Starting phenix.real_space_refine
on Wed Mar 12 11:27:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xtq_33452/03_2025/7xtq_33452.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xtq_33452/03_2025/7xtq_33452.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xtq_33452/03_2025/7xtq_33452.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xtq_33452/03_2025/7xtq_33452.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xtq_33452/03_2025/7xtq_33452.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xtq_33452/03_2025/7xtq_33452.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.033
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: 5
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     Cl      2      4.86       5
     C    5066      2.51       5
     N    1420      2.21       5
     O    1476      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8010
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1897
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 229, 1886
          Classifications: {'peptide': 229}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 222}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "C"
        Number of residues, atoms: 229, 1886
          Classifications: {'peptide': 229}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 222}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 1910
    Chain: "B"
      Number of atoms: 2612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2612
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "R"
      Number of atoms: 2063
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2063
          Classifications: {'peptide': 273}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 21, 'TRANS': 251}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "R"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'H8I': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 380 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2CARG A 380 " occ=0.62
  Time building chain proxies: 5.97, per 1000 atoms: 0.75
  Number of scatterers: 8010
  At special positions: 0
  Unit cell: (77.064, 114.582, 122.694, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      46     16.00
     O    1476      8.00
     N    1420      7.00
     C    5066      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 155 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.01
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1916

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 10 sheets defined
      40.5% alpha, 20.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 4.409A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 4.269A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.732A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 2 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.631A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 21 through 42
      removed outlier: 3.980A  pdb=" N   ASP R  42 " --> pdb=" O   GLY R  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 48 through 67
    Processing helix  chain 'R' and resid 68 through 75
      Proline residue:  R  72  - end of helix
      removed outlier: 4.452A  pdb=" N   TRP R  75 " --> pdb=" O   PRO R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 81 through 116
      Proline residue:  R  92  - end of helix
    Processing helix  chain 'R' and resid 123 through 141
      removed outlier: 3.754A  pdb=" N   ALA R 127 " --> pdb=" O   SER R 123 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY R 134 " --> pdb=" O   LEU R 130 " (cutoff:3.500A)
      Proline residue:  R 135  - end of helix
    Processing helix  chain 'R' and resid 156 through 161
    Processing helix  chain 'R' and resid 162 through 174
      removed outlier: 3.975A  pdb=" N   LEU R 174 " --> pdb=" O   VAL R 170 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 207
      removed outlier: 3.732A  pdb=" N   LEU R 202 " --> pdb=" O   ASP R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 212 through 252
      removed outlier: 4.603A  pdb=" N   GLY R 238 " --> pdb=" O   GLY R 234 " (cutoff:3.500A)
      Proline residue:  R 239  - end of helix
      removed outlier: 4.192A  pdb=" N   GLU R 252 " --> pdb=" O   VAL R 248 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 261 through 282
      removed outlier: 3.701A  pdb=" N   LEU R 265 " --> pdb=" O   THR R 261 " (cutoff:3.500A)
      Proline residue:  R 277  - end of helix
    Processing helix  chain 'R' and resid 284 through 289
      removed outlier: 3.522A  pdb=" N   THR R 288 " --> pdb=" O   ASP R 284 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.695A  pdb=" N   ASP A 223 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.491A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.633A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.096A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.216A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.013A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.924A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.885A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.510A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151
      removed outlier: 3.672A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.515A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 4.056A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.657A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.621A  pdb=" N   GLN N   5 " --> pdb=" O   ALA N  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 3.520A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.950A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    1156 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.33

  Time building geometry restraints manager: 2.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2581
        1.34 -     1.45: 1237
        1.45 -     1.57: 4298
        1.57 -     1.69: 0
        1.69 -     1.81: 65
  Bond restraints: 8181
  Sorted by residual:
  bond pdb=" C1  H8I R 401 "
       pdb=" N2  H8I R 401 "
    ideal  model  delta    sigma   weight residual
    1.352  1.407 -0.055 2.00e-02 2.50e+03 7.51e+00
  bond pdb=" C3  H8I R 401 "
       pdb=" N1  H8I R 401 "
    ideal  model  delta    sigma   weight residual
    1.309  1.355 -0.046 2.00e-02 2.50e+03 5.31e+00
  bond pdb=" C7  H8I R 401 "
       pdb=" O1  H8I R 401 "
    ideal  model  delta    sigma   weight residual
    1.365  1.403 -0.038 2.00e-02 2.50e+03 3.70e+00
  bond pdb=" C7  H8I R 401 "
       pdb=" C8  H8I R 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.424 -0.034 2.00e-02 2.50e+03 2.95e+00
  bond pdb=" C2  H8I R 401 "
       pdb=" C3  H8I R 401 "
    ideal  model  delta    sigma   weight residual
    1.396  1.424 -0.028 2.00e-02 2.50e+03 2.02e+00
  ... (remaining 8176 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.76: 10977
        2.76 -     5.52: 106
        5.52 -     8.29: 20
        8.29 -    11.05: 3
       11.05 -    13.81: 1
  Bond angle restraints: 11107
  Sorted by residual:
  angle pdb=" C2  H8I R 401 "
        pdb=" C1  H8I R 401 "
        pdb=" N2  H8I R 401 "
      ideal   model   delta    sigma   weight residual
     117.71  131.52  -13.81 3.00e+00 1.11e-01 2.12e+01
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     113.20  109.63    3.57 9.60e-01 1.09e+00 1.39e+01
  angle pdb=" N   GLN B   9 "
        pdb=" CA  GLN B   9 "
        pdb=" CB  GLN B   9 "
      ideal   model   delta    sigma   weight residual
     110.28  115.61   -5.33 1.55e+00 4.16e-01 1.18e+01
  angle pdb=" C3  H8I R 401 "
        pdb=" O1  H8I R 401 "
        pdb=" C7  H8I R 401 "
      ideal   model   delta    sigma   weight residual
     119.25  129.24   -9.99 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" C   PRO A 321 "
        pdb=" N   GLU A 322 "
        pdb=" CA  GLU A 322 "
      ideal   model   delta    sigma   weight residual
     121.54  127.76   -6.22 1.91e+00 2.74e-01 1.06e+01
  ... (remaining 11102 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 4501
       17.64 -    35.28: 326
       35.28 -    52.92: 51
       52.92 -    70.55: 9
       70.55 -    88.19: 4
  Dihedral angle restraints: 4891
    sinusoidal: 1920
      harmonic: 2971
  Sorted by residual:
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   50.97   42.03     1      1.00e+01 1.00e-02 2.47e+01
  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  160.67   19.33     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  PRO B 194 "
           pdb=" C   PRO B 194 "
           pdb=" N   ASP B 195 "
           pdb=" CA  ASP B 195 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.07   15.93     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 4888 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 796
       0.037 -    0.074: 307
       0.074 -    0.111: 112
       0.111 -    0.148: 22
       0.148 -    0.185: 5
  Chirality restraints: 1242
  Sorted by residual:
  chirality pdb=" CA  GLN A  31 "
            pdb=" N   GLN A  31 "
            pdb=" C   GLN A  31 "
            pdb=" CB  GLN A  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.60e-01
  chirality pdb=" CB  THR B 223 "
            pdb=" CA  THR B 223 "
            pdb=" OG1 THR B 223 "
            pdb=" CG2 THR B 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.19 2.00e-01 2.50e+01 8.59e-01
  chirality pdb=" CA  ILE B 232 "
            pdb=" N   ILE B 232 "
            pdb=" C   ILE B 232 "
            pdb=" CB  ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.46e-01
  ... (remaining 1239 not shown)

  Planarity restraints: 1431
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 134 "    0.036 5.00e-02 4.00e+02   5.50e-02 4.85e+00
        pdb=" N   PRO R 135 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO R 135 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO R 135 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 228 "   -0.181 9.50e-02 1.11e+02   8.14e-02 4.28e+00
        pdb=" NE  ARG A 228 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 228 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 228 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 228 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 320 "   -0.031 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO A 321 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 321 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 321 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1428 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 471
        2.73 -     3.27: 7767
        3.27 -     3.82: 13060
        3.82 -     4.36: 14743
        4.36 -     4.90: 26436
  Nonbonded interactions: 62477
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" O   MET B 325 "
            pdb=" OD1 ASN B 340 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.273 3.040
  ... (remaining 62472 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.38 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:             60.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.420
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   87.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
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      :  0.004   0.055   8181  Z= 0.240
  Angle     :  0.745  13.809  11107  Z= 0.371
  Chirality :  0.046   0.185   1242
  Planarity :  0.005   0.081   1431
  Dihedral  : 12.535  88.193   2966
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.26), residues: 1016
  helix:  1.49 (0.25), residues: 399
  sheet: -0.69 (0.34), residues: 215
  loop : -1.79 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 281 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.023   0.002   PHE A 212 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.008   0.000   ARG A 228 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.855 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.6377 (mm-30) cc_final: 0.6096 (mm-30)
REVERT: A  209 GLU cc_start: 0.6027 (tp30) cc_final: 0.5750 (tp30)
REVERT: A  210 THR cc_start: 0.8203 (p) cc_final: 0.7399 (m)
REVERT: A  228 ARG cc_start: 0.7563 (ptm-80) cc_final: 0.7231 (ptt180)
REVERT: A  299 GLU cc_start: 0.7339 (tp30) cc_final: 0.6947 (tp30)
REVERT: A  392 GLU cc_start: 0.7115 (tp30) cc_final: 0.6546 (tp30)
REVERT: B   83 ASP cc_start: 0.7800 (t0) cc_final: 0.7335 (t70)
REVERT: B  148 CYS cc_start: 0.7185 (t) cc_final: 0.6952 (t)
REVERT: B  170 ASP cc_start: 0.6873 (t0) cc_final: 0.6569 (t0)
REVERT: B  197 ARG cc_start: 0.7076 (mtp180) cc_final: 0.6439 (mtp180)
REVERT: B  214 ARG cc_start: 0.7301 (ptt90) cc_final: 0.6357 (ptt90)
REVERT: G   21 MET cc_start: 0.6969 (tmm) cc_final: 0.6692 (tmm)
REVERT: N   31 ASN cc_start: 0.8264 (m110) cc_final: 0.8024 (m110)
REVERT: N   43 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7855 (mmmt)
REVERT: R  248 VAL cc_start: 0.7218 (t) cc_final: 0.6969 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.3083
  time to fit residues: 79.4138
Evaluate side-chains
  181 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 75 optimal weight:   10.0000
   chunk 42 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A 213 GLN
B 119 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.130736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.108583 restraints weight = 22362.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 3.80
r_work: 0.3194 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3146
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3145
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.1133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8181  Z= 0.324
  Angle     :  0.679  12.137  11107  Z= 0.333
  Chirality :  0.046   0.168   1242
  Planarity :  0.005   0.056   1431
  Dihedral  :  5.337  65.437   1145
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  9.72 %
    Favored  : 88.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.26), residues: 1016
  helix:  1.92 (0.26), residues: 387
  sheet: -0.45 (0.33), residues: 218
  loop : -1.74 (0.28), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.021   0.002   PHE N 108 
 TYR   0.019   0.002   TYR N  60 
 ARG   0.005   0.000   ARG A 228 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 191
  time to evaluate  : 0.852 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6469 (mm-30)
REVERT: A  209 GLU cc_start: 0.6910 (tp30) cc_final: 0.6548 (tp30)
REVERT: A  210 THR cc_start: 0.8167 (p) cc_final: 0.7587 (m)
REVERT: A  230 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7135 (mm-30)
REVERT: A  392 GLU cc_start: 0.7844 (tp30) cc_final: 0.7559 (tp30)
REVERT: B   40 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7824 (p)
REVERT: B   48 ARG cc_start: 0.8514 (mmt180) cc_final: 0.8238 (mmt-90)
REVERT: B   52 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7929 (mtt90)
REVERT: B  127 LYS cc_start: 0.7762 (mptt) cc_final: 0.7457 (mptt)
REVERT: B  197 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7464 (mtp180)
REVERT: B  214 ARG cc_start: 0.7945 (ptt90) cc_final: 0.7118 (ptt90)
REVERT: B  327 VAL cc_start: 0.8204 (t) cc_final: 0.7904 (p)
REVERT: G   21 MET cc_start: 0.7513 (tmm) cc_final: 0.7137 (tmm)
REVERT: G   38 MET cc_start: 0.7524 (ttp) cc_final: 0.7319 (ttm)
REVERT: N   31 ASN cc_start: 0.8508 (m110) cc_final: 0.8220 (m-40)
REVERT: N   43 LYS cc_start: 0.8261 (mmmt) cc_final: 0.7882 (mmmt)
REVERT: R   58 LEU cc_start: 0.7396 (mt) cc_final: 0.7192 (mm)
  outliers start: 12
  outliers final: 8
  residues processed: 195
  average time/residue: 0.2887
  time to fit residues: 70.0199
Evaluate side-chains
  195 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 186
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  170 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 14 optimal weight:    0.2980
   chunk 66 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 119 ASN
B 295 ASN
G  44 HIS
N  39 GLN
R 107 HIS
R 154 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.136175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.113444 restraints weight = 24814.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 3.91
r_work: 0.3234 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8181  Z= 0.191
  Angle     :  0.599  10.867  11107  Z= 0.290
  Chirality :  0.043   0.160   1242
  Planarity :  0.004   0.051   1431
  Dihedral  :  5.014  65.379   1145
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 12.80 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.26), residues: 1016
  helix:  2.13 (0.26), residues: 394
  sheet: -0.35 (0.33), residues: 218
  loop : -1.64 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.015   0.001   PHE B 241 
 TYR   0.013   0.001   TYR A 339 
 ARG   0.006   0.000   ARG R 187 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 193
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6446 (mm-30)
REVERT: A  209 GLU cc_start: 0.7013 (tp30) cc_final: 0.6653 (tp30)
REVERT: A  210 THR cc_start: 0.8229 (p) cc_final: 0.7695 (m)
REVERT: A  392 GLU cc_start: 0.7846 (tp30) cc_final: 0.7566 (tp30)
REVERT: B   48 ARG cc_start: 0.8523 (mmt180) cc_final: 0.8279 (mmt-90)
REVERT: B  126 LEU cc_start: 0.8257 (mm) cc_final: 0.7996 (mp)
REVERT: B  197 ARG cc_start: 0.7933 (mtp180) cc_final: 0.7392 (mtp180)
REVERT: B  327 VAL cc_start: 0.8196 (t) cc_final: 0.7907 (p)
REVERT: G   21 MET cc_start: 0.7550 (tmm) cc_final: 0.7173 (tmm)
REVERT: N   31 ASN cc_start: 0.8400 (m110) cc_final: 0.8050 (m-40)
REVERT: N   43 LYS cc_start: 0.8237 (mmmt) cc_final: 0.7865 (mmmt)
REVERT: N   60 TYR cc_start: 0.8598 (m-80) cc_final: 0.8199 (m-80)
REVERT: R   80 ARG cc_start: 0.7752 (ttm-80) cc_final: 0.7482 (ttm-80)
  outliers start: 14
  outliers final: 8
  residues processed: 199
  average time/residue: 0.2870
  time to fit residues: 72.5706
Evaluate side-chains
  188 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 180
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  170 VAL
Chi-restraints excluded: chain R residue  231 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 93 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0980
   chunk 39 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 4 optimal weight:    0.4980
   chunk 87 optimal weight:    0.0470
   chunk 91 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0000
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.2682

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.137031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.115367 restraints weight = 19154.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 3.43
r_work: 0.3305 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3283
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3283
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8181  Z= 0.132
  Angle     :  0.560   8.865  11107  Z= 0.268
  Chirality :  0.041   0.147   1242
  Planarity :  0.004   0.050   1431
  Dihedral  :  4.707  65.283   1145
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 14.93 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.26), residues: 1016
  helix:  2.30 (0.26), residues: 400
  sheet: -0.34 (0.33), residues: 219
  loop : -1.43 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.014   0.001   PHE B 234 
 TYR   0.013   0.001   TYR A 339 
 ARG   0.005   0.000   ARG R 187 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 168
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7760 (ttm110)
REVERT: B   48 ARG cc_start: 0.8470 (mmt180) cc_final: 0.8211 (mmt-90)
REVERT: B   61 MET cc_start: 0.7530 (ppp) cc_final: 0.7250 (ppp)
REVERT: B  126 LEU cc_start: 0.7758 (mm) cc_final: 0.7412 (mt)
REVERT: B  219 ARG cc_start: 0.7979 (mmt90) cc_final: 0.7744 (ttm-80)
REVERT: B  292 PHE cc_start: 0.7736 (m-10) cc_final: 0.7412 (m-80)
REVERT: G   21 MET cc_start: 0.7429 (tmm) cc_final: 0.7046 (tmm)
REVERT: N   31 ASN cc_start: 0.8365 (m110) cc_final: 0.8038 (m-40)
REVERT: N   43 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7879 (mmmt)
REVERT: N   60 TYR cc_start: 0.8544 (m-80) cc_final: 0.8311 (m-80)
REVERT: R  112 MET cc_start: 0.7946 (mmt) cc_final: 0.7583 (mpp)
  outliers start: 11
  outliers final: 7
  residues processed: 174
  average time/residue: 0.2814
  time to fit residues: 63.5786
Evaluate side-chains
  176 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 169
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  146 TRP
Chi-restraints excluded: chain R residue  170 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 68 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 15 optimal weight:    0.4980
   chunk 64 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 24 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.131123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.108225 restraints weight = 24332.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 4.14
r_work: 0.3152 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8181  Z= 0.194
  Angle     :  0.584  10.024  11107  Z= 0.281
  Chirality :  0.042   0.145   1242
  Planarity :  0.004   0.049   1431
  Dihedral  :  4.753  66.283   1145
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 15.88 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.27), residues: 1016
  helix:  2.29 (0.26), residues: 400
  sheet: -0.25 (0.33), residues: 227
  loop : -1.30 (0.29), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.014   0.002   PHE B 241 
 TYR   0.012   0.001   TYR A 339 
 ARG   0.006   0.000   ARG R 187 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 187
  time to evaluate  : 1.719 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6406 (mm-30)
REVERT: A  209 GLU cc_start: 0.7082 (tp30) cc_final: 0.6737 (tp30)
REVERT: A  210 THR cc_start: 0.8195 (m) cc_final: 0.7362 (m)
REVERT: A  231 ARG cc_start: 0.8573 (ptp90) cc_final: 0.8361 (ptp-170)
REVERT: A  392 GLU cc_start: 0.7911 (tp30) cc_final: 0.7594 (tp30)
REVERT: B   40 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7870 (p)
REVERT: B   48 ARG cc_start: 0.8529 (mmt180) cc_final: 0.8316 (mmt-90)
REVERT: B  126 LEU cc_start: 0.7907 (mm) cc_final: 0.7632 (mt)
REVERT: B  214 ARG cc_start: 0.7910 (ptt90) cc_final: 0.7674 (ptt90)
REVERT: B  219 ARG cc_start: 0.8002 (mmt90) cc_final: 0.7729 (ttm-80)
REVERT: B  292 PHE cc_start: 0.7941 (m-10) cc_final: 0.7609 (m-80)
REVERT: B  318 LEU cc_start: 0.8111 (tp) cc_final: 0.7894 (tt)
REVERT: B  327 VAL cc_start: 0.8159 (t) cc_final: 0.7886 (p)
REVERT: G   21 MET cc_start: 0.7579 (tmm) cc_final: 0.7146 (tmm)
REVERT: N   31 ASN cc_start: 0.8382 (m110) cc_final: 0.8019 (m-40)
REVERT: N   43 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7843 (mmmt)
REVERT: N   60 TYR cc_start: 0.8603 (m-80) cc_final: 0.8278 (m-80)
REVERT: R  112 MET cc_start: 0.7971 (mmt) cc_final: 0.7595 (mpp)
  outliers start: 15
  outliers final: 8
  residues processed: 193
  average time/residue: 0.4083
  time to fit residues: 99.6867
Evaluate side-chains
  194 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 185
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  146 TRP
Chi-restraints excluded: chain R residue  170 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0970
   chunk 55 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 83 optimal weight:    0.0170
   chunk 81 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.4416

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

Flipped N/Q/H residues before XYZ refinement:
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.136503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.112810 restraints weight = 29384.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 4.34
r_work: 0.3221 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3182
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3182
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8181  Z= 0.142
  Angle     :  0.555   8.525  11107  Z= 0.264
  Chirality :  0.040   0.139   1242
  Planarity :  0.004   0.048   1431
  Dihedral  :  4.561  65.704   1145
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 17.18 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.27), residues: 1016
  helix:  2.39 (0.26), residues: 400
  sheet: -0.15 (0.33), residues: 228
  loop : -1.18 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.011   0.001   PHE B 241 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.005   0.000   ARG A 228 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 169
  time to evaluate  : 0.663 
Fit side-chains
REVERT: A  228 ARG cc_start: 0.7845 (ptm-80) cc_final: 0.7498 (ptt180)
REVERT: B   40 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7893 (p)
REVERT: B   61 MET cc_start: 0.7710 (ppp) cc_final: 0.7433 (ppp)
REVERT: B  126 LEU cc_start: 0.7744 (mm) cc_final: 0.7455 (mt)
REVERT: B  214 ARG cc_start: 0.7978 (ptt90) cc_final: 0.7718 (ptt90)
REVERT: B  219 ARG cc_start: 0.8035 (mmt90) cc_final: 0.7797 (ttm-80)
REVERT: B  263 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8177 (p)
REVERT: B  292 PHE cc_start: 0.7856 (m-10) cc_final: 0.7573 (m-80)
REVERT: G   21 MET cc_start: 0.7569 (tmm) cc_final: 0.7157 (tmm)
REVERT: N   31 ASN cc_start: 0.8394 (m110) cc_final: 0.8076 (m-40)
REVERT: N   43 LYS cc_start: 0.8250 (mmmt) cc_final: 0.7877 (mmmt)
REVERT: N   60 TYR cc_start: 0.8580 (m-80) cc_final: 0.8380 (m-80)
REVERT: R  112 MET cc_start: 0.8030 (mmt) cc_final: 0.7660 (mpp)
  outliers start: 14
  outliers final: 8
  residues processed: 176
  average time/residue: 0.2858
  time to fit residues: 63.8952
Evaluate side-chains
  179 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 169
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  146 TRP
Chi-restraints excluded: chain R residue  170 VAL
Chi-restraints excluded: chain R residue  185 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 85 optimal weight:    0.0010
   chunk 20 optimal weight:    0.4980
   chunk 70 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 99 optimal weight:    0.0060
   chunk 71 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0670
   chunk 77 optimal weight:    0.9980
   overall best weight:    0.2940

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

Flipped N/Q/H residues before XYZ refinement:
B  54 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.138901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.116194 restraints weight = 22408.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 3.72
r_work: 0.3273 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8181  Z= 0.130
  Angle     :  0.549   7.789  11107  Z= 0.261
  Chirality :  0.041   0.141   1242
  Planarity :  0.004   0.047   1431
  Dihedral  :  4.428  65.371   1145
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 17.89 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.27), residues: 1016
  helix:  2.47 (0.26), residues: 400
  sheet: -0.14 (0.34), residues: 230
  loop : -1.11 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.000   HIS A 220 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.006   0.000   ARG R 187 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 173
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 ARG cc_start: 0.7813 (ptm-80) cc_final: 0.7442 (ptt180)
REVERT: B   40 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7859 (p)
REVERT: B   61 MET cc_start: 0.7582 (ppp) cc_final: 0.7287 (ppp)
REVERT: B  126 LEU cc_start: 0.7680 (mm) cc_final: 0.7398 (mt)
REVERT: B  214 ARG cc_start: 0.7917 (ptt90) cc_final: 0.7445 (ptt90)
REVERT: B  219 ARG cc_start: 0.8015 (mmt90) cc_final: 0.7721 (ttm-80)
REVERT: B  263 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8167 (p)
REVERT: B  292 PHE cc_start: 0.7803 (m-10) cc_final: 0.7537 (m-80)
REVERT: B  298 ASP cc_start: 0.8184 (t0) cc_final: 0.7982 (t0)
REVERT: B  300 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8181 (mp)
REVERT: G   21 MET cc_start: 0.7509 (tmm) cc_final: 0.7156 (tmm)
REVERT: N   31 ASN cc_start: 0.8303 (m110) cc_final: 0.8006 (m-40)
REVERT: N   43 LYS cc_start: 0.8233 (mmmt) cc_final: 0.7871 (mmmt)
REVERT: R  112 MET cc_start: 0.7893 (mmt) cc_final: 0.7510 (mpp)
  outliers start: 16
  outliers final: 9
  residues processed: 181
  average time/residue: 0.2799
  time to fit residues: 65.2263
Evaluate side-chains
  181 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 169
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  146 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0980
   chunk 57 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 70 optimal weight:    4.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
N  39 GLN
R 119 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.137142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.115766 restraints weight = 17852.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 3.24
r_work: 0.3296 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3226
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3226
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8181  Z= 0.185
  Angle     :  0.581   8.816  11107  Z= 0.276
  Chirality :  0.042   0.136   1242
  Planarity :  0.004   0.048   1431
  Dihedral  :  4.482  65.273   1145
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 19.19 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.27), residues: 1016
  helix:  2.42 (0.26), residues: 400
  sheet: -0.06 (0.34), residues: 227
  loop : -1.16 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.012   0.001   PHE B 241 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.006   0.000   ARG R 187 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 179
  time to evaluate  : 0.791 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6342 (mm-30)
REVERT: A  209 GLU cc_start: 0.6925 (tp30) cc_final: 0.6642 (tp30)
REVERT: A  228 ARG cc_start: 0.7955 (ptm-80) cc_final: 0.7556 (ptt180)
REVERT: A  392 GLU cc_start: 0.7753 (tp30) cc_final: 0.7484 (tp30)
REVERT: B   40 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7920 (p)
REVERT: B   61 MET cc_start: 0.7510 (ppp) cc_final: 0.7292 (ppp)
REVERT: B  126 LEU cc_start: 0.7800 (mm) cc_final: 0.7548 (mt)
REVERT: B  214 ARG cc_start: 0.7906 (ptt90) cc_final: 0.7451 (ptt90)
REVERT: B  263 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8175 (p)
REVERT: B  292 PHE cc_start: 0.7886 (m-10) cc_final: 0.7615 (m-80)
REVERT: B  300 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8198 (mp)
REVERT: G   21 MET cc_start: 0.7469 (tmm) cc_final: 0.7150 (tmm)
REVERT: N   31 ASN cc_start: 0.8328 (m110) cc_final: 0.8008 (m-40)
REVERT: N   43 LYS cc_start: 0.8238 (mmmt) cc_final: 0.7909 (mmmt)
REVERT: R   90 LEU cc_start: 0.7266 (pp) cc_final: 0.6683 (mt)
REVERT: R  112 MET cc_start: 0.7949 (mmt) cc_final: 0.7566 (mpp)
  outliers start: 15
  outliers final: 11
  residues processed: 188
  average time/residue: 0.2575
  time to fit residues: 61.7554
Evaluate side-chains
  186 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 172
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  146 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 75 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0980
   chunk 55 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 78 optimal weight:    0.0870
   overall best weight:    0.5760

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

Flipped N/Q/H residues before XYZ refinement:
N  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.137863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.114018 restraints weight = 29227.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 4.33
r_work: 0.3213 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8181  Z= 0.163
  Angle     :  0.575   9.185  11107  Z= 0.274
  Chirality :  0.041   0.139   1242
  Planarity :  0.004   0.051   1431
  Dihedral  :  4.462  65.241   1145
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 19.91 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.27), residues: 1016
  helix:  2.48 (0.26), residues: 400
  sheet: -0.01 (0.34), residues: 227
  loop : -1.14 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.012   0.001   PHE B 241 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.005   0.000   ARG R 187 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 174
  time to evaluate  : 0.853 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6409 (mm-30)
REVERT: A  209 GLU cc_start: 0.7082 (tp30) cc_final: 0.6824 (tp30)
REVERT: A  228 ARG cc_start: 0.7931 (ptm-80) cc_final: 0.7561 (ptt180)
REVERT: A  392 GLU cc_start: 0.7843 (tp30) cc_final: 0.7551 (tp30)
REVERT: B   40 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.7946 (p)
REVERT: B  126 LEU cc_start: 0.7830 (mm) cc_final: 0.7571 (mt)
REVERT: B  214 ARG cc_start: 0.7998 (ptt90) cc_final: 0.7503 (ptt90)
REVERT: B  263 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8185 (p)
REVERT: B  292 PHE cc_start: 0.7918 (m-10) cc_final: 0.7661 (m-80)
REVERT: G   21 MET cc_start: 0.7623 (tmm) cc_final: 0.7198 (tmm)
REVERT: N   31 ASN cc_start: 0.8339 (m110) cc_final: 0.8029 (m-40)
REVERT: N   43 LYS cc_start: 0.8247 (mmmt) cc_final: 0.7915 (mmmt)
REVERT: R   90 LEU cc_start: 0.7377 (pp) cc_final: 0.6597 (mt)
REVERT: R  112 MET cc_start: 0.8034 (mmt) cc_final: 0.7655 (mpp)
  outliers start: 14
  outliers final: 10
  residues processed: 181
  average time/residue: 0.2648
  time to fit residues: 60.9734
Evaluate side-chains
  184 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 172
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  146 TRP
Chi-restraints excluded: chain R residue  185 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 91 optimal weight:    0.2980
   chunk 10 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.133100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.110767 restraints weight = 25200.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 3.74
r_work: 0.3208 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3194
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3194
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8181  Z= 0.257
  Angle     :  0.628  10.190  11107  Z= 0.302
  Chirality :  0.043   0.147   1242
  Planarity :  0.004   0.057   1431
  Dihedral  :  4.689  66.032   1145
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 20.73 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.27), residues: 1016
  helix:  2.33 (0.26), residues: 400
  sheet: -0.14 (0.34), residues: 228
  loop : -1.16 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.017   0.002   PHE N 108 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.006   0.000   ARG R 187 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 197
  time to evaluate  : 0.872 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6479 (mm-30)
REVERT: A  209 GLU cc_start: 0.7029 (tp30) cc_final: 0.6805 (tp30)
REVERT: A  210 THR cc_start: 0.8269 (m) cc_final: 0.7659 (m)
REVERT: A  228 ARG cc_start: 0.8037 (ptm-80) cc_final: 0.7635 (ptt180)
REVERT: A  392 GLU cc_start: 0.7882 (tp30) cc_final: 0.7593 (tp30)
REVERT: B   40 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7948 (p)
REVERT: B  126 LEU cc_start: 0.8068 (mm) cc_final: 0.7806 (mt)
REVERT: B  194 PRO cc_start: 0.8626 (Cg_exo) cc_final: 0.8391 (Cg_endo)
REVERT: B  214 ARG cc_start: 0.7915 (ptt90) cc_final: 0.7429 (ptt90)
REVERT: G   21 MET cc_start: 0.7486 (tmm) cc_final: 0.7083 (tmm)
REVERT: N   31 ASN cc_start: 0.8390 (m110) cc_final: 0.8178 (m-40)
REVERT: N   43 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7862 (mmmt)
REVERT: R   90 LEU cc_start: 0.7299 (pp) cc_final: 0.6575 (mt)
REVERT: R  112 MET cc_start: 0.7988 (mmt) cc_final: 0.7601 (mpp)
  outliers start: 13
  outliers final: 11
  residues processed: 203
  average time/residue: 0.2921
  time to fit residues: 74.0743
Evaluate side-chains
  207 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 195
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  146 TRP
Chi-restraints excluded: chain R residue  185 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 98 optimal weight:    0.0030
   chunk 81 optimal weight:    0.9980
   chunk 99 optimal weight:    0.0070
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.4608

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

Flipped N/Q/H residues before XYZ refinement:
N  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.137076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.114396 restraints weight = 23691.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 3.87
r_work: 0.3231 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3199
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8181  Z= 0.155
  Angle     :  0.584  10.144  11107  Z= 0.278
  Chirality :  0.041   0.142   1242
  Planarity :  0.004   0.052   1431
  Dihedral  :  4.501  65.965   1145
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 20.97 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.27), residues: 1016
  helix:  2.48 (0.26), residues: 400
  sheet: -0.08 (0.35), residues: 228
  loop : -1.10 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.011   0.001   PHE B 241 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.005   0.000   ARG R 187 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5110.61 seconds
wall clock time: 91 minutes 56.26 seconds (5516.26 seconds total)