Starting phenix.real_space_refine
on Sun Jul 27 20:46:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vla_32022/07_2025/7vla_32022.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vla_32022/07_2025/7vla_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vla_32022/07_2025/7vla_32022.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vla_32022/07_2025/7vla_32022.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vla_32022/07_2025/7vla_32022.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vla_32022/07_2025/7vla_32022.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.31, per 1000 atoms: 0.76
  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: 2.67
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 1.20
  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: 3.35

  Time building geometry restraints manager: 3.13 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:             0.820
  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:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     28.170
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:15.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.120
-------------------------------------------------------------------------------
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 : 9.80
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.24), residues: 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
 TRP   0.067   0.003   TRP R 176 
 HIS   0.007   0.002   HIS A 213 
 PHE   0.023   0.003   PHE R 316 
 TYR   0.022   0.002   TYR S 103 
 ARG   0.012   0.001   ARG B  68 

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

*********************** 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  : 1.075 
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: 1.4972
  time to fit residues: 278.3792
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  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 90 optimal weight:    8.9990
   chunk 50 optimal weight:    0.7980
   chunk 30 optimal weight:    0.4980
   chunk 60 optimal weight:   30.0000
   chunk 48 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
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 = 0.4094 r_free = 0.4094 target = 0.185785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.133689 restraints weight = 17319.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.36
r_work: 0.3043 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2877
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2877
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9896  Z= 0.150
  Angle     :  0.621   9.171  13406  Z= 0.333
  Chirality :  0.044   0.184   1512
  Planarity :  0.005   0.048   1683
  Dihedral  :  5.949  57.556   1389
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  8.51 %
    Favored  : 90.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.24), residues: 1209
  helix:  2.13 (0.25), residues: 415
  sheet:  1.02 (0.30), residues: 297
  loop : -0.46 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP R 176 
 HIS   0.005   0.001   HIS R 186 
 PHE   0.024   0.002   PHE R  85 
 TYR   0.022   0.002   TYR A 296 
 ARG   0.006   0.001   ARG B  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04757 (  502)
  hydrogen bonds       : angle       5.07181 ( 1399)
  SS BOND              : bond        0.00457 (    7)
  SS BOND              : angle       2.11878 (   14)
  covalent geometry    : bond        0.00334 ( 9889)
  covalent geometry    : angle       0.61765 (13392)

*********************** 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
  157 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  297 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7185 (mm-30)
REVERT: A  318 GLU cc_start: 0.8130 (tp30) cc_final: 0.7868 (tp30)
REVERT: A  349 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7624 (tttp)
REVERT: B  176 GLN cc_start: 0.9182 (tt0) cc_final: 0.8950 (tt0)
REVERT: B  280 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8223 (tttt)
REVERT: S  234 GLU cc_start: 0.8873 (pt0) cc_final: 0.8553 (pt0)
  outliers start: 14
  outliers final: 3
  residues processed: 148
  average time/residue: 1.4315
  time to fit residues: 224.9152
Evaluate side-chains
  138 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 133
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  280 LYS
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 34 optimal weight:    0.3980
   chunk 71 optimal weight:    2.9990
   chunk 80 optimal weight:    0.0170
   chunk 114 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0870
   chunk 7 optimal weight:    7.9990
   chunk 52 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.4196

-------------------------------------------------------------------------------
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**
A 195 HIS
A 244 HIS
B  32 GLN
B  88 ASN
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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.188169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.155643 restraints weight = 22610.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 4.33
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3731
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3731 r_free = 0.3731    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3731 r_free = 0.3731    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3731
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.1903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9896  Z= 0.110
  Angle     :  0.529   7.209  13406  Z= 0.286
  Chirality :  0.042   0.179   1512
  Planarity :  0.004   0.044   1683
  Dihedral  :  5.413  51.393   1389
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  9.07 %
    Favored  : 89.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.24), residues: 1209
  helix:  2.52 (0.25), residues: 410
  sheet:  1.06 (0.29), residues: 301
  loop : -0.49 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP R 176 
 HIS   0.004   0.001   HIS R 186 
 PHE   0.019   0.001   PHE R 264 
 TYR   0.021   0.001   TYR A 296 
 ARG   0.006   0.000   ARG B  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03948 (  502)
  hydrogen bonds       : angle       4.73632 ( 1399)
  SS BOND              : bond        0.00375 (    7)
  SS BOND              : angle       1.71372 (   14)
  covalent geometry    : bond        0.00223 ( 9889)
  covalent geometry    : angle       0.52634 (13392)

*********************** 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
  167 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 152
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.7032 (tt0)
REVERT: B  214 ARG cc_start: 0.7218 (mmt-90) cc_final: 0.6879 (mmt180)
REVERT: R  239 ARG cc_start: 0.7207 (ttm170) cc_final: 0.6912 (ptp-110)
  outliers start: 15
  outliers final: 2
  residues processed: 160
  average time/residue: 1.3767
  time to fit residues: 234.3376
Evaluate side-chains
  141 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 138
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  332 VAL
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 108 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 11 optimal weight:    0.1980
   chunk 65 optimal weight:   30.0000
   chunk 79 optimal weight:    2.9990
   chunk 90 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 112 optimal weight:    4.9990
   chunk 73 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 195 HIS
B  32 GLN
B 176 GLN
B 340 ASN
G  18 GLN
** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.184227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.150982 restraints weight = 20379.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 4.24
r_work: 0.2821 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2795
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2795 r_free = 0.2795    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2795 r_free = 0.2795    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2795
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9896  Z= 0.163
  Angle     :  0.588   7.207  13406  Z= 0.315
  Chirality :  0.044   0.177   1512
  Planarity :  0.004   0.044   1683
  Dihedral  :  5.468  47.553   1389
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  9.64 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.24), residues: 1209
  helix:  2.38 (0.25), residues: 415
  sheet:  0.93 (0.29), residues: 296
  loop : -0.58 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP R 176 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.018   0.002   PHE R 101 
 TYR   0.029   0.002   TYR A 296 
 ARG   0.004   0.000   ARG B  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04549 (  502)
  hydrogen bonds       : angle       4.82295 ( 1399)
  SS BOND              : bond        0.00537 (    7)
  SS BOND              : angle       1.93194 (   14)
  covalent geometry    : bond        0.00377 ( 9889)
  covalent geometry    : angle       0.58454 (13392)

*********************** 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
  161 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7656 (tt0)
REVERT: B   42 ARG cc_start: 0.7650 (tpt170) cc_final: 0.7333 (tpp-160)
REVERT: B   65 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8256 (p)
REVERT: B  176 GLN cc_start: 0.9226 (tt0) cc_final: 0.8986 (tt0)
REVERT: G   20 LYS cc_start: 0.8381 (mtmt) cc_final: 0.8149 (mtpp)
REVERT: R  239 ARG cc_start: 0.7707 (ttm170) cc_final: 0.7192 (ptp-110)
  outliers start: 25
  outliers final: 10
  residues processed: 147
  average time/residue: 1.5100
  time to fit residues: 235.5096
Evaluate side-chains
  143 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
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   65 THR
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  227 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   62 ASP
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  192 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 118 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 117 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4097 r_free = 0.4097 target = 0.185865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.152774 restraints weight = 21616.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 4.26
r_work: 0.2856 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2834
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2834
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9896  Z= 0.122
  Angle     :  0.538   8.421  13406  Z= 0.287
  Chirality :  0.042   0.173   1512
  Planarity :  0.004   0.044   1683
  Dihedral  :  5.234  45.346   1389
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 10.59 %
    Favored  : 87.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.24), residues: 1209
  helix:  2.52 (0.25), residues: 414
  sheet:  0.85 (0.29), residues: 299
  loop : -0.56 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP R 176 
 HIS   0.003   0.001   HIS R 186 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.024   0.001   TYR A 296 
 ARG   0.003   0.000   ARG S 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04011 (  502)
  hydrogen bonds       : angle       4.66395 ( 1399)
  SS BOND              : bond        0.00435 (    7)
  SS BOND              : angle       1.73239 (   14)
  covalent geometry    : bond        0.00267 ( 9889)
  covalent geometry    : angle       0.53497 (13392)

*********************** 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
  157 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 1.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.7666 (mppt) cc_final: 0.7426 (pptt)
REVERT: B   42 ARG cc_start: 0.7609 (tpt170) cc_final: 0.7295 (tpp-160)
REVERT: B  172 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8184 (tp30)
REVERT: R  239 ARG cc_start: 0.7705 (ttm170) cc_final: 0.7172 (ptp-110)
  outliers start: 21
  outliers final: 8
  residues processed: 147
  average time/residue: 1.4521
  time to fit residues: 227.3620
Evaluate side-chains
  141 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 133
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  229 ARG
Chi-restraints excluded: chain R residue  250 LEU
Chi-restraints excluded: chain R residue  311 TYR
Chi-restraints excluded: chain S residue  162 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 88 optimal weight:    0.8980
   chunk 74 optimal weight:    8.9990
   chunk 33 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 106 optimal weight:    0.7980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4096 r_free = 0.4096 target = 0.185789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.136753 restraints weight = 17964.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.50
r_work: 0.3085 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3008
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3008 r_free = 0.3008    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3008 r_free = 0.3008    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3008
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9896  Z= 0.124
  Angle     :  0.533   7.131  13406  Z= 0.286
  Chirality :  0.042   0.169   1512
  Planarity :  0.004   0.044   1683
  Dihedral  :  5.156  43.923   1389
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 11.53 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.24), residues: 1209
  helix:  2.60 (0.25), residues: 414
  sheet:  0.81 (0.29), residues: 301
  loop : -0.54 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP R 176 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.017   0.001   PHE R 101 
 TYR   0.024   0.001   TYR A 296 
 ARG   0.003   0.000   ARG S 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04005 (  502)
  hydrogen bonds       : angle       4.63071 ( 1399)
  SS BOND              : bond        0.00459 (    7)
  SS BOND              : angle       1.73405 (   14)
  covalent geometry    : bond        0.00276 ( 9889)
  covalent geometry    : angle       0.53059 (13392)

*********************** 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
  157 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7435 (tt0)
REVERT: B   75 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7653 (mm110)
REVERT: R  239 ARG cc_start: 0.7719 (ttm170) cc_final: 0.7229 (ptp-110)
  outliers start: 23
  outliers final: 10
  residues processed: 143
  average time/residue: 1.4540
  time to fit residues: 220.7298
Evaluate side-chains
  145 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 133
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
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  240 MET
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain R residue  227 LEU
Chi-restraints excluded: chain R residue  229 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
Chi-restraints excluded: chain S residue  162 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 96 optimal weight:    0.0170
   chunk 108 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 89 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 75 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.6218

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.186825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.137311 restraints weight = 18305.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.61
r_work: 0.3098 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3009
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3009
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2368

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     :  0.522   7.490  13406  Z= 0.278
  Chirality :  0.041   0.166   1512
  Planarity :  0.004   0.044   1683
  Dihedral  :  5.027  42.759   1389
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 12.19 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.24), residues: 1209
  helix:  2.66 (0.25), residues: 414
  sheet:  0.86 (0.29), residues: 306
  loop : -0.54 (0.26), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP R 176 
 HIS   0.003   0.001   HIS R 186 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.023   0.001   TYR A 296 
 ARG   0.003   0.000   ARG S 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03730 (  502)
  hydrogen bonds       : angle       4.53407 ( 1399)
  SS BOND              : bond        0.00420 (    7)
  SS BOND              : angle       1.65860 (   14)
  covalent geometry    : bond        0.00240 ( 9889)
  covalent geometry    : angle       0.51983 (13392)

*********************** 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
  157 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7457 (tt0)
REVERT: A   51 LYS cc_start: 0.7807 (pptt) cc_final: 0.7602 (mppt)
REVERT: G   20 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8287 (mtpp)
  outliers start: 20
  outliers final: 7
  residues processed: 146
  average time/residue: 1.4111
  time to fit residues: 219.0804
Evaluate side-chains
  139 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
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  112 VAL
Chi-restraints excluded: chain R residue  250 LEU
Chi-restraints excluded: chain R residue  257 LEU
Chi-restraints excluded: chain R residue  311 TYR
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 34 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9980
   chunk 105 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 48 optimal weight:    0.4980
   chunk 43 optimal weight:    0.6980
   chunk 9 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9990
   chunk 108 optimal weight:    0.3980
   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 ** 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 = 0.4087 r_free = 0.4087 target = 0.184931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.131821 restraints weight = 11763.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 1.80
r_work: 0.3182 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3009
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3009
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9896  Z= 0.113
  Angle     :  0.523   7.566  13406  Z= 0.279
  Chirality :  0.041   0.162   1512
  Planarity :  0.004   0.045   1683
  Dihedral  :  4.978  41.972   1389
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.48 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.24), residues: 1209
  helix:  2.66 (0.25), residues: 415
  sheet:  0.93 (0.29), residues: 304
  loop : -0.55 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 176 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.019   0.001   PHE R 101 
 TYR   0.024   0.001   TYR A 296 
 ARG   0.005   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03713 (  502)
  hydrogen bonds       : angle       4.51019 ( 1399)
  SS BOND              : bond        0.00451 (    7)
  SS BOND              : angle       1.68078 (   14)
  covalent geometry    : bond        0.00245 ( 9889)
  covalent geometry    : angle       0.52079 (13392)

*********************** 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
  152 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 1.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7408 (tt0)
REVERT: A   51 LYS cc_start: 0.7732 (pptt) cc_final: 0.7519 (mppt)
REVERT: G   20 LYS cc_start: 0.8561 (mtmt) cc_final: 0.8291 (mtpp)
  outliers start: 18
  outliers final: 8
  residues processed: 142
  average time/residue: 1.5375
  time to fit residues: 232.1625
Evaluate side-chains
  140 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 131
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
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  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain R residue  257 LEU
Chi-restraints excluded: chain R residue  311 TYR
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 98 optimal weight:    7.9990
   chunk 14 optimal weight:    0.0970
   chunk 107 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 29 optimal weight:    0.5980
   chunk 60 optimal weight:   30.0000
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.2980
   chunk 9 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
** B 340 ASN ** 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 = 0.4073 r_free = 0.4073 target = 0.183451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.131843 restraints weight = 16278.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 2.23
r_work: 0.3097 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9896  Z= 0.133
  Angle     :  0.555   8.184  13406  Z= 0.293
  Chirality :  0.042   0.164   1512
  Planarity :  0.004   0.045   1683
  Dihedral  :  5.063  41.892   1389
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.67 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.24), residues: 1209
  helix:  2.60 (0.25), residues: 415
  sheet:  0.91 (0.29), residues: 304
  loop : -0.56 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 176 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.024   0.001   TYR A 296 
 ARG   0.005   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03969 (  502)
  hydrogen bonds       : angle       4.59001 ( 1399)
  SS BOND              : bond        0.00505 (    7)
  SS BOND              : angle       1.76880 (   14)
  covalent geometry    : bond        0.00303 ( 9889)
  covalent geometry    : angle       0.55220 (13392)

*********************** 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: 18
    poor density    : 130
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7569 (tt0)
REVERT: B   75 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7730 (mm110)
REVERT: B  172 GLU cc_start: 0.8293 (tp30) cc_final: 0.8067 (mt-10)
REVERT: G   20 LYS cc_start: 0.8619 (mtmt) cc_final: 0.8343 (mtpp)
REVERT: R  239 ARG cc_start: 0.7707 (ttm170) cc_final: 0.7289 (ptp-110)
REVERT: R  301 TYR cc_start: 0.8425 (m-80) cc_final: 0.8160 (m-80)
  outliers start: 18
  outliers final: 12
  residues processed: 139
  average time/residue: 1.4019
  time to fit residues: 207.2989
Evaluate side-chains
  144 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
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   75 GLN
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  257 LEU
Chi-restraints excluded: chain R residue  311 TYR
Chi-restraints excluded: chain S residue  113 GLN
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  186 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 104 optimal weight:    0.0870
   chunk 41 optimal weight:    0.0030
   chunk 62 optimal weight:    5.9990
   chunk 89 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 107 optimal weight:    0.8980
   chunk 69 optimal weight:    4.9990
   chunk 118 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    0.5972

-------------------------------------------------------------------------------
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 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.185282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.152469 restraints weight = 20342.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 4.30
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3740
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3740 r_free = 0.3740    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3740 r_free = 0.3740    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3740
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9896  Z= 0.109
  Angle     :  0.521   7.829  13406  Z= 0.277
  Chirality :  0.041   0.159   1512
  Planarity :  0.004   0.044   1683
  Dihedral  :  4.946  41.848   1389
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 13.14 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.24), residues: 1209
  helix:  2.68 (0.25), residues: 415
  sheet:  0.92 (0.29), residues: 304
  loop : -0.51 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 176 
 HIS   0.003   0.001   HIS R 186 
 PHE   0.019   0.001   PHE R 101 
 TYR   0.024   0.001   TYR A 296 
 ARG   0.005   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03605 (  502)
  hydrogen bonds       : angle       4.48367 ( 1399)
  SS BOND              : bond        0.00423 (    7)
  SS BOND              : angle       1.63424 (   14)
  covalent geometry    : bond        0.00236 ( 9889)
  covalent geometry    : angle       0.51905 (13392)

********************** 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
  143 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7061 (tt0)
REVERT: R  239 ARG cc_start: 0.7348 (ttm170) cc_final: 0.7076 (ptp-110)
  outliers start: 13
  outliers final: 8
  residues processed: 136
  average time/residue: 1.4177
  time to fit residues: 204.8386
Evaluate side-chains
  137 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
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  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain R residue  257 LEU
Chi-restraints excluded: chain R residue  311 TYR
Chi-restraints excluded: chain S residue  113 GLN
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 103 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0270
   chunk 48 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 29 optimal weight:    0.2980
   overall best weight:    0.5640

-------------------------------------------------------------------------------
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 = 0.4093 r_free = 0.4093 target = 0.185536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.137978 restraints weight = 19885.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.75
r_work: 0.3077 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3000
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    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 = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3000
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.2569

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= 0.108
  Angle     :  0.521   7.832  13406  Z= 0.276
  Chirality :  0.041   0.160   1512
  Planarity :  0.004   0.044   1683
  Dihedral  :  4.891  41.245   1389
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 13.42 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.24), residues: 1209
  helix:  2.70 (0.25), residues: 415
  sheet:  0.93 (0.29), residues: 304
  loop : -0.48 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 176 
 HIS   0.002   0.001   HIS R 186 
 PHE   0.012   0.001   PHE R  83 
 TYR   0.024   0.001   TYR A 296 
 ARG   0.005   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03572 (  502)
  hydrogen bonds       : angle       4.45371 ( 1399)
  SS BOND              : bond        0.00424 (    7)
  SS BOND              : angle       1.65601 (   14)
  covalent geometry    : bond        0.00234 ( 9889)
  covalent geometry    : angle       0.51858 (13392)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9631.78 seconds
wall clock time: 166 minutes 23.02 seconds (9983.02 seconds total)