Starting phenix.real_space_refine
on Tue Jul 29 04:07:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x2f_32966/07_2025/7x2f_32966.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x2f_32966/07_2025/7x2f_32966.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x2f_32966/07_2025/7x2f_32966.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x2f_32966/07_2025/7x2f_32966.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x2f_32966/07_2025/7x2f_32966.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x2f_32966/07_2025/7x2f_32966.cif"
  }
  resolution = 3.0
  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=   0.106
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3031 atoms to isotropic.
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      54      5.16       5
     Cl      2      4.86       5
     C    5252      2.51       5
     N    1429      2.21       5
     O    1512      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8249
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "F"
      Number of atoms: 2242
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2242
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 9, 'TRANS': 272}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 1896
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1896
          Classifications: {'peptide': 228}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 971
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2609
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 341, 2599
          Classifications: {'peptide': 341}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
      Conformer: "B"
        Number of residues, atoms: 341, 2599
          Classifications: {'peptide': 341}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
          bond proxies already assigned to first conformer: 2633
    Chain: "D"
      Number of atoms: 434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 434
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "F"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 97
          Unusual residues: {'CLR': 2, 'G4C': 1, 'LDP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 6.43, per 1000 atoms: 0.78
  Number of scatterers: 8249
  At special positions: 0
  Unit cell: (78.264, 101.091, 128.266, 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      54     16.00
     O    1512      8.00
     N    1429      7.00
     C    5252      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS F  96 " - pdb=" SG  CYS F 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  99 " - pdb=" SG  CYS E 107 " 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: 2.29
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1966

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 10 sheets defined
      45.2% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'F' and resid 21 through 51
    Processing helix  chain 'F' and resid 51 through 57
      removed outlier: 4.033A  pdb=" N   ARG F  55 " --> pdb=" O   PHE F  51 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   LYS F  57 " --> pdb=" O   HIS F  53 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 59 through 77
      removed outlier: 4.081A  pdb=" N   VAL F  63 " --> pdb=" O   THR F  59 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 77 through 88
    Processing helix  chain 'F' and resid 94 through 126
      removed outlier: 4.063A  pdb=" N   ILE F  98 " --> pdb=" O   SER F  94 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ALA F 101 " --> pdb=" O   ASN F  97 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ASN F 113 " --> pdb=" O   ALA F 109 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 127 through 135
      removed outlier: 3.836A  pdb=" N   GLU F 132 " --> pdb=" O   PRO F 128 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ARG F 133 " --> pdb=" O   PHE F 129 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 136 through 161
      removed outlier: 3.554A  pdb=" N   VAL F 152 " --> pdb=" O   TRP F 148 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ILE F 157 " --> pdb=" O   LEU F 153 " (cutoff:3.500A)
      Proline residue:  F 158  - end of helix
      removed outlier: 3.586A  pdb=" N   LEU F 161 " --> pdb=" O   ILE F 157 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 191 through 203
      removed outlier: 3.825A  pdb=" N   ILE F 196 " --> pdb=" O   ARG F 192 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ILE F 201 " --> pdb=" O   SER F 197 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 203 through 241
      removed outlier: 3.802A  pdb=" N   MET F 210 " --> pdb=" O   PRO F 206 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU F 231 " --> pdb=" O   ARG F 227 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 265 through 299
      removed outlier: 4.042A  pdb=" N   PHE F 281 " --> pdb=" O   ILE F 277 " (cutoff:3.500A)
      Proline residue:  F 287  - end of helix
      Proline residue:  F 296  - end of helix
    Processing helix  chain 'F' and resid 309 through 332
      removed outlier: 3.892A  pdb=" N   ASN F 323 " --> pdb=" O   PHE F 319 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   SER F 324 " --> pdb=" O   GLY F 320 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   SER F 325 " --> pdb=" O   TRP F 321 " (cutoff:3.500A)
      Proline residue:  F 328  - end of helix
    Processing helix  chain 'F' and resid 334 through 346
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.606A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 232 through 239
      removed outlier: 3.625A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.038A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.684A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.670A  pdb=" N   TYR E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 4.011A  pdb=" N   THR E  91 " --> pdb=" O   PRO E  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 25
      removed outlier: 3.934A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'D' and resid 9 through 24
      removed outlier: 3.578A  pdb=" N   GLU D  17 " --> pdb=" O   ARG D  13 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.563A  pdb=" N   LEU D  37 " --> pdb=" O   ALA D  33 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   HIS D  44 " --> pdb=" O   TYR D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 48
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 8.985A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.846A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AA3, first strand: chain 'E' and resid 11 through 12
      removed outlier: 6.097A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.737A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.771A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.086A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.430A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.910A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.923A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.606A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.521A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.752A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.606A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)

    426 hydrogen bonds defined for protein.
    1221 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: 2.77

  Time building geometry restraints manager: 2.64 seconds

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

  Histogram of bond lengths:
        1.12 -     1.26: 1326
        1.26 -     1.40: 2139
        1.40 -     1.54: 4786
        1.54 -     1.68: 101
        1.68 -     1.82: 75
  Bond restraints: 8427
  Sorted by residual:
  bond pdb=" C   ARG F 130 "
       pdb=" O   ARG F 130 "
    ideal  model  delta    sigma   weight residual
    1.237  1.121  0.115 1.17e-02 7.31e+03 9.70e+01
  bond pdb=" C05 G4C F 502 "
       pdb=" N04 G4C F 502 "
    ideal  model  delta    sigma   weight residual
    1.355  1.511 -0.156 2.00e-02 2.50e+03 6.08e+01
  bond pdb=" CA  ARG F 130 "
       pdb=" C   ARG F 130 "
    ideal  model  delta    sigma   weight residual
    1.523  1.430  0.093 1.30e-02 5.92e+03 5.13e+01
  bond pdb=" CA  TYR B 145 "
       pdb=" CB  TYR B 145 "
    ideal  model  delta    sigma   weight residual
    1.527  1.431  0.096 1.44e-02 4.82e+03 4.47e+01
  bond pdb=" CA  ARG F 130 "
       pdb=" CB  ARG F 130 "
    ideal  model  delta    sigma   weight residual
    1.528  1.435  0.094 1.56e-02 4.11e+03 3.60e+01
  ... (remaining 8422 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 11177
        2.45 -     4.90: 216
        4.90 -     7.35: 32
        7.35 -     9.79: 7
        9.79 -    12.24: 2
  Bond angle restraints: 11434
  Sorted by residual:
  angle pdb=" C   ARG F 130 "
        pdb=" CA  ARG F 130 "
        pdb=" CB  ARG F 130 "
      ideal   model   delta    sigma   weight residual
     110.79   99.41   11.38 1.66e+00 3.63e-01 4.70e+01
  angle pdb=" N   GLU A 344 "
        pdb=" CA  GLU A 344 "
        pdb=" CB  GLU A 344 "
      ideal   model   delta    sigma   weight residual
     110.28  119.54   -9.26 1.55e+00 4.16e-01 3.57e+01
  angle pdb=" N   ARG A 232 "
        pdb=" CA  ARG A 232 "
        pdb=" C   ARG A 232 "
      ideal   model   delta    sigma   weight residual
     111.04  118.60   -7.56 1.55e+00 4.16e-01 2.38e+01
  angle pdb=" O   GLY B 144 "
        pdb=" C   GLY B 144 "
        pdb=" N   TYR B 145 "
      ideal   model   delta    sigma   weight residual
     123.65  119.24    4.41 9.20e-01 1.18e+00 2.30e+01
  angle pdb=" C   GLY B 144 "
        pdb=" N   TYR B 145 "
        pdb=" CA  TYR B 145 "
      ideal   model   delta    sigma   weight residual
     121.29  113.85    7.44 1.74e+00 3.30e-01 1.83e+01
  ... (remaining 11429 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 4682
       17.93 -    35.85: 373
       35.85 -    53.78: 54
       53.78 -    71.71: 10
       71.71 -    89.64: 4
  Dihedral angle restraints: 5123
    sinusoidal: 2093
      harmonic: 3030
  Sorted by residual:
  dihedral pdb=" C   ARG F 130 "
           pdb=" N   ARG F 130 "
           pdb=" CA  ARG F 130 "
           pdb=" CB  ARG F 130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -108.59  -14.01     0      2.50e+00 1.60e-01 3.14e+01
  dihedral pdb=" CA  ASN A 254 "
           pdb=" C   ASN A 254 "
           pdb=" N   ARG A 265 "
           pdb=" CA  ARG A 265 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.80   24.20     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  96 "
           pdb=" CB  CYS E  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.69   37.31     1      1.00e+01 1.00e-02 1.96e+01
  ... (remaining 5120 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1142
       0.076 -    0.152: 132
       0.152 -    0.228: 10
       0.228 -    0.303: 2
       0.303 -    0.379: 3
  Chirality restraints: 1289
  Sorted by residual:
  chirality pdb=" CA  TYR B 145 "
            pdb=" N   TYR B 145 "
            pdb=" C   TYR B 145 "
            pdb=" CB  TYR B 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.59e+00
  chirality pdb=" C13 CLR F 501 "
            pdb=" C12 CLR F 501 "
            pdb=" C14 CLR F 501 "
            pdb=" C17 CLR F 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.57   -0.37 2.00e-01 2.50e+01 3.34e+00
  chirality pdb=" C13 CLR F 503 "
            pdb=" C12 CLR F 503 "
            pdb=" C14 CLR F 503 "
            pdb=" C17 CLR F 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.58   -0.35 2.00e-01 2.50e+01 3.05e+00
  ... (remaining 1286 not shown)

  Planarity restraints: 1443
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.026 2.00e-02 2.50e+03   2.18e-02 9.47e+00
        pdb=" CG  TYR B  59 "    0.054 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 145 "   -0.030 2.00e-02 2.50e+03   2.05e-02 8.40e+00
        pdb=" CG  TYR B 145 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 145 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 145 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 145 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 145 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 145 "   -0.028 2.00e-02 2.50e+03
        pdb=" OH  TYR B 145 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  25 "   -0.013 2.00e-02 2.50e+03   2.51e-02 6.32e+00
        pdb=" C   LYS A  25 "    0.043 2.00e-02 2.50e+03
        pdb=" O   LYS A  25 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ILE A  26 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1440 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 324
        2.71 -     3.26: 8343
        3.26 -     3.81: 13470
        3.81 -     4.35: 17006
        4.35 -     4.90: 28942
  Nonbonded interactions: 68085
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" OG  SER F 198 "
            pdb=" O2  LDP F 504 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" NE2 HIS B 225 "
            pdb=" OG1 THR B 243 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OE1 GLN A  35 "
            pdb=" NH2 ARG A  38 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.236 3.040
  ... (remaining 68080 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:             0.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     25.810
  Find NCS groups from input model:        0.100
  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:21.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.156   8430  Z= 0.341
  Angle     :  0.830  12.242  11440  Z= 0.456
  Chirality :  0.053   0.379   1289
  Planarity :  0.005   0.047   1443
  Dihedral  : 12.875  89.636   3148
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.34 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.20 %
  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: -0.87 (0.25), residues: 1021
  helix:  0.04 (0.25), residues: 403
  sheet: -0.60 (0.32), residues: 216
  loop : -1.05 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 297 
 HIS   0.012   0.002   HIS A 220 
 PHE   0.041   0.002   PHE A 340 
 TYR   0.054   0.002   TYR B  59 
 ARG   0.005   0.000   ARG E  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14493 (  426)
  hydrogen bonds       : angle       6.67063 ( 1221)
  SS BOND              : bond        0.00055 (    3)
  SS BOND              : angle       1.19481 (    6)
  covalent geometry    : bond        0.00642 ( 8427)
  covalent geometry    : angle       0.82975 (11434)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8258 (tp-100) cc_final: 0.7826 (tp40)
REVERT: A  315 PHE cc_start: 0.7254 (t80) cc_final: 0.6856 (t80)
REVERT: E   60 TYR cc_start: 0.8383 (m-80) cc_final: 0.8112 (m-80)
REVERT: E   69 THR cc_start: 0.7751 (p) cc_final: 0.7543 (t)
REVERT: B  259 GLN cc_start: 0.8072 (pt0) cc_final: 0.7802 (pt0)
REVERT: D   38 MET cc_start: 0.6412 (mmt) cc_final: 0.5838 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 145
  average time/residue: 1.0500
  time to fit residues: 163.5868
Evaluate side-chains
  107 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 51 optimal weight:   20.0000
   chunk 40 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 58 optimal weight:    0.1980
   chunk 91 optimal weight:    0.8980
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.182983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.133874 restraints weight = 21277.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 4.16
r_work: 0.3479 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3468
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3468 r_free = 0.3468    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3468 r_free = 0.3468    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3468
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6782
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8430  Z= 0.129
  Angle     :  0.565   7.666  11440  Z= 0.299
  Chirality :  0.043   0.153   1289
  Planarity :  0.004   0.044   1443
  Dihedral  :  6.189  86.777   1288
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 11.69 %
    Favored  : 86.38 %
  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:  0.43 (0.25), residues: 1021
  helix:  1.44 (0.25), residues: 408
  sheet: -0.20 (0.31), residues: 229
  loop : -0.57 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 169 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.028   0.002   PHE A 340 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.003   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04327 (  426)
  hydrogen bonds       : angle       4.74356 ( 1221)
  SS BOND              : bond        0.00579 (    3)
  SS BOND              : angle       0.60539 (    6)
  covalent geometry    : bond        0.00285 ( 8427)
  covalent geometry    : angle       0.56505 (11434)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.911 
Fit side-chains
REVERT: F  163 TRP cc_start: 0.7461 (m-10) cc_final: 0.7201 (m-10)
REVERT: F  269 LYS cc_start: 0.6929 (tppt) cc_final: 0.6661 (tttp)
REVERT: A  315 PHE cc_start: 0.7067 (t80) cc_final: 0.6783 (t80)
REVERT: A  317 ARG cc_start: 0.8575 (mtm110) cc_final: 0.8221 (mtm110)
REVERT: E   60 TYR cc_start: 0.8326 (m-80) cc_final: 0.8094 (m-80)
REVERT: E   83 MET cc_start: 0.6420 (mtm) cc_final: 0.6000 (mtp)
REVERT: B  156 GLN cc_start: 0.6634 (mp10) cc_final: 0.6387 (mp10)
REVERT: B  195 ASP cc_start: 0.6814 (p0) cc_final: 0.6502 (p0)
REVERT: B  259 GLN cc_start: 0.6978 (pt0) cc_final: 0.6610 (pt0)
REVERT: D   38 MET cc_start: 0.5497 (mmt) cc_final: 0.5214 (mpt)
  outliers start: 17
  outliers final: 8
  residues processed: 124
  average time/residue: 0.9879
  time to fit residues: 132.5175
Evaluate side-chains
  109 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  105 MET
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain E residue  114 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue  269 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 58 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   overall best weight:    1.2182

-------------------------------------------------------------------------------
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 = 0.4133 r_free = 0.4133 target = 0.182253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.128108 restraints weight = 30504.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 5.31
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3568
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3568 r_free = 0.3568    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3568 r_free = 0.3568    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3568
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6463
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8430  Z= 0.144
  Angle     :  0.551   8.579  11440  Z= 0.291
  Chirality :  0.043   0.146   1289
  Planarity :  0.004   0.044   1443
  Dihedral  :  6.074  85.360   1288
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.53 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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:  0.75 (0.26), residues: 1021
  helix:  1.76 (0.26), residues: 414
  sheet: -0.09 (0.31), residues: 225
  loop : -0.46 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  82 
 HIS   0.005   0.001   HIS F  53 
 PHE   0.016   0.002   PHE A 212 
 TYR   0.011   0.001   TYR B 111 
 ARG   0.004   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04133 (  426)
  hydrogen bonds       : angle       4.46158 ( 1221)
  SS BOND              : bond        0.00602 (    3)
  SS BOND              : angle       2.28136 (    6)
  covalent geometry    : bond        0.00338 ( 8427)
  covalent geometry    : angle       0.54858 (11434)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 1.893 
Fit side-chains
REVERT: F  163 TRP cc_start: 0.7198 (m-10) cc_final: 0.6966 (m-10)
REVERT: F  269 LYS cc_start: 0.6749 (tppt) cc_final: 0.6430 (tttp)
REVERT: A  315 PHE cc_start: 0.6678 (t80) cc_final: 0.6443 (t80)
REVERT: A  317 ARG cc_start: 0.8559 (mtm110) cc_final: 0.8108 (mtm110)
REVERT: A  344 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6475 (mp0)
REVERT: E   83 MET cc_start: 0.6230 (mtm) cc_final: 0.5983 (mtp)
REVERT: B  156 GLN cc_start: 0.6209 (mp10) cc_final: 0.5902 (mp10)
REVERT: B  184 THR cc_start: 0.8485 (p) cc_final: 0.8251 (t)
REVERT: B  259 GLN cc_start: 0.6872 (pt0) cc_final: 0.6515 (pt0)
REVERT: D   38 MET cc_start: 0.5522 (mmt) cc_final: 0.5095 (mpt)
  outliers start: 19
  outliers final: 11
  residues processed: 121
  average time/residue: 1.0452
  time to fit residues: 137.0812
Evaluate side-chains
  110 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  212 VAL
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain E residue  114 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  269 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 79 optimal weight:    0.0030
   chunk 41 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   chunk 77 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0370
   chunk 36 optimal weight:    0.5980
   chunk 92 optimal weight:    5.9990
   overall best weight:    0.9272

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

Flipped N/Q/H residues before XYZ refinement:
E  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.181833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.129141 restraints weight = 30216.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 5.15
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3586
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3586
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6476
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8430  Z= 0.124
  Angle     :  0.527   9.009  11440  Z= 0.277
  Chirality :  0.041   0.144   1289
  Planarity :  0.003   0.042   1443
  Dihedral  :  5.814  83.521   1288
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.10 %
    Favored  : 82.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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:  0.98 (0.26), residues: 1021
  helix:  2.03 (0.26), residues: 413
  sheet:  0.05 (0.32), residues: 220
  loop : -0.45 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  82 
 HIS   0.005   0.001   HIS F  53 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.020   0.001   TYR E  60 
 ARG   0.003   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03830 (  426)
  hydrogen bonds       : angle       4.28216 ( 1221)
  SS BOND              : bond        0.00276 (    3)
  SS BOND              : angle       1.52932 (    6)
  covalent geometry    : bond        0.00286 ( 8427)
  covalent geometry    : angle       0.52570 (11434)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.809 
Fit side-chains
REVERT: F  163 TRP cc_start: 0.7300 (m-10) cc_final: 0.7041 (m-10)
REVERT: F  269 LYS cc_start: 0.6830 (tppt) cc_final: 0.6511 (tttp)
REVERT: F  333 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7245 (m-10)
REVERT: A  317 ARG cc_start: 0.8565 (mtm110) cc_final: 0.8102 (mtm110)
REVERT: A  344 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6372 (mp0)
REVERT: E   83 MET cc_start: 0.6377 (mtm) cc_final: 0.6108 (mtp)
REVERT: B   59 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7345 (m-80)
REVERT: B  156 GLN cc_start: 0.6151 (mp10) cc_final: 0.5857 (mp10)
REVERT: B  161 SER cc_start: 0.8236 (t) cc_final: 0.7584 (p)
REVERT: B  259 GLN cc_start: 0.6969 (pt0) cc_final: 0.6650 (pt0)
REVERT: D   38 MET cc_start: 0.5329 (mmt) cc_final: 0.4978 (mpt)
  outliers start: 22
  outliers final: 12
  residues processed: 128
  average time/residue: 0.8697
  time to fit residues: 121.1903
Evaluate side-chains
  118 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  212 VAL
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  269 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 57 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9990
   chunk 44 optimal weight:    6.9990
   chunk 28 optimal weight:    8.9990
   chunk 66 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.179711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.129770 restraints weight = 20082.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 4.10
r_work: 0.3392 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3417
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3417 r_free = 0.3417    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3417 r_free = 0.3417    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3417
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6600
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8430  Z= 0.142
  Angle     :  0.528   5.934  11440  Z= 0.281
  Chirality :  0.042   0.147   1289
  Planarity :  0.003   0.042   1443
  Dihedral  :  5.733  81.595   1288
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 16.57 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.26), residues: 1021
  helix:  2.11 (0.26), residues: 413
  sheet: -0.01 (0.32), residues: 223
  loop : -0.38 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.007   0.001   HIS F  53 
 PHE   0.021   0.002   PHE A 315 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.003   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03910 (  426)
  hydrogen bonds       : angle       4.26464 ( 1221)
  SS BOND              : bond        0.00220 (    3)
  SS BOND              : angle       1.42871 (    6)
  covalent geometry    : bond        0.00332 ( 8427)
  covalent geometry    : angle       0.52665 (11434)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.816 
Fit side-chains
REVERT: F  163 TRP cc_start: 0.7588 (m-10) cc_final: 0.7329 (m-10)
REVERT: F  269 LYS cc_start: 0.6988 (tppt) cc_final: 0.6781 (tttp)
REVERT: F  333 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7183 (m-10)
REVERT: A   29 GLN cc_start: 0.7946 (tp-100) cc_final: 0.7504 (tp40)
REVERT: A   31 GLN cc_start: 0.7411 (tp-100) cc_final: 0.7095 (tp40)
REVERT: A  213 GLN cc_start: 0.8431 (mt0) cc_final: 0.8219 (tt0)
REVERT: A  227 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8064 (mp10)
REVERT: A  317 ARG cc_start: 0.8572 (mtm110) cc_final: 0.8119 (mtm110)
REVERT: A  344 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6482 (mp0)
REVERT: E   83 MET cc_start: 0.6481 (mtm) cc_final: 0.6198 (mtp)
REVERT: B   59 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7769 (m-80)
REVERT: B  156 GLN cc_start: 0.6271 (mp10) cc_final: 0.5971 (mp10)
REVERT: B  161 SER cc_start: 0.8276 (t) cc_final: 0.7674 (p)
REVERT: B  259 GLN cc_start: 0.6655 (pt0) cc_final: 0.6336 (pt0)
REVERT: D   38 MET cc_start: 0.5546 (mmt) cc_final: 0.5134 (mpt)
  outliers start: 23
  outliers final: 14
  residues processed: 129
  average time/residue: 0.9422
  time to fit residues: 131.7334
Evaluate side-chains
  129 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  155 SER
Chi-restraints excluded: chain F residue  212 VAL
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  227 GLN
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 70 optimal weight:    0.3980
   chunk 16 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 52 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0570
   chunk 56 optimal weight:    8.9990
   chunk 48 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.8500

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

Flipped N/Q/H residues before XYZ refinement:
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
A 294 GLN
B  75 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.180343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.129106 restraints weight = 29633.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 4.92
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3598
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3598 r_free = 0.3598    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3598 r_free = 0.3598    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3598
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6688
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8430  Z= 0.117
  Angle     :  0.516   9.545  11440  Z= 0.271
  Chirality :  0.041   0.142   1289
  Planarity :  0.003   0.041   1443
  Dihedral  :  5.555  79.257   1288
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 17.03 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.26), residues: 1021
  helix:  2.19 (0.26), residues: 413
  sheet:  0.03 (0.33), residues: 223
  loop : -0.32 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  82 
 HIS   0.007   0.001   HIS F  53 
 PHE   0.033   0.001   PHE A 315 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.003   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03674 (  426)
  hydrogen bonds       : angle       4.17272 ( 1221)
  SS BOND              : bond        0.00230 (    3)
  SS BOND              : angle       1.21965 (    6)
  covalent geometry    : bond        0.00270 ( 8427)
  covalent geometry    : angle       0.51556 (11434)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.896 
Fit side-chains
REVERT: F  163 TRP cc_start: 0.7521 (m-10) cc_final: 0.7278 (m-10)
REVERT: F  269 LYS cc_start: 0.7087 (tppt) cc_final: 0.6791 (tttm)
REVERT: F  333 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7400 (m-10)
REVERT: A   29 GLN cc_start: 0.8038 (tp-100) cc_final: 0.7580 (tp40)
REVERT: A   31 GLN cc_start: 0.7552 (tp-100) cc_final: 0.7165 (tp40)
REVERT: A  213 GLN cc_start: 0.8349 (mt0) cc_final: 0.8117 (tt0)
REVERT: A  317 ARG cc_start: 0.8618 (mtm110) cc_final: 0.8155 (mtm110)
REVERT: E   83 MET cc_start: 0.6487 (mtm) cc_final: 0.6230 (mtp)
REVERT: B   59 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.7517 (m-80)
REVERT: B  156 GLN cc_start: 0.6112 (mp10) cc_final: 0.5794 (mp10)
REVERT: B  161 SER cc_start: 0.8360 (t) cc_final: 0.7799 (p)
REVERT: B  259 GLN cc_start: 0.6819 (pt0) cc_final: 0.6506 (pt0)
REVERT: D   38 MET cc_start: 0.5662 (mmt) cc_final: 0.5167 (mpt)
  outliers start: 23
  outliers final: 14
  residues processed: 131
  average time/residue: 0.9250
  time to fit residues: 131.8333
Evaluate side-chains
  128 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 98 optimal weight:    9.9990
   chunk 94 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.178239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.132123 restraints weight = 26638.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 4.64
r_work: 0.3386 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3399
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3399
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6855
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8430  Z= 0.136
  Angle     :  0.524   6.774  11440  Z= 0.277
  Chirality :  0.042   0.147   1289
  Planarity :  0.003   0.041   1443
  Dihedral  :  5.534  77.226   1288
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 17.14 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.27), residues: 1021
  helix:  2.22 (0.26), residues: 411
  sheet: -0.00 (0.33), residues: 223
  loop : -0.32 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.008   0.001   HIS F  53 
 PHE   0.035   0.002   PHE A 315 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.003   0.000   ARG A 231 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03815 (  426)
  hydrogen bonds       : angle       4.18614 ( 1221)
  SS BOND              : bond        0.00265 (    3)
  SS BOND              : angle       1.27678 (    6)
  covalent geometry    : bond        0.00318 ( 8427)
  covalent geometry    : angle       0.52352 (11434)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 0.822 
Fit side-chains
REVERT: F  163 TRP cc_start: 0.7798 (m-10) cc_final: 0.7591 (m-10)
REVERT: F  269 LYS cc_start: 0.7241 (tppt) cc_final: 0.7019 (tttp)
REVERT: F  333 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7270 (m-10)
REVERT: A   29 GLN cc_start: 0.8058 (tp-100) cc_final: 0.7593 (tp40)
REVERT: A   31 GLN cc_start: 0.7531 (tp-100) cc_final: 0.7198 (tp40)
REVERT: A  227 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8235 (mp10)
REVERT: A  317 ARG cc_start: 0.8609 (mtm110) cc_final: 0.8134 (mtm110)
REVERT: E   83 MET cc_start: 0.6603 (mtm) cc_final: 0.6310 (mtp)
REVERT: B  156 GLN cc_start: 0.6511 (mp10) cc_final: 0.6276 (mp10)
REVERT: B  161 SER cc_start: 0.8535 (t) cc_final: 0.8014 (p)
REVERT: B  259 GLN cc_start: 0.6766 (pt0) cc_final: 0.6501 (pt0)
REVERT: D   38 MET cc_start: 0.5710 (mmt) cc_final: 0.5232 (mpt)
  outliers start: 28
  outliers final: 18
  residues processed: 127
  average time/residue: 0.9299
  time to fit residues: 128.1048
Evaluate side-chains
  124 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  155 SER
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  212 VAL
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  227 GLN
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 97 optimal weight:    8.9990
   chunk 89 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9990
   chunk 83 optimal weight:    0.5980
   chunk 74 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.177801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.131496 restraints weight = 27146.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 4.67
r_work: 0.3376 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3389
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3389
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6876
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8430  Z= 0.142
  Angle     :  0.541   9.928  11440  Z= 0.284
  Chirality :  0.042   0.157   1289
  Planarity :  0.003   0.040   1443
  Dihedral  :  5.538  75.178   1288
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.39 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.27), residues: 1021
  helix:  2.24 (0.26), residues: 410
  sheet: -0.04 (0.33), residues: 223
  loop : -0.32 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.008   0.001   HIS F  53 
 PHE   0.036   0.002   PHE A 315 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.003   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  426)
  hydrogen bonds       : angle       4.17583 ( 1221)
  SS BOND              : bond        0.00313 (    3)
  SS BOND              : angle       1.23287 (    6)
  covalent geometry    : bond        0.00334 ( 8427)
  covalent geometry    : angle       0.54049 (11434)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 1.249 
Fit side-chains
REVERT: F  163 TRP cc_start: 0.7751 (m-10) cc_final: 0.6943 (m100)
REVERT: F  333 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7253 (m-10)
REVERT: A   29 GLN cc_start: 0.8056 (tp-100) cc_final: 0.7597 (tp40)
REVERT: A   31 GLN cc_start: 0.7551 (tp-100) cc_final: 0.7207 (tp40)
REVERT: A  284 THR cc_start: 0.8831 (p) cc_final: 0.8422 (t)
REVERT: A  368 ASP cc_start: 0.7266 (t70) cc_final: 0.7013 (t70)
REVERT: B  156 GLN cc_start: 0.6518 (mp10) cc_final: 0.6262 (mp10)
REVERT: B  161 SER cc_start: 0.8544 (t) cc_final: 0.8080 (p)
REVERT: B  259 GLN cc_start: 0.6766 (pt0) cc_final: 0.6507 (pt0)
REVERT: D   38 MET cc_start: 0.5618 (mmt) cc_final: 0.5129 (mpt)
  outliers start: 23
  outliers final: 18
  residues processed: 117
  average time/residue: 1.0563
  time to fit residues: 134.5708
Evaluate side-chains
  119 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  212 VAL
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 15 optimal weight:    6.9990
   chunk 22 optimal weight:    0.7980
   chunk 90 optimal weight:   10.0000
   chunk 86 optimal weight:    0.1980
   chunk 77 optimal weight:    0.9990
   chunk 80 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
E  31 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.180872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.130935 restraints weight = 22293.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 4.30
r_work: 0.3446 rms_B_bonded: 4.64 restraints_weight: 0.5000
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3431
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3431 r_free = 0.3431    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3431 r_free = 0.3431    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3431
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6772
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8430  Z= 0.112
  Angle     :  0.516   7.515  11440  Z= 0.271
  Chirality :  0.041   0.160   1289
  Planarity :  0.003   0.041   1443
  Dihedral  :  5.331  72.938   1288
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 19.18 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.27), residues: 1021
  helix:  2.30 (0.26), residues: 409
  sheet: -0.06 (0.33), residues: 223
  loop : -0.31 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  82 
 HIS   0.008   0.001   HIS F  53 
 PHE   0.035   0.001   PHE A 315 
 TYR   0.007   0.001   TYR A 339 
 ARG   0.008   0.000   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03587 (  426)
  hydrogen bonds       : angle       4.08625 ( 1221)
  SS BOND              : bond        0.00273 (    3)
  SS BOND              : angle       1.02572 (    6)
  covalent geometry    : bond        0.00253 ( 8427)
  covalent geometry    : angle       0.51538 (11434)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
REVERT: F  163 TRP cc_start: 0.7735 (m-10) cc_final: 0.6939 (m100)
REVERT: F  333 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7129 (m-10)
REVERT: A   29 GLN cc_start: 0.8060 (tp-100) cc_final: 0.7596 (tp40)
REVERT: A   31 GLN cc_start: 0.7534 (tp-100) cc_final: 0.7165 (tp40)
REVERT: A  284 THR cc_start: 0.8797 (p) cc_final: 0.8389 (t)
REVERT: A  368 ASP cc_start: 0.7130 (t70) cc_final: 0.6878 (t70)
REVERT: B  156 GLN cc_start: 0.6447 (mp10) cc_final: 0.6178 (mp10)
REVERT: B  161 SER cc_start: 0.8423 (t) cc_final: 0.8021 (p)
REVERT: B  259 GLN cc_start: 0.6843 (pt0) cc_final: 0.6569 (pt0)
REVERT: D   38 MET cc_start: 0.5497 (mmt) cc_final: 0.5000 (mpt)
  outliers start: 17
  outliers final: 14
  residues processed: 118
  average time/residue: 0.9288
  time to fit residues: 118.6338
Evaluate side-chains
  118 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 20 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   chunk 92 optimal weight:    3.9990
   chunk 95 optimal weight:    0.0670
   chunk 64 optimal weight:    6.9990
   chunk 56 optimal weight:    0.8980
   chunk 88 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.3122

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

Flipped N/Q/H residues before XYZ refinement:
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
A 294 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.178172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.130674 restraints weight = 14947.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 3.37
r_work: 0.3453 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3471
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3471
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6870
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8430  Z= 0.144
  Angle     :  0.550   9.782  11440  Z= 0.287
  Chirality :  0.042   0.143   1289
  Planarity :  0.003   0.041   1443
  Dihedral  :  5.402  71.061   1288
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 19.52 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.27), residues: 1021
  helix:  2.26 (0.26), residues: 410
  sheet: -0.04 (0.33), residues: 223
  loop : -0.33 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.009   0.001   HIS F  53 
 PHE   0.037   0.002   PHE A 315 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.007   0.000   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03842 (  426)
  hydrogen bonds       : angle       4.15591 ( 1221)
  SS BOND              : bond        0.00318 (    3)
  SS BOND              : angle       1.18264 (    6)
  covalent geometry    : bond        0.00340 ( 8427)
  covalent geometry    : angle       0.54903 (11434)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 1.515 
Fit side-chains
REVERT: F   35 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7428 (mm)
REVERT: F  163 TRP cc_start: 0.7724 (m-10) cc_final: 0.6900 (m100)
REVERT: F  333 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7279 (m-10)
REVERT: A   31 GLN cc_start: 0.7539 (tp-100) cc_final: 0.7172 (tp40)
REVERT: A  284 THR cc_start: 0.8802 (p) cc_final: 0.8388 (t)
REVERT: A  356 ARG cc_start: 0.7899 (ttp-110) cc_final: 0.7637 (ttp-110)
REVERT: A  368 ASP cc_start: 0.7280 (t70) cc_final: 0.7045 (t70)
REVERT: B  156 GLN cc_start: 0.6522 (mp10) cc_final: 0.6249 (mp10)
REVERT: B  161 SER cc_start: 0.8541 (t) cc_final: 0.8109 (p)
REVERT: B  259 GLN cc_start: 0.6921 (pt0) cc_final: 0.6657 (pt0)
REVERT: D   38 MET cc_start: 0.5551 (mmt) cc_final: 0.5062 (mpt)
  outliers start: 18
  outliers final: 13
  residues processed: 113
  average time/residue: 1.3135
  time to fit residues: 162.7357
Evaluate side-chains
  120 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 86 optimal weight:    5.9990
   chunk 55 optimal weight:   10.0000
   chunk 96 optimal weight:   10.0000
   chunk 84 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
E  31 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.179730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.130649 restraints weight = 18213.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 4.11
r_work: 0.3526 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3521
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3521 r_free = 0.3521    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3521 r_free = 0.3521    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3521
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.2898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8430  Z= 0.121
  Angle     :  0.521   7.896  11440  Z= 0.275
  Chirality :  0.041   0.138   1289
  Planarity :  0.003   0.041   1443
  Dihedral  :  5.287  69.104   1288
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 19.52 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.27), residues: 1021
  helix:  2.33 (0.26), residues: 409
  sheet: -0.06 (0.33), residues: 223
  loop : -0.33 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  82 
 HIS   0.008   0.001   HIS F  53 
 PHE   0.037   0.001   PHE A 315 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.007   0.000   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03674 (  426)
  hydrogen bonds       : angle       4.09597 ( 1221)
  SS BOND              : bond        0.00327 (    3)
  SS BOND              : angle       0.99888 (    6)
  covalent geometry    : bond        0.00280 ( 8427)
  covalent geometry    : angle       0.52093 (11434)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6137.64 seconds
wall clock time: 108 minutes 53.95 seconds (6533.95 seconds total)