Starting phenix.real_space_refine
on Tue Mar  3 21:04:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7trk_26099/03_2026/7trk_26099.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7trk_26099/03_2026/7trk_26099.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7trk_26099/03_2026/7trk_26099.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7trk_26099/03_2026/7trk_26099.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7trk_26099/03_2026/7trk_26099.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7trk_26099/03_2026/7trk_26099.cif"
  }
  resolution = 2.8
  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=   0.002
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      63      5.16       5
     C    5523      2.51       5
     N    1457      2.21       5
     O    1616      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 8659
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2106
          Classifications: {'peptide': 271}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 10, 'TRANS': 260}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 23
    Chain: "B"
      Number of atoms: 2579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2579
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "G"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 418
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "H"
      Number of atoms: 1778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1778
          Classifications: {'peptide': 235}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 224}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "A"
      Number of atoms: 1764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1764
          Classifications: {'peptide': 225}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 40
          Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 38
    Chain: "R"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'IXO': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.97, per 1000 atoms: 0.23
  Number of scatterers: 8659
  At special positions: 0
  Unit cell: (92.96, 118.69, 122.84, 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      63     16.00
     O    1616      8.00
     N    1457      7.00
     C    5523      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 426 " - pdb=" SG  CYS R 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 347.4 milliseconds
  

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2112

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 13 sheets defined
      38.2% alpha, 23.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'R' and resid 32 through 60
      removed outlier: 3.689A  pdb=" N   ASN R  60 " --> pdb=" O   SER R  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 65 through 96
      removed outlier: 4.148A  pdb=" N   PHE R  70 " --> pdb=" O   VAL R  66 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU R  71 " --> pdb=" O   ASN R  67 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   MET R  86 " --> pdb=" O   GLY R  82 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   ASN R  87 " --> pdb=" O   ALA R  83 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU R  88 " --> pdb=" O   PHE R  84 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 101 through 136
      removed outlier: 3.540A  pdb=" N   CYS R 105 " --> pdb=" O   GLY R 101 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ASP R 106 " --> pdb=" O   ALA R 102 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   LEU R 107 " --> pdb=" O   VAL R 103 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 138 through 144
      removed outlier: 4.522A  pdb=" N   ALA R 142 " --> pdb=" O   LEU R 138 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 145 through 176
      Proline residue:  R 166  - end of helix
      removed outlier: 5.203A  pdb=" N   GLN R 172 " --> pdb=" O   ILE R 168 " (cutoff:3.500A)
      removed outlier: 5.068A  pdb=" N   PHE R 173 " --> pdb=" O   LEU R 169 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 187 through 191
      removed outlier: 3.949A  pdb=" N   LEU R 190 " --> pdb=" O   ILE R 187 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   SER R 191 " --> pdb=" O   GLN R 188 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 187 through 191'
    Processing helix  chain 'R' and resid 192 through 204
      removed outlier: 3.544A  pdb=" N   THR R 196 " --> pdb=" O   ASN R 192 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 204 through 221
    Processing helix  chain 'R' and resid 393 through 424
      removed outlier: 3.814A  pdb=" N   PHE R 409 " --> pdb=" O   ILE R 405 " (cutoff:3.500A)
      Proline residue:  R 415  - end of helix
    Processing helix  chain 'R' and resid 431 through 454
      removed outlier: 4.280A  pdb=" N   SER R 446 " --> pdb=" O   CYS R 442 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   THR R 447 " --> pdb=" O   TYR R 443 " (cutoff:3.500A)
      Proline residue:  R 450  - end of helix
    Processing helix  chain 'R' and resid 457 through 466
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.588A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 35
    Processing helix  chain 'G' and resid 8 through 23
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 53 through 56
      removed outlier: 4.215A  pdb=" N   GLY H  56 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 53 through 56'
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.588A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.668A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.414A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.903A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.896A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 331 through 351
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.656A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.520A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.876A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.084A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.811A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.924A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.155A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 192
      removed outlier: 6.601A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.570A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.675A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12
      removed outlier: 5.988A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 5.730A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.056A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12
      removed outlier: 5.988A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 141
      removed outlier: 3.662A  pdb=" N   ALA H 211 " --> pdb=" O   SER H 208 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148
      removed outlier: 3.909A  pdb=" N   GLU H 246 " --> pdb=" O   VAL H 147 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   TYR H 190 " --> pdb=" O   LEU H 174 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   TRP H 176 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.224A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)

    451 hydrogen bonds defined for protein.
    1284 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.49

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1402
        1.32 -     1.44: 2469
        1.44 -     1.57: 4880
        1.57 -     1.69: 1
        1.69 -     1.81: 91
  Bond restraints: 8843
  Sorted by residual:
  bond pdb=" C10 IXO R 501 "
       pdb=" N11 IXO R 501 "
    ideal  model  delta    sigma   weight residual
    1.270  1.469 -0.199 2.00e-02 2.50e+03 9.91e+01
  bond pdb=" C10 IXO R 501 "
       pdb=" C14 IXO R 501 "
    ideal  model  delta    sigma   weight residual
    1.492  1.345  0.147 2.00e-02 2.50e+03 5.41e+01
  bond pdb=" C13 IXO R 501 "
       pdb=" O12 IXO R 501 "
    ideal  model  delta    sigma   weight residual
    1.439  1.542 -0.103 2.00e-02 2.50e+03 2.67e+01
  bond pdb=" C10 IXO R 501 "
       pdb=" O09 IXO R 501 "
    ideal  model  delta    sigma   weight residual
    1.325  1.406 -0.081 2.00e-02 2.50e+03 1.64e+01
  bond pdb=" C07 IXO R 501 "
       pdb=" C08 IXO R 501 "
    ideal  model  delta    sigma   weight residual
    1.454  1.534 -0.080 2.00e-02 2.50e+03 1.61e+01
  ... (remaining 8838 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 11309
        1.73 -     3.47: 598
        3.47 -     5.20: 82
        5.20 -     6.94: 22
        6.94 -     8.67: 5
  Bond angle restraints: 12016
  Sorted by residual:
  angle pdb=" C   ASP B 333 "
        pdb=" N   SER B 334 "
        pdb=" CA  SER B 334 "
      ideal   model   delta    sigma   weight residual
     123.93  129.45   -5.52 1.54e+00 4.22e-01 1.28e+01
  angle pdb=" C   ARG H 191 "
        pdb=" N   MET H 192 "
        pdb=" CA  MET H 192 "
      ideal   model   delta    sigma   weight residual
     121.54  128.34   -6.80 1.91e+00 2.74e-01 1.27e+01
  angle pdb=" C   TYR R  92 "
        pdb=" N   ILE R  93 "
        pdb=" CA  ILE R  93 "
      ideal   model   delta    sigma   weight residual
     121.35  115.87    5.48 1.58e+00 4.01e-01 1.20e+01
  angle pdb=" C   ASP H 201 "
        pdb=" N   ARG H 202 "
        pdb=" CA  ARG H 202 "
      ideal   model   delta    sigma   weight residual
     120.38  125.08   -4.70 1.46e+00 4.69e-01 1.04e+01
  angle pdb=" N   SER R 191 "
        pdb=" CA  SER R 191 "
        pdb=" C   SER R 191 "
      ideal   model   delta    sigma   weight residual
     112.45  108.07    4.38 1.39e+00 5.18e-01 9.95e+00
  ... (remaining 12011 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.04: 4999
       21.04 -    42.08: 182
       42.08 -    63.12: 25
       63.12 -    84.16: 5
       84.16 -   105.21: 1
  Dihedral angle restraints: 5212
    sinusoidal: 1940
      harmonic: 3272
  Sorted by residual:
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.06   19.94     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" CA  GLN B 259 "
           pdb=" C   GLN B 259 "
           pdb=" N   GLU B 260 "
           pdb=" CA  GLU B 260 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.34   18.66     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" C05 IXO R 501 "
           pdb=" C06 IXO R 501 "
           pdb=" C07 IXO R 501 "
           pdb=" C08 IXO R 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -178.63  -73.42 -105.21     1      3.00e+01 1.11e-03 1.35e+01
  ... (remaining 5209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1091
       0.065 -    0.131: 245
       0.131 -    0.196: 44
       0.196 -    0.261: 5
       0.261 -    0.327: 3
  Chirality restraints: 1388
  Sorted by residual:
  chirality pdb=" CB  VAL B  71 "
            pdb=" CA  VAL B  71 "
            pdb=" CG1 VAL B  71 "
            pdb=" CG2 VAL B  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" CB  ILE R  94 "
            pdb=" CA  ILE R  94 "
            pdb=" CG1 ILE R  94 "
            pdb=" CG2 ILE R  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" CA  PHE R 189 "
            pdb=" N   PHE R 189 "
            pdb=" C   PHE R 189 "
            pdb=" CB  PHE R 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.75e+00
  ... (remaining 1385 not shown)

  Planarity restraints: 1511
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 196 "    0.014 2.00e-02 2.50e+03   2.74e-02 7.50e+00
        pdb=" C   THR R 196 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   THR R 196 "    0.018 2.00e-02 2.50e+03
        pdb=" N   PHE R 197 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.044 5.00e-02 4.00e+02   6.67e-02 7.12e+00
        pdb=" N   PRO B 236 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 189 "    0.025 2.00e-02 2.50e+03   1.93e-02 6.54e+00
        pdb=" CG  PHE R 189 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 189 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 189 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 189 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 189 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 189 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1508 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1839
        2.78 -     3.31: 7711
        3.31 -     3.84: 14682
        3.84 -     4.37: 17795
        4.37 -     4.90: 30654
  Nonbonded interactions: 72681
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OD2 ASP R 112 "
            pdb=" OH  TYR R 443 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OH  TYR H 175 "
            pdb=" OE2 GLU A   8 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   GLU R 395 "
            pdb=" OG1 THR R 399 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OG  SER H 161 "
            pdb=" O   LYS H 163 "
     model   vdw
     2.306 3.040
  ... (remaining 72676 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:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.980
  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:6.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
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   0.199   8847  Z= 0.296
  Angle     :  0.888   8.674  12024  Z= 0.511
  Chirality :  0.058   0.327   1388
  Planarity :  0.007   0.067   1511
  Dihedral  : 11.327 105.205   3088
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 2.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.52 %
    Favored  : 98.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.00 (0.23), residues: 1110
  helix: -0.71 (0.24), residues: 395
  sheet:  0.33 (0.30), residues: 278
  loop : -1.13 (0.26), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H 191 
 TYR   0.019   0.002   TYR R 416 
 PHE   0.044   0.003   PHE R 189 
 TRP   0.025   0.003   TRP B  82 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00610 ( 8843)
  covalent geometry    : angle       0.88762 (12016)
  SS BOND              : bond        0.00322 (    4)
  SS BOND              : angle       1.00702 (    8)
  hydrogen bonds       : bond        0.13273 (  447)
  hydrogen bonds       : angle       6.13157 ( 1284)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 198
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   64 GLN cc_start: 0.8344 (mt0) cc_final: 0.7735 (mt0)
REVERT: R  107 LEU cc_start: 0.8106 (mt) cc_final: 0.7737 (tm)
REVERT: R  143 ARG cc_start: 0.7998 (ptm160) cc_final: 0.7517 (mtm110)
REVERT: R  223 ARG cc_start: 0.8449 (ptp-170) cc_final: 0.8089 (ptm160)
REVERT: R  465 ARG cc_start: 0.7863 (ttt90) cc_final: 0.6987 (tpt170)
REVERT: B   10 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8477 (tp30)
REVERT: B   61 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8609 (ppp)
REVERT: B  254 ASP cc_start: 0.8202 (t70) cc_final: 0.7950 (t0)
REVERT: G   20 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8602 (mtmp)
REVERT: G   24 ASN cc_start: 0.9040 (m-40) cc_final: 0.8769 (m-40)
REVERT: H  148 PRO cc_start: 0.9326 (Cg_exo) cc_final: 0.9053 (Cg_endo)
REVERT: H  192 MET cc_start: 0.8923 (ttp) cc_final: 0.8720 (ttm)
REVERT: H  223 ASP cc_start: 0.8921 (m-30) cc_final: 0.8696 (m-30)
REVERT: H  234 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7731 (mt-10)
REVERT: H  244 LYS cc_start: 0.9176 (tttt) cc_final: 0.8835 (ttmm)
REVERT: A    9 ASP cc_start: 0.8497 (m-30) cc_final: 0.8085 (m-30)
REVERT: A   24 ARG cc_start: 0.7956 (ttm110) cc_final: 0.7738 (ttm110)
REVERT: A  188 HIS cc_start: 0.8046 (m-70) cc_final: 0.7654 (m-70)
REVERT: A  329 THR cc_start: 0.8189 (m) cc_final: 0.7963 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 198
  average time/residue: 0.7313
  time to fit residues: 151.6311
Evaluate side-chains
  141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    0.7980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
R  60 ASN
R 117 ASN
R 172 GLN
R 192 ASN
B  13 GLN
B  75 GLN
B 340 ASN
G  18 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.091230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.063264 restraints weight = 16639.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.2807 rms_B_bonded: 2.81
r_work: 0.2674 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2551 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8847  Z= 0.134
  Angle     :  0.543   7.969  12024  Z= 0.296
  Chirality :  0.042   0.138   1388
  Planarity :  0.004   0.047   1511
  Dihedral  :  4.841  40.650   1223
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  9.63 %
    Favored  : 88.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  0.28 (0.24), residues: 1110
  helix:  0.95 (0.26), residues: 398
  sheet:  0.44 (0.30), residues: 280
  loop : -0.61 (0.27), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 144 
 TYR   0.016   0.001   TYR H 190 
 PHE   0.017   0.001   PHE R 189 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8843)
  covalent geometry    : angle       0.54335 (12016)
  SS BOND              : bond        0.00310 (    4)
  SS BOND              : angle       0.61270 (    8)
  hydrogen bonds       : bond        0.04168 (  447)
  hydrogen bonds       : angle       4.62444 ( 1284)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 152
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   64 GLN cc_start: 0.8258 (mt0) cc_final: 0.7686 (mt0)
REVERT: R  107 LEU cc_start: 0.8139 (mt) cc_final: 0.7817 (tm)
REVERT: R  143 ARG cc_start: 0.7788 (ptm160) cc_final: 0.7404 (mtm110)
REVERT: R  223 ARG cc_start: 0.8643 (ptp-170) cc_final: 0.8336 (ptm160)
REVERT: R  465 ARG cc_start: 0.7873 (ttt90) cc_final: 0.6952 (tpt170)
REVERT: B   10 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8636 (tp30)
REVERT: B   13 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8139 (tm-30)
REVERT: B   17 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8781 (tm-30)
REVERT: B   61 MET cc_start: 0.9471 (ppp) cc_final: 0.9190 (ppp)
REVERT: B  215 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8568 (mp0)
REVERT: B  217 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7948 (pmt)
REVERT: B  254 ASP cc_start: 0.8692 (t70) cc_final: 0.8396 (t0)
REVERT: G   20 LYS cc_start: 0.8868 (mtmm) cc_final: 0.8534 (mtmp)
REVERT: G   24 ASN cc_start: 0.9336 (m-40) cc_final: 0.9086 (m-40)
REVERT: G   58 GLU cc_start: 0.8764 (pm20) cc_final: 0.8521 (pm20)
REVERT: H  160 ARG cc_start: 0.8273 (mtm110) cc_final: 0.7850 (mtp85)
REVERT: H  220 GLU cc_start: 0.8773 (tt0) cc_final: 0.8397 (mm-30)
REVERT: H  223 ASP cc_start: 0.9056 (m-30) cc_final: 0.7851 (m-30)
REVERT: H  234 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8529 (mt-10)
REVERT: A  242 ARG cc_start: 0.8905 (mmm-85) cc_final: 0.8603 (mmm-85)
REVERT: A  329 THR cc_start: 0.8295 (m) cc_final: 0.8050 (t)
  outliers start: 15
  outliers final: 4
  residues processed: 161
  average time/residue: 0.7382
  time to fit residues: 124.7317
Evaluate side-chains
  141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 135
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  159 LEU
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 71 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   chunk 16 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 340 ASN
G  18 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.090269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.062207 restraints weight = 16669.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.2779 rms_B_bonded: 2.84
r_work: 0.2642 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2515 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8847  Z= 0.171
  Angle     :  0.547   7.351  12024  Z= 0.296
  Chirality :  0.043   0.138   1388
  Planarity :  0.004   0.044   1511
  Dihedral  :  4.494  29.223   1220
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.47 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  0.70 (0.25), residues: 1110
  helix:  1.47 (0.27), residues: 398
  sheet:  0.48 (0.30), residues: 281
  loop : -0.43 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 214 
 TYR   0.017   0.001   TYR R  89 
 PHE   0.017   0.001   PHE R 189 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 8843)
  covalent geometry    : angle       0.54742 (12016)
  SS BOND              : bond        0.00341 (    4)
  SS BOND              : angle       0.65421 (    8)
  hydrogen bonds       : bond        0.04028 (  447)
  hydrogen bonds       : angle       4.39392 ( 1284)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 0.298 
Fit side-chains
REVERT: R   64 GLN cc_start: 0.8274 (mt0) cc_final: 0.7704 (mt0)
REVERT: R  107 LEU cc_start: 0.8186 (mt) cc_final: 0.7914 (tm)
REVERT: R  143 ARG cc_start: 0.7721 (ptm160) cc_final: 0.7365 (mtm110)
REVERT: R  148 MET cc_start: 0.7410 (tpp) cc_final: 0.7064 (tpp)
REVERT: R  223 ARG cc_start: 0.8596 (ptp-170) cc_final: 0.8367 (ptm160)
REVERT: R  395 GLU cc_start: 0.7418 (tt0) cc_final: 0.6844 (tt0)
REVERT: R  407 LEU cc_start: 0.8022 (tp) cc_final: 0.7805 (mm)
REVERT: R  439 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.6943 (m-80)
REVERT: R  465 ARG cc_start: 0.7925 (ttt90) cc_final: 0.7031 (tpt170)
REVERT: B   10 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8512 (tp30)
REVERT: B   13 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8000 (pp30)
REVERT: B   17 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8834 (tm-30)
REVERT: B  215 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8537 (mp0)
REVERT: B  254 ASP cc_start: 0.8671 (t70) cc_final: 0.8344 (t0)
REVERT: G   20 LYS cc_start: 0.8837 (mtmm) cc_final: 0.8535 (mtmp)
REVERT: G   24 ASN cc_start: 0.9365 (m-40) cc_final: 0.9106 (m-40)
REVERT: G   58 GLU cc_start: 0.8810 (pm20) cc_final: 0.8491 (pm20)
REVERT: H  140 MET cc_start: 0.9457 (OUTLIER) cc_final: 0.8929 (mmm)
REVERT: H  234 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8486 (mt-10)
REVERT: A  261 ASP cc_start: 0.9437 (p0) cc_final: 0.9208 (p0)
REVERT: A  329 THR cc_start: 0.8378 (m) cc_final: 0.8145 (t)
  outliers start: 17
  outliers final: 6
  residues processed: 153
  average time/residue: 0.7577
  time to fit residues: 121.4512
Evaluate side-chains
  139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  159 LEU
Chi-restraints excluded: chain R residue  439 TYR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain H residue  140 MET
Chi-restraints excluded: chain H residue  154 SER
Chi-restraints excluded: chain H residue  186 GLN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 101 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 105 optimal weight:    0.9980
   chunk 102 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 104 optimal weight:    6.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
B  75 GLN
G  18 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.090356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.062357 restraints weight = 16804.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.2783 rms_B_bonded: 2.84
r_work: 0.2646 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2520 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8847  Z= 0.154
  Angle     :  0.544   9.632  12024  Z= 0.291
  Chirality :  0.042   0.139   1388
  Planarity :  0.004   0.043   1511
  Dihedral  :  4.428  27.051   1220
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 11.80 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  0.87 (0.25), residues: 1110
  helix:  1.68 (0.27), residues: 398
  sheet:  0.44 (0.30), residues: 283
  loop : -0.29 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 219 
 TYR   0.017   0.001   TYR A 296 
 PHE   0.017   0.001   PHE R 189 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8843)
  covalent geometry    : angle       0.54444 (12016)
  SS BOND              : bond        0.00306 (    4)
  SS BOND              : angle       0.56659 (    8)
  hydrogen bonds       : bond        0.03858 (  447)
  hydrogen bonds       : angle       4.30635 ( 1284)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   64 GLN cc_start: 0.8281 (mt0) cc_final: 0.7684 (mt0)
REVERT: R  107 LEU cc_start: 0.8185 (mt) cc_final: 0.7905 (tm)
REVERT: R  143 ARG cc_start: 0.7706 (ptm160) cc_final: 0.7320 (mtm110)
REVERT: R  148 MET cc_start: 0.7340 (tpp) cc_final: 0.6852 (tpp)
REVERT: R  152 MET cc_start: 0.7991 (mtm) cc_final: 0.7754 (mtp)
REVERT: R  217 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.8271 (m-70)
REVERT: R  223 ARG cc_start: 0.8562 (ptp-170) cc_final: 0.8207 (ptm160)
REVERT: R  395 GLU cc_start: 0.7451 (tt0) cc_final: 0.7232 (tt0)
REVERT: R  439 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6994 (m-80)
REVERT: R  465 ARG cc_start: 0.7927 (ttt90) cc_final: 0.7035 (tpt170)
REVERT: B   10 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8476 (tp30)
REVERT: B   13 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8065 (pp30)
REVERT: B   17 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8843 (tm-30)
REVERT: B  254 ASP cc_start: 0.8644 (t70) cc_final: 0.8313 (t0)
REVERT: G   20 LYS cc_start: 0.8852 (mtmm) cc_final: 0.8587 (mtmp)
REVERT: G   24 ASN cc_start: 0.9351 (m-40) cc_final: 0.9065 (m110)
REVERT: G   58 GLU cc_start: 0.8834 (pm20) cc_final: 0.8480 (pm20)
REVERT: H  140 MET cc_start: 0.9439 (OUTLIER) cc_final: 0.8964 (mmm)
REVERT: H  160 ARG cc_start: 0.8117 (mtm110) cc_final: 0.7482 (mtp-110)
REVERT: H  234 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8476 (mt-10)
REVERT: A  261 ASP cc_start: 0.9454 (p0) cc_final: 0.9230 (p0)
REVERT: A  329 THR cc_start: 0.8356 (m) cc_final: 0.8116 (t)
  outliers start: 23
  outliers final: 10
  residues processed: 151
  average time/residue: 0.7248
  time to fit residues: 115.0671
Evaluate side-chains
  147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  159 LEU
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain R residue  217 HIS
Chi-restraints excluded: chain R residue  439 TYR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain H residue  140 MET
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
G  18 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.090197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.062309 restraints weight = 16843.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.2784 rms_B_bonded: 2.83
r_work: 0.2648 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2522 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8847  Z= 0.154
  Angle     :  0.544   9.632  12024  Z= 0.291
  Chirality :  0.042   0.139   1388
  Planarity :  0.004   0.043   1511
  Dihedral  :  4.428  27.051   1220
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.29 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  0.87 (0.25), residues: 1110
  helix:  1.68 (0.27), residues: 398
  sheet:  0.44 (0.30), residues: 283
  loop : -0.29 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 219 
 TYR   0.017   0.001   TYR A 296 
 PHE   0.017   0.001   PHE R 189 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8843)
  covalent geometry    : angle       0.54443 (12016)
  SS BOND              : bond        0.00306 (    4)
  SS BOND              : angle       0.56658 (    8)
  hydrogen bonds       : bond        0.03858 (  447)
  hydrogen bonds       : angle       4.30635 ( 1284)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   64 GLN cc_start: 0.8287 (mt0) cc_final: 0.7696 (mt0)
REVERT: R  107 LEU cc_start: 0.8186 (mt) cc_final: 0.7905 (tm)
REVERT: R  143 ARG cc_start: 0.7708 (ptm160) cc_final: 0.7321 (mtm110)
REVERT: R  148 MET cc_start: 0.7336 (tpp) cc_final: 0.6847 (tpp)
REVERT: R  152 MET cc_start: 0.7990 (mtm) cc_final: 0.7753 (mtp)
REVERT: R  217 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.8269 (m-70)
REVERT: R  223 ARG cc_start: 0.8564 (ptp-170) cc_final: 0.8210 (ptm160)
REVERT: R  395 GLU cc_start: 0.7452 (tt0) cc_final: 0.7230 (tt0)
REVERT: R  439 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.6996 (m-80)
REVERT: R  465 ARG cc_start: 0.7924 (ttt90) cc_final: 0.7031 (tpt170)
REVERT: B   10 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8472 (tp30)
REVERT: B   13 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8062 (pp30)
REVERT: B   17 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8844 (tm-30)
REVERT: B  254 ASP cc_start: 0.8639 (t70) cc_final: 0.8307 (t0)
REVERT: G   20 LYS cc_start: 0.8851 (mtmm) cc_final: 0.8581 (mtmp)
REVERT: G   24 ASN cc_start: 0.9350 (m-40) cc_final: 0.9063 (m110)
REVERT: G   58 GLU cc_start: 0.8834 (pm20) cc_final: 0.8475 (pm20)
REVERT: H  140 MET cc_start: 0.9438 (OUTLIER) cc_final: 0.8964 (mmm)
REVERT: H  160 ARG cc_start: 0.8122 (mtm110) cc_final: 0.7488 (mtp-110)
REVERT: H  234 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8488 (mt-10)
REVERT: A  261 ASP cc_start: 0.9450 (p0) cc_final: 0.9225 (p0)
REVERT: A  329 THR cc_start: 0.8352 (m) cc_final: 0.8114 (t)
  outliers start: 14
  outliers final: 10
  residues processed: 140
  average time/residue: 0.7781
  time to fit residues: 114.0824
Evaluate side-chains
  147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  159 LEU
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain R residue  217 HIS
Chi-restraints excluded: chain R residue  439 TYR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain H residue  140 MET
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 107 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   chunk 5 optimal weight:    4.9990
   chunk 87 optimal weight:    0.0040
   chunk 15 optimal weight:    5.9990
   chunk 106 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   chunk 43 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    1.5596

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
G  18 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.090197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.062316 restraints weight = 16746.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.2784 rms_B_bonded: 2.83
r_work: 0.2648 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2522 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8847  Z= 0.154
  Angle     :  0.544   9.632  12024  Z= 0.291
  Chirality :  0.042   0.139   1388
  Planarity :  0.004   0.043   1511
  Dihedral  :  4.428  27.051   1220
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.29 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  0.87 (0.25), residues: 1110
  helix:  1.68 (0.27), residues: 398
  sheet:  0.44 (0.30), residues: 283
  loop : -0.29 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 219 
 TYR   0.017   0.001   TYR A 296 
 PHE   0.017   0.001   PHE R 189 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8843)
  covalent geometry    : angle       0.54443 (12016)
  SS BOND              : bond        0.00306 (    4)
  SS BOND              : angle       0.56658 (    8)
  hydrogen bonds       : bond        0.03858 (  447)
  hydrogen bonds       : angle       4.30635 ( 1284)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   64 GLN cc_start: 0.8282 (mt0) cc_final: 0.7692 (mt0)
REVERT: R  107 LEU cc_start: 0.8185 (mt) cc_final: 0.7904 (tm)
REVERT: R  143 ARG cc_start: 0.7708 (ptm160) cc_final: 0.7321 (mtm110)
REVERT: R  148 MET cc_start: 0.7330 (tpp) cc_final: 0.6841 (tpp)
REVERT: R  152 MET cc_start: 0.7985 (mtm) cc_final: 0.7747 (mtp)
REVERT: R  217 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.8267 (m-70)
REVERT: R  223 ARG cc_start: 0.8563 (ptp-170) cc_final: 0.8207 (ptm160)
REVERT: R  395 GLU cc_start: 0.7450 (tt0) cc_final: 0.7227 (tt0)
REVERT: R  439 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6994 (m-80)
REVERT: R  465 ARG cc_start: 0.7923 (ttt90) cc_final: 0.7029 (tpt170)
REVERT: B   10 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8470 (tp30)
REVERT: B   13 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8061 (pp30)
REVERT: B   17 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8842 (tm-30)
REVERT: B  254 ASP cc_start: 0.8639 (t70) cc_final: 0.8307 (t0)
REVERT: G   20 LYS cc_start: 0.8849 (mtmm) cc_final: 0.8579 (mtmp)
REVERT: G   24 ASN cc_start: 0.9351 (m-40) cc_final: 0.9064 (m110)
REVERT: G   58 GLU cc_start: 0.8835 (pm20) cc_final: 0.8477 (pm20)
REVERT: H  140 MET cc_start: 0.9438 (OUTLIER) cc_final: 0.8962 (mmm)
REVERT: H  160 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7487 (mtp-110)
REVERT: H  234 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8487 (mt-10)
REVERT: A  261 ASP cc_start: 0.9452 (p0) cc_final: 0.9227 (p0)
REVERT: A  329 THR cc_start: 0.8354 (m) cc_final: 0.8116 (t)
  outliers start: 14
  outliers final: 10
  residues processed: 140
  average time/residue: 0.7412
  time to fit residues: 108.6681
Evaluate side-chains
  147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  159 LEU
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain R residue  217 HIS
Chi-restraints excluded: chain R residue  439 TYR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain H residue  140 MET
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 104 optimal weight:   10.0000
   chunk 73 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 91 optimal weight:    6.9990
   chunk 65 optimal weight:    8.9990
   chunk 57 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 86 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
G  18 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.090197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.062286 restraints weight = 16905.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.2783 rms_B_bonded: 2.84
r_work: 0.2647 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2521 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8847  Z= 0.154
  Angle     :  0.544   9.632  12024  Z= 0.291
  Chirality :  0.042   0.139   1388
  Planarity :  0.004   0.043   1511
  Dihedral  :  4.428  27.051   1220
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.29 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  0.87 (0.25), residues: 1110
  helix:  1.68 (0.27), residues: 398
  sheet:  0.44 (0.30), residues: 283
  loop : -0.29 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 219 
 TYR   0.017   0.001   TYR A 296 
 PHE   0.017   0.001   PHE R 189 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8843)
  covalent geometry    : angle       0.54443 (12016)
  SS BOND              : bond        0.00306 (    4)
  SS BOND              : angle       0.56658 (    8)
  hydrogen bonds       : bond        0.03858 (  447)
  hydrogen bonds       : angle       4.30635 ( 1284)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   64 GLN cc_start: 0.8282 (mt0) cc_final: 0.7692 (mt0)
REVERT: R  107 LEU cc_start: 0.8185 (mt) cc_final: 0.7904 (tm)
REVERT: R  143 ARG cc_start: 0.7708 (ptm160) cc_final: 0.7321 (mtm110)
REVERT: R  148 MET cc_start: 0.7330 (tpp) cc_final: 0.6841 (tpp)
REVERT: R  152 MET cc_start: 0.7985 (mtm) cc_final: 0.7747 (mtp)
REVERT: R  217 HIS cc_start: 0.8501 (OUTLIER) cc_final: 0.8268 (m-70)
REVERT: R  223 ARG cc_start: 0.8562 (ptp-170) cc_final: 0.8207 (ptm160)
REVERT: R  395 GLU cc_start: 0.7450 (tt0) cc_final: 0.7227 (tt0)
REVERT: R  439 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.6994 (m-80)
REVERT: R  465 ARG cc_start: 0.7923 (ttt90) cc_final: 0.7029 (tpt170)
REVERT: B   10 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8470 (tp30)
REVERT: B   13 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8061 (pp30)
REVERT: B   17 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8843 (tm-30)
REVERT: B  254 ASP cc_start: 0.8640 (t70) cc_final: 0.8309 (t0)
REVERT: G   20 LYS cc_start: 0.8850 (mtmm) cc_final: 0.8580 (mtmp)
REVERT: G   24 ASN cc_start: 0.9352 (m-40) cc_final: 0.9064 (m110)
REVERT: G   58 GLU cc_start: 0.8836 (pm20) cc_final: 0.8478 (pm20)
REVERT: H  140 MET cc_start: 0.9438 (OUTLIER) cc_final: 0.8963 (mmm)
REVERT: H  160 ARG cc_start: 0.8122 (mtm110) cc_final: 0.7488 (mtp-110)
REVERT: H  234 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8488 (mt-10)
REVERT: A  261 ASP cc_start: 0.9452 (p0) cc_final: 0.9227 (p0)
REVERT: A  329 THR cc_start: 0.8354 (m) cc_final: 0.8116 (t)
  outliers start: 14
  outliers final: 10
  residues processed: 140
  average time/residue: 0.7642
  time to fit residues: 111.9636
Evaluate side-chains
  147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  159 LEU
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain R residue  217 HIS
Chi-restraints excluded: chain R residue  439 TYR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain H residue  140 MET
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9980
   chunk 106 optimal weight:    0.3980
   chunk 54 optimal weight:    5.9990
   chunk 98 optimal weight:    8.9990
   chunk 95 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
G  18 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.090197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.062343 restraints weight = 16646.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.2785 rms_B_bonded: 2.82
r_work: 0.2648 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2523 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8847  Z= 0.154
  Angle     :  0.544   9.632  12024  Z= 0.291
  Chirality :  0.042   0.139   1388
  Planarity :  0.004   0.043   1511
  Dihedral  :  4.428  27.051   1220
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.29 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  0.87 (0.25), residues: 1110
  helix:  1.68 (0.27), residues: 398
  sheet:  0.44 (0.30), residues: 283
  loop : -0.29 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 219 
 TYR   0.017   0.001   TYR A 296 
 PHE   0.017   0.001   PHE R 189 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8843)
  covalent geometry    : angle       0.54443 (12016)
  SS BOND              : bond        0.00306 (    4)
  SS BOND              : angle       0.56658 (    8)
  hydrogen bonds       : bond        0.03858 (  447)
  hydrogen bonds       : angle       4.30635 ( 1284)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   64 GLN cc_start: 0.8280 (mt0) cc_final: 0.7690 (mt0)
REVERT: R  107 LEU cc_start: 0.8185 (mt) cc_final: 0.7904 (tm)
REVERT: R  143 ARG cc_start: 0.7709 (ptm160) cc_final: 0.7321 (mtm110)
REVERT: R  148 MET cc_start: 0.7330 (tpp) cc_final: 0.6840 (tpp)
REVERT: R  152 MET cc_start: 0.7984 (mtm) cc_final: 0.7746 (mtp)
REVERT: R  217 HIS cc_start: 0.8501 (OUTLIER) cc_final: 0.8267 (m-70)
REVERT: R  223 ARG cc_start: 0.8561 (ptp-170) cc_final: 0.8205 (ptm160)
REVERT: R  395 GLU cc_start: 0.7452 (tt0) cc_final: 0.7229 (tt0)
REVERT: R  439 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6993 (m-80)
REVERT: R  465 ARG cc_start: 0.7923 (ttt90) cc_final: 0.7029 (tpt170)
REVERT: B   10 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8470 (tp30)
REVERT: B   13 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8060 (pp30)
REVERT: B   17 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8842 (tm-30)
REVERT: B  254 ASP cc_start: 0.8639 (t70) cc_final: 0.8307 (t0)
REVERT: G   20 LYS cc_start: 0.8850 (mtmm) cc_final: 0.8580 (mtmp)
REVERT: G   24 ASN cc_start: 0.9352 (m-40) cc_final: 0.9064 (m110)
REVERT: G   58 GLU cc_start: 0.8835 (pm20) cc_final: 0.8478 (pm20)
REVERT: H  140 MET cc_start: 0.9438 (OUTLIER) cc_final: 0.8963 (mmm)
REVERT: H  160 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7488 (mtp-110)
REVERT: H  234 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8486 (mt-10)
REVERT: A  261 ASP cc_start: 0.9451 (p0) cc_final: 0.9226 (p0)
REVERT: A  329 THR cc_start: 0.8352 (m) cc_final: 0.8115 (t)
  outliers start: 14
  outliers final: 10
  residues processed: 140
  average time/residue: 0.7287
  time to fit residues: 106.9331
Evaluate side-chains
  147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  159 LEU
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain R residue  217 HIS
Chi-restraints excluded: chain R residue  439 TYR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain H residue  140 MET
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 94 optimal weight:    1.9990
   chunk 28 optimal weight:    7.9990
   chunk 107 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 98 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
G  18 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.090197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.062298 restraints weight = 16813.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.2783 rms_B_bonded: 2.84
r_work: 0.2647 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2521 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8847  Z= 0.154
  Angle     :  0.544   9.632  12024  Z= 0.291
  Chirality :  0.042   0.139   1388
  Planarity :  0.004   0.043   1511
  Dihedral  :  4.428  27.051   1220
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.29 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  0.87 (0.25), residues: 1110
  helix:  1.68 (0.27), residues: 398
  sheet:  0.44 (0.30), residues: 283
  loop : -0.29 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 219 
 TYR   0.017   0.001   TYR A 296 
 PHE   0.017   0.001   PHE R 189 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8843)
  covalent geometry    : angle       0.54443 (12016)
  SS BOND              : bond        0.00306 (    4)
  SS BOND              : angle       0.56658 (    8)
  hydrogen bonds       : bond        0.03858 (  447)
  hydrogen bonds       : angle       4.30635 ( 1284)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   64 GLN cc_start: 0.8291 (mt0) cc_final: 0.7699 (mt0)
REVERT: R  107 LEU cc_start: 0.8186 (mt) cc_final: 0.7905 (tm)
REVERT: R  143 ARG cc_start: 0.7710 (ptm160) cc_final: 0.7323 (mtm110)
REVERT: R  148 MET cc_start: 0.7341 (tpp) cc_final: 0.6853 (tpp)
REVERT: R  152 MET cc_start: 0.7993 (mtm) cc_final: 0.7756 (mtp)
REVERT: R  217 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.8271 (m-70)
REVERT: R  223 ARG cc_start: 0.8566 (ptp-170) cc_final: 0.8211 (ptm160)
REVERT: R  395 GLU cc_start: 0.7452 (tt0) cc_final: 0.7230 (tt0)
REVERT: R  439 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.6998 (m-80)
REVERT: R  465 ARG cc_start: 0.7924 (ttt90) cc_final: 0.7033 (tpt170)
REVERT: B   10 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8473 (tp30)
REVERT: B   13 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8063 (pp30)
REVERT: B   17 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8846 (tm-30)
REVERT: B  254 ASP cc_start: 0.8641 (t70) cc_final: 0.8309 (t0)
REVERT: G   20 LYS cc_start: 0.8852 (mtmm) cc_final: 0.8581 (mtmp)
REVERT: G   24 ASN cc_start: 0.9349 (m-40) cc_final: 0.9062 (m110)
REVERT: G   58 GLU cc_start: 0.8833 (pm20) cc_final: 0.8475 (pm20)
REVERT: H  140 MET cc_start: 0.9438 (OUTLIER) cc_final: 0.8965 (mmm)
REVERT: H  160 ARG cc_start: 0.8123 (mtm110) cc_final: 0.7489 (mtp-110)
REVERT: H  234 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8488 (mt-10)
REVERT: A  261 ASP cc_start: 0.9449 (p0) cc_final: 0.9224 (p0)
REVERT: A  329 THR cc_start: 0.8352 (m) cc_final: 0.8114 (t)
  outliers start: 14
  outliers final: 10
  residues processed: 140
  average time/residue: 0.7794
  time to fit residues: 114.3153
Evaluate side-chains
  147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  159 LEU
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain R residue  217 HIS
Chi-restraints excluded: chain R residue  439 TYR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain H residue  140 MET
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 104 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9990
   chunk 108 optimal weight:    0.2980
   chunk 96 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 77 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 79 optimal weight:    8.9990
   chunk 62 optimal weight:    0.5980
   chunk 15 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
G  18 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.090197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.062321 restraints weight = 16718.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.2784 rms_B_bonded: 2.83
r_work: 0.2648 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2522 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8847  Z= 0.154
  Angle     :  0.544   9.632  12024  Z= 0.291
  Chirality :  0.042   0.139   1388
  Planarity :  0.004   0.043   1511
  Dihedral  :  4.428  27.051   1220
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.29 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  0.87 (0.25), residues: 1110
  helix:  1.68 (0.27), residues: 398
  sheet:  0.44 (0.30), residues: 283
  loop : -0.29 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 219 
 TYR   0.017   0.001   TYR A 296 
 PHE   0.017   0.001   PHE R 189 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8843)
  covalent geometry    : angle       0.54443 (12016)
  SS BOND              : bond        0.00306 (    4)
  SS BOND              : angle       0.56658 (    8)
  hydrogen bonds       : bond        0.03858 (  447)
  hydrogen bonds       : angle       4.30635 ( 1284)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   64 GLN cc_start: 0.8280 (mt0) cc_final: 0.7690 (mt0)
REVERT: R  107 LEU cc_start: 0.8184 (mt) cc_final: 0.7904 (tm)
REVERT: R  143 ARG cc_start: 0.7707 (ptm160) cc_final: 0.7320 (mtm110)
REVERT: R  148 MET cc_start: 0.7329 (tpp) cc_final: 0.6840 (tpp)
REVERT: R  152 MET cc_start: 0.7984 (mtm) cc_final: 0.7746 (mtp)
REVERT: R  217 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.8266 (m-70)
REVERT: R  223 ARG cc_start: 0.8562 (ptp-170) cc_final: 0.8206 (ptm160)
REVERT: R  395 GLU cc_start: 0.7450 (tt0) cc_final: 0.7227 (tt0)
REVERT: R  439 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6993 (m-80)
REVERT: R  465 ARG cc_start: 0.7922 (ttt90) cc_final: 0.7029 (tpt170)
REVERT: B   10 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8470 (tp30)
REVERT: B   13 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8061 (pp30)
REVERT: B   17 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8841 (tm-30)
REVERT: B  254 ASP cc_start: 0.8640 (t70) cc_final: 0.8308 (t0)
REVERT: G   20 LYS cc_start: 0.8849 (mtmm) cc_final: 0.8579 (mtmp)
REVERT: G   24 ASN cc_start: 0.9352 (m-40) cc_final: 0.9064 (m110)
REVERT: G   58 GLU cc_start: 0.8836 (pm20) cc_final: 0.8478 (pm20)
REVERT: H  140 MET cc_start: 0.9438 (OUTLIER) cc_final: 0.8962 (mmm)
REVERT: H  160 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7487 (mtp-110)
REVERT: H  234 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8487 (mt-10)
REVERT: A  261 ASP cc_start: 0.9452 (p0) cc_final: 0.9227 (p0)
REVERT: A  329 THR cc_start: 0.8353 (m) cc_final: 0.8116 (t)
  outliers start: 14
  outliers final: 10
  residues processed: 140
  average time/residue: 0.7605
  time to fit residues: 111.6717
Evaluate side-chains
  147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  159 LEU
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain R residue  217 HIS
Chi-restraints excluded: chain R residue  439 TYR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain H residue  140 MET
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 108 optimal weight:    0.2980
   chunk 96 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 98 optimal weight:    7.9990
   chunk 101 optimal weight:    4.9990
   chunk 92 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
G  18 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.090197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.062346 restraints weight = 16626.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.2785 rms_B_bonded: 2.82
r_work: 0.2648 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2523 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8847  Z= 0.154
  Angle     :  0.544   9.632  12024  Z= 0.291
  Chirality :  0.042   0.139   1388
  Planarity :  0.004   0.043   1511
  Dihedral  :  4.428  27.051   1220
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.29 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  0.87 (0.25), residues: 1110
  helix:  1.68 (0.27), residues: 398
  sheet:  0.44 (0.30), residues: 283
  loop : -0.29 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 219 
 TYR   0.017   0.001   TYR A 296 
 PHE   0.017   0.001   PHE R 189 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8843)
  covalent geometry    : angle       0.54443 (12016)
  SS BOND              : bond        0.00306 (    4)
  SS BOND              : angle       0.56658 (    8)
  hydrogen bonds       : bond        0.03858 (  447)
  hydrogen bonds       : angle       4.30635 ( 1284)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3851.10 seconds
wall clock time: 66 minutes 8.95 seconds (3968.95 seconds total)