0.168   1512
  Planarity :  0.004   0.045   1683
  Dihedral  :  5.214  42.160   1389
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.33 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.24), residues: 1209
  helix:  2.56 (0.25), residues: 415
  sheet:  0.90 (0.29), residues: 302
  loop : -0.57 (0.26), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 219 
 TYR   0.024   0.002   TYR A 296 
 PHE   0.015   0.002   PHE B 234 
 TRP   0.009   0.001   TRP R  90 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 9889)
  covalent geometry    : angle       0.58550 (13392)
  SS BOND              : bond        0.00588 (    7)
  SS BOND              : angle       1.87167 (   14)
  hydrogen bonds       : bond        0.04399 (  502)
  hydrogen bonds       : angle       4.70522 ( 1399)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7606 (tt0)
REVERT: B  172 GLU cc_start: 0.8313 (tp30) cc_final: 0.8109 (mt-10)
REVERT: B  293 ASN cc_start: 0.8475 (p0) cc_final: 0.8148 (p0)
REVERT: R  239 ARG cc_start: 0.7626 (ttm170) cc_final: 0.7200 (ptp-110)
REVERT: R  313 ARG cc_start: 0.6208 (mtt-85) cc_final: 0.5856 (mtt90)
REVERT: S  160 ARG cc_start: 0.8016 (ttm110) cc_final: 0.7581 (mtp85)
  outliers start: 16
  outliers final: 9
  residues processed: 136
  average time/residue: 0.6780
  time to fit residues: 97.6933
Evaluate side-chains
  139 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain R residue  257 LEU
Chi-restraints excluded: chain R residue  287 GLU
Chi-restraints excluded: chain S residue  162 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   chunk 114 optimal weight:    0.0970
   chunk 44 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 91 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 87 optimal weight:    6.9990
   chunk 107 optimal weight:    0.7980
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.180578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.129573 restraints weight = 18227.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 2.60
r_work: 0.3028 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2851
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2851
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9896  Z= 0.171
  Angle     :  0.601   9.239  13406  Z= 0.316
  Chirality :  0.043   0.169   1512
  Planarity :  0.004   0.045   1683
  Dihedral  :  5.312  43.117   1389
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.33 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.24), residues: 1209
  helix:  2.47 (0.25), residues: 415
  sheet:  0.94 (0.29), residues: 299
  loop : -0.64 (0.26), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 219 
 TYR   0.024   0.002   TYR A 296 
 PHE   0.018   0.002   PHE R 101 
 TRP   0.008   0.001   TRP R  90 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 9889)
  covalent geometry    : angle       0.59771 (13392)
  SS BOND              : bond        0.00626 (    7)
  SS BOND              : angle       1.92994 (   14)
  hydrogen bonds       : bond        0.04471 (  502)
  hydrogen bonds       : angle       4.74212 ( 1399)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7721 (tt0)
REVERT: A   51 LYS cc_start: 0.7715 (pptt) cc_final: 0.7481 (mppt)
REVERT: B  172 GLU cc_start: 0.8343 (tp30) cc_final: 0.8055 (mt-10)
REVERT: B  293 ASN cc_start: 0.8618 (p0) cc_final: 0.8316 (p0)
REVERT: R  239 ARG cc_start: 0.7817 (ttm170) cc_final: 0.7332 (ptp-110)
REVERT: R  313 ARG cc_start: 0.6397 (mtt-85) cc_final: 0.5939 (mtt90)
REVERT: S  160 ARG cc_start: 0.8181 (ttm110) cc_final: 0.7710 (mtp85)
  outliers start: 16
  outliers final: 11
  residues processed: 139
  average time/residue: 0.7267
  time to fit residues: 106.7170
Evaluate side-chains
  141 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain R residue  250 LEU
Chi-restraints excluded: chain R residue  257 LEU
Chi-restraints excluded: chain R residue  287 GLU
Chi-restraints excluded: chain R residue  311 TYR
Chi-restraints excluded: chain S residue  162 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 25 optimal weight:    0.4980
   chunk 83 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 37 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 84 optimal weight:    3.9990
   chunk 62 optimal weight:    7.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.182871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.132374 restraints weight = 16686.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.34
r_work: 0.3072 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2887
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2887 r_free = 0.2887    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2887 r_free = 0.2887    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2887
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9896  Z= 0.120
  Angle     :  0.547   8.877  13406  Z= 0.288
  Chirality :  0.041   0.164   1512
  Planarity :  0.004   0.044   1683
  Dihedral  :  5.096  43.129   1389
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 13.99 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.24), residues: 1209
  helix:  2.61 (0.25), residues: 415
  sheet:  0.92 (0.29), residues: 301
  loop : -0.57 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 219 
 TYR   0.024   0.001   TYR A 296 
 PHE   0.012   0.001   PHE A 189 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9889)
  covalent geometry    : angle       0.54453 (13392)
  SS BOND              : bond        0.00475 (    7)
  SS BOND              : angle       1.69429 (   14)
  hydrogen bonds       : bond        0.03877 (  502)
  hydrogen bonds       : angle       4.58635 ( 1399)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7684 (tt0)
REVERT: A   51 LYS cc_start: 0.7706 (pptt) cc_final: 0.7474 (mppt)
REVERT: B  172 GLU cc_start: 0.8340 (tp30) cc_final: 0.8005 (mt-10)
REVERT: B  293 ASN cc_start: 0.8487 (p0) cc_final: 0.8156 (p0)
REVERT: R  239 ARG cc_start: 0.7793 (ttm170) cc_final: 0.7311 (ptp-110)
REVERT: R  313 ARG cc_start: 0.6348 (mtt-85) cc_final: 0.5892 (mtt90)
REVERT: S  160 ARG cc_start: 0.8142 (ttm110) cc_final: 0.7646 (mtp85)
REVERT: S  234 GLU cc_start: 0.8905 (pt0) cc_final: 0.8526 (pt0)
  outliers start: 11
  outliers final: 9
  residues processed: 135
  average time/residue: 0.7265
  time to fit residues: 103.7033
Evaluate side-chains
  140 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain R residue  250 LEU
Chi-restraints excluded: chain R residue  257 LEU
Chi-restraints excluded: chain R residue  287 GLU
Chi-restraints excluded: chain R residue  311 TYR
Chi-restraints excluded: chain S residue  162 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 74 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0010
   chunk 57 optimal weight:    3.9990
   chunk 112 optimal weight:    3.9990
   chunk 91 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    1.9994

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.179622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.126926 restraints weight = 15337.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.22
r_work: 0.3045 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2864
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2864
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9896  Z= 0.203
  Angle     :  0.629  10.130  13406  Z= 0.330
  Chirality :  0.045   0.178   1512
  Planarity :  0.004   0.049   1683
  Dihedral  :  5.375  42.806   1389
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 13.61 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.24), residues: 1209
  helix:  2.43 (0.25), residues: 415
  sheet:  0.90 (0.29), residues: 300
  loop : -0.67 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 219 
 TYR   0.026   0.002   TYR A 296 
 PHE   0.017   0.002   PHE R 101 
 TRP   0.009   0.002   TRP R  90 
 HIS   0.006   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 9889)
  covalent geometry    : angle       0.62603 (13392)
  SS BOND              : bond        0.00691 (    7)
  SS BOND              : angle       2.05901 (   14)
  hydrogen bonds       : bond        0.04755 (  502)
  hydrogen bonds       : angle       4.80598 ( 1399)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4643.06 seconds
wall clock time: 79 minutes 36.24 seconds (4776.24 seconds total)