Starting phenix.real_space_refine
on Wed Mar  4 21:13:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xz5_33525/03_2026/7xz5_33525_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xz5_33525/03_2026/7xz5_33525.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xz5_33525/03_2026/7xz5_33525.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xz5_33525/03_2026/7xz5_33525.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xz5_33525/03_2026/7xz5_33525_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xz5_33525/03_2026/7xz5_33525_neut_trim.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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: 6
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      56      5.16       5
     C    5243      2.51       5
     N    1433      2.21       5
     O    1534      1.98       5
     H    8189      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16456
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 3910
          Classifications: {'peptide': 237}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 230}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "B"
      Number of atoms: 5108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 5108
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 885
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 1909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 1909
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 4609
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 4609
          Classifications: {'peptide': 292}
          Link IDs: {'PTRANS': 9, 'TRANS': 282}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'LSC': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.56, per 1000 atoms: 0.16
  Number of scatterers: 16456
  At special positions: 0
  Unit cell: (100.674, 99.603, 116.739, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      56     16.00
     P       1     15.00
     O    1534      8.00
     N    1433      7.00
     C    5243      6.00
     H    8189      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  78 " - pdb=" SG  CYS R 155 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 251 " - pdb=" SG  CYS R 254 " distance=2.05

  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: 1.42
  Conformation dependent library (CDL) restraints added in 470.7 milliseconds
  

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1970

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      43.3% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 39
      removed outlier: 3.519A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 233 through 239
    Processing helix  chain 'A' and resid 264 through 279
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.985A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 318
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 4.112A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 391
      removed outlier: 4.623A  pdb=" N   ARG A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.824A  pdb=" N   ALA G  12 " --> pdb=" O   SER G   8 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 2 through 36
      removed outlier: 4.035A  pdb=" N   ILE R  10 " --> pdb=" O   SER R   6 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 39 through 61
      removed outlier: 3.995A  pdb=" N   PHE R  43 " --> pdb=" O   VAL R  39 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LEU R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 61 through 66
      removed outlier: 3.500A  pdb=" N   GLN R  65 " --> pdb=" O   LEU R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 73 through 109
      removed outlier: 4.783A  pdb=" N   LEU R  77 " --> pdb=" O   THR R  73 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ARG R  81 " --> pdb=" O   LEU R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 109 through 117
      removed outlier: 3.550A  pdb=" N   LEU R 114 " --> pdb=" O   PRO R 110 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 118 through 143
      Proline residue:  R 140  - end of helix
    Processing helix  chain 'R' and resid 162 through 172
      removed outlier: 4.073A  pdb=" N   VAL R 166 " --> pdb=" O   HIS R 162 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 173 through 210
    Processing helix  chain 'R' and resid 221 through 251
      removed outlier: 3.932A  pdb=" N   VAL R 229 " --> pdb=" O   ARG R 225 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU R 236 " --> pdb=" O   GLY R 232 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   TRP R 238 " --> pdb=" O   PHE R 234 " (cutoff:3.500A)
      Proline residue:  R 240  - end of helix
    Processing helix  chain 'R' and resid 256 through 261
      removed outlier: 3.789A  pdb=" N   GLU R 261 " --> pdb=" O   TYR R 257 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 263 through 279
      removed outlier: 3.774A  pdb=" N   LEU R 267 " --> pdb=" O   TYR R 263 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   GLY R 268 " --> pdb=" O   LEU R 264 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ASN R 271 " --> pdb=" O   LEU R 267 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   SER R 272 " --> pdb=" O   GLY R 268 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   LEU R 273 " --> pdb=" O   VAL R 269 " (cutoff:3.500A)
      Proline residue:  R 276  - end of helix
    Processing helix  chain 'R' and resid 283 through 299
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 9.719A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.432A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.614A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.699A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.473A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.107A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.376A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 4.091A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   GLY B 202 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.460A  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: 6.356A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.923A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 7.046A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    442 hydrogen bonds defined for protein.
    1251 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: 3.50

  Time building geometry restraints manager: 1.96 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6948
        1.03 -     1.23: 1279
        1.23 -     1.42: 3757
        1.42 -     1.62: 4552
        1.62 -     1.82: 81
  Bond restraints: 16617
  Sorted by residual:
  bond pdb=" ND1 HIS R 162 "
       pdb=" CE1 HIS R 162 "
    ideal  model  delta    sigma   weight residual
    1.321  1.233  0.088 1.00e-02 1.00e+04 7.67e+01
  bond pdb=" CE1 HIS R 164 "
       pdb=" NE2 HIS R 164 "
    ideal  model  delta    sigma   weight residual
    1.321  1.233  0.088 1.00e-02 1.00e+04 7.66e+01
  bond pdb=" CD2 HIS R 164 "
       pdb=" NE2 HIS R 164 "
    ideal  model  delta    sigma   weight residual
    1.374  1.287  0.087 1.10e-02 8.26e+03 6.29e+01
  bond pdb=" CZ  ARG R 103 "
       pdb=" NH2 ARG R 103 "
    ideal  model  delta    sigma   weight residual
    1.330  1.230  0.100 1.30e-02 5.92e+03 5.86e+01
  bond pdb=" CZ  ARG R  81 "
       pdb=" NH2 ARG R  81 "
    ideal  model  delta    sigma   weight residual
    1.330  1.231  0.099 1.30e-02 5.92e+03 5.82e+01
  ... (remaining 16612 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.05: 29118
        5.05 -    10.11: 769
       10.11 -    15.16: 8
       15.16 -    20.22: 1
       20.22 -    25.27: 1
  Bond angle restraints: 29897
  Sorted by residual:
  angle pdb=" N   PRO N 100 "
        pdb=" CA  PRO N 100 "
        pdb=" C   PRO N 100 "
      ideal   model   delta    sigma   weight residual
     113.78  127.83  -14.05 1.62e+00 3.81e-01 7.52e+01
  angle pdb=" C21 LSC R 401 "
        pdb=" C22 LSC R 401 "
        pdb=" O23 LSC R 401 "
      ideal   model   delta    sigma   weight residual
     108.44  133.71  -25.27 3.00e+00 1.11e-01 7.10e+01
  angle pdb=" C   LEU R 267 "
        pdb=" N   GLY R 268 "
        pdb=" CA  GLY R 268 "
      ideal   model   delta    sigma   weight residual
     119.94  128.10   -8.16 1.11e+00 8.12e-01 5.41e+01
  angle pdb=" CA  PHE R 181 "
        pdb=" CB  PHE R 181 "
        pdb=" CG  PHE R 181 "
      ideal   model   delta    sigma   weight residual
     113.80  121.13   -7.33 1.00e+00 1.00e+00 5.37e+01
  angle pdb=" C   ALA R 159 "
        pdb=" N   VAL R 160 "
        pdb=" CA  VAL R 160 "
      ideal   model   delta    sigma   weight residual
     121.97  134.89  -12.92 1.80e+00 3.09e-01 5.15e+01
  ... (remaining 29892 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.91: 7516
       27.91 -    55.82: 271
       55.82 -    83.73: 49
       83.73 -   111.64: 6
      111.64 -   139.55: 2
  Dihedral angle restraints: 7844
    sinusoidal: 4233
      harmonic: 3611
  Sorted by residual:
  dihedral pdb=" C   TYR R 185 "
           pdb=" N   TYR R 185 "
           pdb=" CA  TYR R 185 "
           pdb=" CB  TYR R 185 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.73   12.13     0      2.50e+00 1.60e-01 2.35e+01
  dihedral pdb=" C   PHE R 138 "
           pdb=" N   PHE R 138 "
           pdb=" CA  PHE R 138 "
           pdb=" CB  PHE R 138 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.28   11.68     0      2.50e+00 1.60e-01 2.18e+01
  dihedral pdb=" C   GLU R 261 "
           pdb=" N   GLU R 261 "
           pdb=" CA  GLU R 261 "
           pdb=" CB  GLU R 261 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.20   11.60     0      2.50e+00 1.60e-01 2.15e+01
  ... (remaining 7841 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.140: 1100
       0.140 -    0.281: 10
       0.281 -    0.421: 16
       0.421 -    0.562: 102
       0.562 -    0.702: 61
  Chirality restraints: 1289
  Sorted by residual:
  chirality pdb=" CG  LEU R 139 "
            pdb=" CB  LEU R 139 "
            pdb=" CD1 LEU R 139 "
            pdb=" CD2 LEU R 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.89   -0.70 2.00e-01 2.50e+01 1.23e+01
  chirality pdb=" CG  LEU R 167 "
            pdb=" CB  LEU R 167 "
            pdb=" CD1 LEU R 167 "
            pdb=" CD2 LEU R 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.89   -0.70 2.00e-01 2.50e+01 1.21e+01
  chirality pdb=" CG  LEU R  77 "
            pdb=" CB  LEU R  77 "
            pdb=" CD1 LEU R  77 "
            pdb=" CD2 LEU R  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.89   -0.70 2.00e-01 2.50e+01 1.21e+01
  ... (remaining 1286 not shown)

  Planarity restraints: 2465
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN R  65 "   -0.097 2.00e-02 2.50e+03   1.06e-01 1.67e+02
        pdb=" CD  GLN R  65 "    0.007 2.00e-02 2.50e+03
        pdb=" OE1 GLN R  65 "    0.093 2.00e-02 2.50e+03
        pdb=" NE2 GLN R  65 "    0.001 2.00e-02 2.50e+03
        pdb="HE21 GLN R  65 "    0.155 2.00e-02 2.50e+03
        pdb="HE22 GLN R  65 "   -0.158 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 265 "   -0.090 2.00e-02 2.50e+03   3.75e-02 5.63e+01
        pdb=" CG  TRP R 265 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 265 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 265 "    0.020 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 265 "    0.045 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 265 "    0.019 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 265 "    0.032 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 265 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 265 "    0.025 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 265 "   -0.002 2.00e-02 2.50e+03
        pdb=" HD1 TRP R 265 "   -0.013 2.00e-02 2.50e+03
        pdb=" HE1 TRP R 265 "    0.048 2.00e-02 2.50e+03
        pdb=" HE3 TRP R 265 "    0.027 2.00e-02 2.50e+03
        pdb=" HZ2 TRP R 265 "   -0.073 2.00e-02 2.50e+03
        pdb=" HZ3 TRP R 265 "    0.005 2.00e-02 2.50e+03
        pdb=" HH2 TRP R 265 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 234 "    0.038 2.00e-02 2.50e+03   4.13e-02 5.13e+01
        pdb=" CG  PHE R 234 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 234 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 234 "    0.019 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 234 "    0.022 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 234 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 234 "    0.029 2.00e-02 2.50e+03
        pdb=" HD1 PHE R 234 "   -0.088 2.00e-02 2.50e+03
        pdb=" HD2 PHE R 234 "    0.015 2.00e-02 2.50e+03
        pdb=" HE1 PHE R 234 "    0.026 2.00e-02 2.50e+03
        pdb=" HE2 PHE R 234 "   -0.081 2.00e-02 2.50e+03
        pdb=" HZ  PHE R 234 "    0.031 2.00e-02 2.50e+03
  ... (remaining 2462 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 870
        2.19 -     2.79: 32990
        2.79 -     3.40: 45187
        3.40 -     4.00: 59077
        4.00 -     4.60: 91879
  Nonbonded interactions: 230003
  Sorted by model distance:
  nonbonded pdb=" H   PHE B 235 "
            pdb=" O   ALA B 240 "
     model   vdw
     1.590 2.450
  nonbonded pdb=" OD1 ASP B 153 "
            pdb=" H   ASN B 155 "
     model   vdw
     1.606 2.450
  nonbonded pdb=" H   GLN R 148 "
            pdb=" O   VAL R 160 "
     model   vdw
     1.624 2.450
  nonbonded pdb=" HG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     1.634 2.450
  nonbonded pdb=" O   ALA R 235 "
            pdb=" HG1 THR R 239 "
     model   vdw
     1.634 2.450
  ... (remaining 229998 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.050
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     15.240
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
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      :  0.020   0.129   8432  Z= 1.037
  Angle     :  1.554  25.271  11409  Z= 1.011
  Chirality :  0.210   0.702   1289
  Planarity :  0.005   0.066   1450
  Dihedral  : 14.345 139.551   3062
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  8.22 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.26), residues: 1036
  helix:  1.59 (0.25), residues: 422
  sheet:  1.31 (0.37), residues: 202
  loop :  0.04 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 197 
 TYR   0.054   0.004   TYR R 257 
 PHE   0.036   0.004   PHE R 234 
 TRP   0.057   0.003   TRP R 265 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.01971 ( 8428)
  covalent geometry    : angle       1.55263 (11401)
  SS BOND              : bond        0.01048 (    4)
  SS BOND              : angle       2.73873 (    8)
  hydrogen bonds       : bond        0.18204 (  442)
  hydrogen bonds       : angle       6.10553 ( 1251)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  171 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   59 ASN cc_start: 0.7478 (t0) cc_final: 0.6865 (t0)
REVERT: R  263 TYR cc_start: 0.6750 (m-80) cc_final: 0.6414 (m-10)
REVERT: R  298 LYS cc_start: 0.6378 (ttmm) cc_final: 0.5947 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.2665
  time to fit residues: 58.8683
Evaluate side-chains
  134 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   overall best weight:    2.8986

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.149246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.110753 restraints weight = 27822.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 2.12
r_work: 0.3123 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8432  Z= 0.220
  Angle     :  0.591   6.700  11409  Z= 0.323
  Chirality :  0.042   0.139   1289
  Planarity :  0.005   0.047   1450
  Dihedral  :  7.540  95.906   1169
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  6.06 %
    Favored  : 92.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.68 (0.27), residues: 1036
  helix:  2.30 (0.25), residues: 416
  sheet:  0.78 (0.37), residues: 204
  loop :  0.12 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 385 
 TYR   0.017   0.002   TYR A  37 
 PHE   0.027   0.002   PHE N 108 
 TRP   0.014   0.002   TRP B 297 
 HIS   0.012   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 ( 8428)
  covalent geometry    : angle       0.58699 (11401)
  SS BOND              : bond        0.00336 (    4)
  SS BOND              : angle       2.65952 (    8)
  hydrogen bonds       : bond        0.04724 (  442)
  hydrogen bonds       : angle       4.77589 ( 1251)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  153 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 144
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 TYR cc_start: 0.5994 (p90) cc_final: 0.5754 (p90)
REVERT: G   21 MET cc_start: 0.7877 (mtp) cc_final: 0.7586 (mtm)
REVERT: R  298 LYS cc_start: 0.6291 (ttmm) cc_final: 0.5876 (mptt)
  outliers start: 9
  outliers final: 9
  residues processed: 152
  average time/residue: 0.2370
  time to fit residues: 47.2933
Evaluate side-chains
  141 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain R residue   23 THR
Chi-restraints excluded: chain R residue  121 VAL
Chi-restraints excluded: chain R residue  166 VAL
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  274 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 79 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:   10.0000
   chunk 13 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 53 optimal weight:    7.9990
   chunk 67 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
N  35 ASN
R  65 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.152049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.113893 restraints weight = 28061.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.12
r_work: 0.3190 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8432  Z= 0.103
  Angle     :  0.466   5.101  11409  Z= 0.250
  Chirality :  0.038   0.137   1289
  Planarity :  0.003   0.039   1450
  Dihedral  :  6.756  83.995   1169
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  7.52 %
    Favored  : 91.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.92 (0.27), residues: 1036
  helix:  2.71 (0.25), residues: 410
  sheet:  0.80 (0.37), residues: 203
  loop :  0.11 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 228 
 TYR   0.009   0.001   TYR R 134 
 PHE   0.011   0.001   PHE N 108 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 8428)
  covalent geometry    : angle       0.46295 (11401)
  SS BOND              : bond        0.00231 (    4)
  SS BOND              : angle       2.12225 (    8)
  hydrogen bonds       : bond        0.04128 (  442)
  hydrogen bonds       : angle       4.37529 ( 1251)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  140 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   21 MET cc_start: 0.7895 (mtp) cc_final: 0.7608 (mtm)
REVERT: R  225 ARG cc_start: 0.7662 (ttt180) cc_final: 0.7455 (ttp80)
REVERT: R  298 LYS cc_start: 0.6238 (ttmm) cc_final: 0.5837 (mptt)
  outliers start: 10
  outliers final: 9
  residues processed: 138
  average time/residue: 0.2524
  time to fit residues: 44.9680
Evaluate side-chains
  135 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 126
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain R residue   23 THR
Chi-restraints excluded: chain R residue  266 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 94 optimal weight:    0.9980
   chunk 85 optimal weight:    6.9990
   chunk 84 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.149016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.110450 restraints weight = 28033.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.12
r_work: 0.3130 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8432  Z= 0.162
  Angle     :  0.500   6.010  11409  Z= 0.271
  Chirality :  0.039   0.132   1289
  Planarity :  0.004   0.040   1450
  Dihedral  :  6.507  78.642   1169
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  8.98 %
    Favored  : 89.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.27), residues: 1036
  helix:  2.48 (0.25), residues: 416
  sheet:  0.65 (0.37), residues: 204
  loop :  0.00 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 283 
 TYR   0.012   0.001   TYR A  37 
 PHE   0.019   0.002   PHE N 108 
 TRP   0.012   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 8428)
  covalent geometry    : angle       0.49683 (11401)
  SS BOND              : bond        0.00208 (    4)
  SS BOND              : angle       2.15518 (    8)
  hydrogen bonds       : bond        0.04288 (  442)
  hydrogen bonds       : angle       4.43312 ( 1251)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  142 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8164 (mmm-85) cc_final: 0.7736 (mtt-85)
REVERT: G   21 MET cc_start: 0.7932 (mtp) cc_final: 0.7630 (mtm)
REVERT: R  298 LYS cc_start: 0.6428 (ttmm) cc_final: 0.6066 (mptt)
  outliers start: 11
  outliers final: 7
  residues processed: 141
  average time/residue: 0.2642
  time to fit residues: 48.0255
Evaluate side-chains
  135 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 128
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   23 THR
Chi-restraints excluded: chain R residue  265 TRP
Chi-restraints excluded: chain R residue  266 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 101 optimal weight:    7.9990
   chunk 77 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 99 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 8 optimal weight:    0.4980
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.148747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.110209 restraints weight = 27912.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.11
r_work: 0.3103 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8432  Z= 0.141
  Angle     :  0.486   5.314  11409  Z= 0.263
  Chirality :  0.039   0.133   1289
  Planarity :  0.004   0.039   1450
  Dihedral  :  6.265  75.648   1169
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  9.99 %
    Favored  : 88.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.62 (0.27), residues: 1036
  helix:  2.45 (0.25), residues: 416
  sheet:  0.70 (0.37), residues: 198
  loop : -0.10 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 103 
 TYR   0.011   0.001   TYR A  37 
 PHE   0.017   0.001   PHE N 108 
 TRP   0.011   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8428)
  covalent geometry    : angle       0.48228 (11401)
  SS BOND              : bond        0.00199 (    4)
  SS BOND              : angle       2.21255 (    8)
  hydrogen bonds       : bond        0.04170 (  442)
  hydrogen bonds       : angle       4.33738 ( 1251)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  141 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8172 (mmm-85) cc_final: 0.7553 (mtm-85)
REVERT: G   21 MET cc_start: 0.7892 (mtp) cc_final: 0.7587 (mtm)
REVERT: R  225 ARG cc_start: 0.7879 (ttp80) cc_final: 0.7289 (ttp-110)
  outliers start: 12
  outliers final: 10
  residues processed: 140
  average time/residue: 0.2733
  time to fit residues: 49.3147
Evaluate side-chains
  136 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue   23 THR
Chi-restraints excluded: chain R residue  121 VAL
Chi-restraints excluded: chain R residue  125 CYS
Chi-restraints excluded: chain R residue  265 TRP
Chi-restraints excluded: chain R residue  266 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 100 optimal weight:    0.1980
   chunk 54 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 24 optimal weight:    8.9990
   chunk 76 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   overall best weight:    2.0388

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.147967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.109300 restraints weight = 28059.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 2.11
r_work: 0.3119 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8432  Z= 0.153
  Angle     :  0.494   6.281  11409  Z= 0.267
  Chirality :  0.039   0.134   1289
  Planarity :  0.004   0.039   1450
  Dihedral  :  6.170  77.718   1169
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 10.66 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.27), residues: 1036
  helix:  2.38 (0.25), residues: 416
  sheet:  0.60 (0.37), residues: 200
  loop : -0.19 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 228 
 TYR   0.012   0.001   TYR R 185 
 PHE   0.019   0.001   PHE N 108 
 TRP   0.013   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8428)
  covalent geometry    : angle       0.49062 (11401)
  SS BOND              : bond        0.00210 (    4)
  SS BOND              : angle       2.34418 (    8)
  hydrogen bonds       : bond        0.04215 (  442)
  hydrogen bonds       : angle       4.34525 ( 1251)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  138 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8189 (mmm-85) cc_final: 0.7489 (mtm-85)
REVERT: A  248 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8491 (p)
REVERT: G   21 MET cc_start: 0.7857 (mtp) cc_final: 0.7557 (mtm)
REVERT: R  225 ARG cc_start: 0.7886 (ttp80) cc_final: 0.7271 (ttp-110)
  outliers start: 13
  outliers final: 11
  residues processed: 137
  average time/residue: 0.2663
  time to fit residues: 47.2095
Evaluate side-chains
  136 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue   23 THR
Chi-restraints excluded: chain R residue  121 VAL
Chi-restraints excluded: chain R residue  125 CYS
Chi-restraints excluded: chain R residue  265 TRP
Chi-restraints excluded: chain R residue  266 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 101 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0980
   chunk 3 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 87 optimal weight:    0.0980
   chunk 71 optimal weight:    0.4980
   chunk 66 optimal weight:    0.0970
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.151023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.112739 restraints weight = 27939.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.11
r_work: 0.3160 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.2948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8432  Z= 0.089
  Angle     :  0.443   4.397  11409  Z= 0.236
  Chirality :  0.038   0.132   1289
  Planarity :  0.003   0.037   1450
  Dihedral  :  5.896  80.515   1169
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 11.90 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.27), residues: 1036
  helix:  2.68 (0.25), residues: 416
  sheet:  0.64 (0.37), residues: 198
  loop : -0.17 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 228 
 TYR   0.009   0.001   TYR A  37 
 PHE   0.009   0.001   PHE R 181 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.002   0.000   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 ( 8428)
  covalent geometry    : angle       0.44026 (11401)
  SS BOND              : bond        0.00406 (    4)
  SS BOND              : angle       1.97171 (    8)
  hydrogen bonds       : bond        0.03657 (  442)
  hydrogen bonds       : angle       4.04199 ( 1251)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  142 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 135
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASN cc_start: 0.7908 (t0) cc_final: 0.7558 (t0)
REVERT: A   20 ARG cc_start: 0.8212 (mmm-85) cc_final: 0.7554 (mtm-85)
REVERT: B  188 MET cc_start: 0.8647 (mmm) cc_final: 0.8441 (mmm)
REVERT: R  225 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7269 (ttp-110)
  outliers start: 7
  outliers final: 5
  residues processed: 142
  average time/residue: 0.2734
  time to fit residues: 49.5714
Evaluate side-chains
  136 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 131
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue  265 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 8 optimal weight:    0.2980
   chunk 95 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 94 optimal weight:    0.9990
   chunk 59 optimal weight:    6.9990
   overall best weight:    2.2588

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.147697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.108850 restraints weight = 28240.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.14
r_work: 0.3104 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.3174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8432  Z= 0.169
  Angle     :  0.509   6.080  11409  Z= 0.273
  Chirality :  0.040   0.133   1289
  Planarity :  0.004   0.042   1450
  Dihedral  :  6.068  75.774   1169
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 12.46 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.27), residues: 1036
  helix:  2.43 (0.25), residues: 416
  sheet:  0.57 (0.36), residues: 203
  loop : -0.21 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 232 
 TYR   0.013   0.001   TYR R 185 
 PHE   0.024   0.002   PHE N 108 
 TRP   0.013   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 8428)
  covalent geometry    : angle       0.50526 (11401)
  SS BOND              : bond        0.00214 (    4)
  SS BOND              : angle       2.50631 (    8)
  hydrogen bonds       : bond        0.04184 (  442)
  hydrogen bonds       : angle       4.29902 ( 1251)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  138 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 129
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8239 (mmm-85) cc_final: 0.7585 (mtm-85)
  outliers start: 9
  outliers final: 8
  residues processed: 138
  average time/residue: 0.2571
  time to fit residues: 45.5891
Evaluate side-chains
  137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue  265 TRP
Chi-restraints excluded: chain R residue  266 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 96 optimal weight:    0.6980
   chunk 80 optimal weight:    4.9990
   chunk 48 optimal weight:    4.9990
   chunk 78 optimal weight:    6.9990
   chunk 42 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 97 optimal weight:    8.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.147350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.108504 restraints weight = 28054.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 2.13
r_work: 0.3095 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8432  Z= 0.175
  Angle     :  0.519   6.113  11409  Z= 0.280
  Chirality :  0.040   0.138   1289
  Planarity :  0.004   0.046   1450
  Dihedral  :  6.122  72.002   1169
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 12.46 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.27 (0.27), residues: 1036
  helix:  2.17 (0.25), residues: 422
  sheet:  0.39 (0.36), residues: 210
  loop : -0.28 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 103 
 TYR   0.014   0.001   TYR R 185 
 PHE   0.021   0.002   PHE N 108 
 TRP   0.013   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 8428)
  covalent geometry    : angle       0.51518 (11401)
  SS BOND              : bond        0.00212 (    4)
  SS BOND              : angle       2.43890 (    8)
  hydrogen bonds       : bond        0.04325 (  442)
  hydrogen bonds       : angle       4.34454 ( 1251)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8243 (mmm-85) cc_final: 0.7582 (mtm-85)
REVERT: A  248 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8460 (p)
  outliers start: 10
  outliers final: 9
  residues processed: 137
  average time/residue: 0.2627
  time to fit residues: 46.1510
Evaluate side-chains
  136 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue  265 TRP
Chi-restraints excluded: chain R residue  266 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 83 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   overall best weight:    1.0382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.149296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.110765 restraints weight = 27955.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 2.11
r_work: 0.3149 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.3250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8432  Z= 0.106
  Angle     :  0.471   5.473  11409  Z= 0.251
  Chirality :  0.038   0.132   1289
  Planarity :  0.003   0.038   1450
  Dihedral  :  5.898  76.626   1169
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 12.68 %
    Favored  : 86.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.27), residues: 1036
  helix:  2.43 (0.25), residues: 422
  sheet:  0.53 (0.36), residues: 202
  loop : -0.27 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 228 
 TYR   0.010   0.001   TYR R 185 
 PHE   0.012   0.001   PHE N 108 
 TRP   0.010   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 8428)
  covalent geometry    : angle       0.46774 (11401)
  SS BOND              : bond        0.00222 (    4)
  SS BOND              : angle       2.08803 (    8)
  hydrogen bonds       : bond        0.03869 (  442)
  hydrogen bonds       : angle       4.11783 ( 1251)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  366 is missing expected H atoms. Skipping.
Evaluate side-chains
  139 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 130
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8171 (mmm-85) cc_final: 0.7484 (mtm-85)
REVERT: A  248 VAL cc_start: 0.8785 (OUTLIER) cc_final: 0.8465 (p)
REVERT: B  188 MET cc_start: 0.8722 (mmm) cc_final: 0.8500 (mmm)
  outliers start: 9
  outliers final: 7
  residues processed: 139
  average time/residue: 0.2873
  time to fit residues: 50.8984
Evaluate side-chains
  137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue  265 TRP
Chi-restraints excluded: chain R residue  266 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 97 optimal weight:    0.1980
   chunk 98 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 19 optimal weight:    0.8980
   chunk 25 optimal weight:    9.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.148695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.110251 restraints weight = 27925.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.10
r_work: 0.3141 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.3294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8432  Z= 0.121
  Angle     :  0.477   5.105  11409  Z= 0.255
  Chirality :  0.039   0.131   1289
  Planarity :  0.003   0.038   1450
  Dihedral  :  5.874  75.576   1169
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 12.57 %
    Favored  : 86.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.27), residues: 1036
  helix:  2.42 (0.25), residues: 422
  sheet:  0.48 (0.36), residues: 203
  loop : -0.28 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 228 
 TYR   0.011   0.001   TYR A  37 
 PHE   0.015   0.001   PHE N 108 
 TRP   0.011   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8428)
  covalent geometry    : angle       0.47337 (11401)
  SS BOND              : bond        0.00216 (    4)
  SS BOND              : angle       2.15565 (    8)
  hydrogen bonds       : bond        0.03906 (  442)
  hydrogen bonds       : angle       4.13488 ( 1251)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4689.38 seconds
wall clock time: 79 minutes 59.37 seconds (4799.37 seconds total)