Starting phenix.real_space_refine
on Sun May 11 18:01:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ikh_35512/05_2025/8ikh_35512_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ikh_35512/05_2025/8ikh_35512.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ikh_35512/05_2025/8ikh_35512.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ikh_35512/05_2025/8ikh_35512.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ikh_35512/05_2025/8ikh_35512_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ikh_35512/05_2025/8ikh_35512_neut.cif"
  }
  resolution = 3.3
  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=   0.010 sd=   0.088
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    5376      2.51       5
     N    1433      2.21       5
     O    1534      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8403
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1675
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1675
          Classifications: {'peptide': 217}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 47
    Chain: "B"
      Number of atoms: 2547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2547
          Classifications: {'peptide': 333}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "C"
      Number of atoms: 406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 406
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "R"
      Number of atoms: 2076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 2076
          Classifications: {'peptide': 265}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 7, 'TRANS': 257}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "S"
      Number of atoms: 1671
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1671
          Classifications: {'peptide': 223}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 10, 'TRANS': 212}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 44
    Chain: "R"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'Q2L': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.06, per 1000 atoms: 0.60
  Number of scatterers: 8403
  At special positions: 0
  Unit cell: (96.12, 128.16, 126.38, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    1534      8.00
     N    1433      7.00
     C    5376      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.10
  Conformation dependent library (CDL) restraints added in 961.3 milliseconds
  

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2042

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 13 sheets defined
      37.1% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 28
      removed outlier: 3.768A  pdb=" N   GLU A  14 " --> pdb=" O   LYS A  10 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ARG A  15 " --> pdb=" O   ALA A  11 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   SER A  16 " --> pdb=" O   ALA A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 54
      removed outlier: 4.238A  pdb=" N   LYS A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   LYS A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 211
      removed outlier: 3.701A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 216
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 277
      removed outlier: 3.807A  pdb=" N   PHE A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 281
      removed outlier: 3.856A  pdb=" N   SER A 281 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 278 through 281'
    Processing helix  chain 'A' and resid 282 through 287
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.700A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
      removed outlier: 3.658A  pdb=" N   PHE A 334 " --> pdb=" O   LYS A 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 22
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 128 through 132
      removed outlier: 3.721A  pdb=" N   GLY B 131 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ASN B 132 " --> pdb=" O   ARG B 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 128 through 132'
    Processing helix  chain 'B' and resid 279 through 282
    Processing helix  chain 'C' and resid 8 through 23
      removed outlier: 3.617A  pdb=" N   GLN C  18 " --> pdb=" O   LYS C  14 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LEU C  19 " --> pdb=" O   LEU C  15 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   LYS C  20 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   MET C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.707A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   HIS C  44 " --> pdb=" O   TYR C  40 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 114 through 116
      No H-bonds generated for 'chain 'R' and resid 114 through 116'
    Processing helix  chain 'R' and resid 117 through 142
    Processing helix  chain 'R' and resid 150 through 172
      removed outlier: 3.767A  pdb=" N   HIS R 154 " --> pdb=" O   ARG R 150 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   TYR R 172 " --> pdb=" O   VAL R 168 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 185 through 220
      removed outlier: 3.611A  pdb=" N   PHE R 189 " --> pdb=" O   SER R 185 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE R 218 " --> pdb=" O   ARG R 214 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 223 through 228
    Processing helix  chain 'R' and resid 234 through 250
      removed outlier: 3.546A  pdb=" N   TRP R 241 " --> pdb=" O   PHE R 237 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 272 through 279
    Processing helix  chain 'R' and resid 281 through 312
      removed outlier: 4.171A  pdb=" N   LEU R 286 " --> pdb=" O   VAL R 282 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 336 through 366
      removed outlier: 3.692A  pdb=" N   ARG R 340 " --> pdb=" O   ARG R 336 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LEU R 347 " --> pdb=" O   LYS R 343 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ILE R 348 " --> pdb=" O   THR R 344 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLY R 357 " --> pdb=" O   ILE R 353 " (cutoff:3.500A)
      Proline residue:  R 358  - end of helix
    Processing helix  chain 'R' and resid 372 through 388
      removed outlier: 3.987A  pdb=" N   MET R 384 " --> pdb=" O   ALA R 380 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LEU R 385 " --> pdb=" O   PHE R 381 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 388 through 401
      Proline residue:  R 394  - end of helix
      removed outlier: 4.304A  pdb=" N   SER R 401 " --> pdb=" O   TYR R 397 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 401 through 408
      removed outlier: 4.028A  pdb=" N   ARG R 405 " --> pdb=" O   SER R 401 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.509A  pdb=" N   PHE S  32 " --> pdb=" O   PHE S  29 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191
      removed outlier: 6.230A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.644A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 8.283A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   LEU A  38 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.593A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.798A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.204A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
      removed outlier: 5.894A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.629A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.022A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.243A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.525A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   LEU B 252 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277
      removed outlier: 6.324A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.760A  pdb=" N   GLN S   3 " --> pdb=" O   SER S  25 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ARG S  18 " --> pdb=" O   MET S  83 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 46 through 51
      removed outlier: 6.724A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 46 through 51
      removed outlier: 6.724A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 144 through 148
    Processing sheet with id=AB4, first strand: chain 'S' and resid 166 through 167

    372 hydrogen bonds defined for protein.
    1059 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: 2.40

  Time building geometry restraints manager: 2.44 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1336
        1.30 -     1.43: 2289
        1.43 -     1.56: 4856
        1.56 -     1.69: 0
        1.69 -     1.81: 87
  Bond restraints: 8568
  Sorted by residual:
  bond pdb=" N11 Q2L R 501 "
       pdb=" O12 Q2L R 501 "
    ideal  model  delta    sigma   weight residual
    1.207  1.402 -0.195 2.00e-02 2.50e+03 9.49e+01
  bond pdb=" N   ARG R 145 "
       pdb=" CA  ARG R 145 "
    ideal  model  delta    sigma   weight residual
    1.459  1.412  0.047 1.06e-02 8.90e+03 1.98e+01
  bond pdb=" CA  ARG R 145 "
       pdb=" C   ARG R 145 "
    ideal  model  delta    sigma   weight residual
    1.524  1.494  0.030 7.00e-03 2.04e+04 1.90e+01
  bond pdb=" N   ASN R 256 "
       pdb=" CA  ASN R 256 "
    ideal  model  delta    sigma   weight residual
    1.457  1.510 -0.052 1.29e-02 6.01e+03 1.65e+01
  bond pdb=" CA  ASP R 272 "
       pdb=" CB  ASP R 272 "
    ideal  model  delta    sigma   weight residual
    1.533  1.480  0.054 1.51e-02 4.39e+03 1.26e+01
  ... (remaining 8563 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 11371
        1.73 -     3.46: 176
        3.46 -     5.19: 34
        5.19 -     6.92: 19
        6.92 -     8.65: 5
  Bond angle restraints: 11605
  Sorted by residual:
  angle pdb=" C   SER R 144 "
        pdb=" N   ARG R 145 "
        pdb=" CA  ARG R 145 "
      ideal   model   delta    sigma   weight residual
     122.44  115.29    7.15 1.19e+00 7.06e-01 3.61e+01
  angle pdb=" N   VAL S  48 "
        pdb=" CA  VAL S  48 "
        pdb=" C   VAL S  48 "
      ideal   model   delta    sigma   weight residual
     113.71  108.67    5.04 9.50e-01 1.11e+00 2.82e+01
  angle pdb=" N   TRP R 279 "
        pdb=" CA  TRP R 279 "
        pdb=" C   TRP R 279 "
      ideal   model   delta    sigma   weight residual
     112.57  106.96    5.61 1.13e+00 7.83e-01 2.46e+01
  angle pdb=" C   GLU R 273 "
        pdb=" N   THR R 274 "
        pdb=" CA  THR R 274 "
      ideal   model   delta    sigma   weight residual
     120.44  114.08    6.36 1.36e+00 5.41e-01 2.19e+01
  angle pdb=" C   CYS R 107 "
        pdb=" N   PHE R 108 "
        pdb=" CA  PHE R 108 "
      ideal   model   delta    sigma   weight residual
     121.26  113.88    7.38 1.59e+00 3.96e-01 2.16e+01
  ... (remaining 11600 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 4426
       16.00 -    32.00: 481
       32.00 -    47.99: 123
       47.99 -    63.99: 19
       63.99 -    79.99: 5
  Dihedral angle restraints: 5054
    sinusoidal: 1900
      harmonic: 3154
  Sorted by residual:
  dihedral pdb=" C   ASP R 272 "
           pdb=" N   ASP R 272 "
           pdb=" CA  ASP R 272 "
           pdb=" CB  ASP R 272 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.32  -13.28     0      2.50e+00 1.60e-01 2.82e+01
  dihedral pdb=" N   ASP R 272 "
           pdb=" C   ASP R 272 "
           pdb=" CA  ASP R 272 "
           pdb=" CB  ASP R 272 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  112.02   10.78     0      2.50e+00 1.60e-01 1.86e+01
  dihedral pdb=" C   LEU R 165 "
           pdb=" N   LEU R 165 "
           pdb=" CA  LEU R 165 "
           pdb=" CB  LEU R 165 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.40  -10.20     0      2.50e+00 1.60e-01 1.66e+01
  ... (remaining 5051 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1198
       0.065 -    0.129: 139
       0.129 -    0.194: 5
       0.194 -    0.258: 4
       0.258 -    0.323: 1
  Chirality restraints: 1347
  Sorted by residual:
  chirality pdb=" CA  ASP R 272 "
            pdb=" N   ASP R 272 "
            pdb=" C   ASP R 272 "
            pdb=" CB  ASP R 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.60e+00
  chirality pdb=" CA  ASN R 256 "
            pdb=" N   ASN R 256 "
            pdb=" C   ASN R 256 "
            pdb=" CB  ASN R 256 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  CYS R 107 "
            pdb=" N   CYS R 107 "
            pdb=" C   CYS R 107 "
            pdb=" CB  CYS R 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 1344 not shown)

  Planarity restraints: 1447
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 165 "    0.014 2.00e-02 2.50e+03   2.75e-02 7.59e+00
        pdb=" C   LEU R 165 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   LEU R 165 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLY R 166 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.035 5.00e-02 4.00e+02   5.37e-02 4.61e+00
        pdb=" N   PRO B 236 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN R 256 "    0.010 2.00e-02 2.50e+03   2.10e-02 4.39e+00
        pdb=" C   ASN R 256 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   ASN R 256 "    0.014 2.00e-02 2.50e+03
        pdb=" N   CYS R 257 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1444 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 473
        2.73 -     3.28: 8073
        3.28 -     3.82: 13117
        3.82 -     4.36: 14548
        4.36 -     4.90: 26352
  Nonbonded interactions: 62563
  Sorted by model distance:
  nonbonded pdb=" O   TRP R 255 "
            pdb=" OD1 ASN R 256 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" O   GLY S   8 "
            pdb=" OG1 THR S 115 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   CYS B 103 "
            pdb=" NH2 ARG B 150 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" O   LEU R 165 "
            pdb=" N   VAL R 168 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" O   GLY S 112 "
            pdb=" OG  SER S 172 "
     model   vdw
     2.256 3.040
  ... (remaining 62558 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.360
  Find NCS groups from input model:        0.090
  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:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7116
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.195   8568  Z= 0.207
  Angle     :  0.614   8.646  11605  Z= 0.339
  Chirality :  0.043   0.323   1347
  Planarity :  0.003   0.054   1447
  Dihedral  : 14.347  79.989   3012
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.68 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.10 %
  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:  0.29 (0.27), residues: 1057
  helix:  1.72 (0.29), residues: 372
  sheet: -0.17 (0.34), residues: 264
  loop : -0.93 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 339 
 HIS   0.008   0.001   HIS R 154 
 PHE   0.017   0.001   PHE S 227 
 TYR   0.009   0.001   TYR S 102 
 ARG   0.004   0.000   ARG A 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13382 (  369)
  hydrogen bonds       : angle       5.29994 ( 1059)
  covalent geometry    : bond        0.00368 ( 8568)
  covalent geometry    : angle       0.61351 (11605)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 130
  time to evaluate  : 0.884 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8352 (tm-30)
REVERT: B  273 ILE cc_start: 0.8539 (mp) cc_final: 0.8300 (mp)
REVERT: R  353 ILE cc_start: 0.7864 (tp) cc_final: 0.7597 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 132
  average time/residue: 0.1948
  time to fit residues: 35.7251
Evaluate side-chains
  105 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  273 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 45 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0470
   chunk 43 optimal weight:    0.3980
   chunk 83 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   chunk 97 optimal weight:    0.0010
   overall best weight:    0.3684

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

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS
** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 220 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.188158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.153418 restraints weight = 12217.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 2.25
r_work: 0.3680 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3556 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.1019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8568  Z= 0.093
  Angle     :  0.489   7.096  11605  Z= 0.253
  Chirality :  0.040   0.200   1347
  Planarity :  0.003   0.054   1447
  Dihedral  :  4.488  35.810   1189
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  7.67 %
    Favored  : 91.09 %
  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:  0.26 (0.27), residues: 1057
  helix:  1.56 (0.28), residues: 385
  sheet: -0.04 (0.34), residues: 259
  loop : -0.98 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 279 
 HIS   0.008   0.001   HIS R 154 
 PHE   0.014   0.001   PHE S  80 
 TYR   0.008   0.001   TYR S 102 
 ARG   0.003   0.000   ARG A 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03143 (  369)
  hydrogen bonds       : angle       4.03190 ( 1059)
  covalent geometry    : bond        0.00200 ( 8568)
  covalent geometry    : angle       0.48923 (11605)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 1.064 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8291 (tm-30)
REVERT: C   18 GLN cc_start: 0.8564 (tp40) cc_final: 0.8161 (tp-100)
REVERT: C   21 MET cc_start: 0.8665 (tpp) cc_final: 0.8105 (ttt)
REVERT: R  110 VAL cc_start: 0.5336 (OUTLIER) cc_final: 0.4957 (m)
REVERT: R  183 LYS cc_start: 0.7265 (mmtm) cc_final: 0.6645 (mtmt)
REVERT: R  353 ILE cc_start: 0.7869 (tp) cc_final: 0.7579 (tp)
REVERT: S  159 ASN cc_start: 0.7725 (t0) cc_final: 0.7097 (t0)
REVERT: S  217 CYS cc_start: 0.2080 (p) cc_final: 0.1550 (t)
REVERT: S  218 MET cc_start: 0.1576 (ptp) cc_final: 0.1080 (ptp)
  outliers start: 11
  outliers final: 8
  residues processed: 120
  average time/residue: 0.1965
  time to fit residues: 32.9652
Evaluate side-chains
  117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue  110 VAL
Chi-restraints excluded: chain R residue  123 SER
Chi-restraints excluded: chain R residue  403 ASP
Chi-restraints excluded: chain S residue  117 LEU
Chi-restraints excluded: chain S residue  225 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 86 optimal weight:   20.0000
   chunk 95 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 47 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
C  18 GLN
** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.176876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.140130 restraints weight = 12308.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 2.25
r_work: 0.3507 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3378 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   8568  Z= 0.232
  Angle     :  0.653   6.722  11605  Z= 0.339
  Chirality :  0.045   0.170   1347
  Planarity :  0.004   0.052   1447
  Dihedral  :  4.999  33.131   1186
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 11.50 %
    Favored  : 86.47 %
  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: -0.17 (0.26), residues: 1057
  helix:  1.28 (0.28), residues: 377
  sheet: -0.19 (0.32), residues: 268
  loop : -1.34 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP S  36 
 HIS   0.011   0.001   HIS R 154 
 PHE   0.034   0.002   PHE B 199 
 TYR   0.019   0.002   TYR B 105 
 ARG   0.007   0.000   ARG A 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04666 (  369)
  hydrogen bonds       : angle       4.47152 ( 1059)
  covalent geometry    : bond        0.00562 ( 8568)
  covalent geometry    : angle       0.65295 (11605)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.939 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8217 (tm-30)
REVERT: C   18 GLN cc_start: 0.8515 (tp-100) cc_final: 0.8301 (tp40)
REVERT: C   21 MET cc_start: 0.8769 (tpp) cc_final: 0.8130 (ttt)
REVERT: R  116 GLN cc_start: 0.6396 (OUTLIER) cc_final: 0.5941 (mp10)
REVERT: R  134 ASN cc_start: 0.6229 (t0) cc_final: 0.5992 (t0)
REVERT: R  353 ILE cc_start: 0.7808 (tp) cc_final: 0.7579 (tp)
REVERT: S   90 ASP cc_start: 0.7639 (m-30) cc_final: 0.7270 (m-30)
REVERT: S  222 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6581 (tt0)
  outliers start: 18
  outliers final: 13
  residues processed: 115
  average time/residue: 0.2099
  time to fit residues: 33.2291
Evaluate side-chains
  113 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain R residue  116 GLN
Chi-restraints excluded: chain R residue  123 SER
Chi-restraints excluded: chain R residue  384 MET
Chi-restraints excluded: chain R residue  403 ASP
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  218 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 73 optimal weight:   20.0000
   chunk 96 optimal weight:   10.0000
   chunk 74 optimal weight:    6.9990
   chunk 87 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.175817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.139492 restraints weight = 12280.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 2.26
r_work: 0.3493 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8568  Z= 0.214
  Angle     :  0.622   6.653  11605  Z= 0.322
  Chirality :  0.044   0.189   1347
  Planarity :  0.004   0.054   1447
  Dihedral  :  4.873  24.743   1186
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 14.54 %
    Favored  : 82.07 %
  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: -0.39 (0.26), residues: 1057
  helix:  1.20 (0.28), residues: 378
  sheet: -0.42 (0.31), residues: 270
  loop : -1.51 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP S  36 
 HIS   0.012   0.001   HIS R 154 
 PHE   0.028   0.002   PHE B 199 
 TYR   0.013   0.002   TYR B 264 
 ARG   0.005   0.000   ARG A 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04395 (  369)
  hydrogen bonds       : angle       4.41175 ( 1059)
  covalent geometry    : bond        0.00517 ( 8568)
  covalent geometry    : angle       0.62183 (11605)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 1.002 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8133 (tm-30)
REVERT: C   18 GLN cc_start: 0.8536 (tp-100) cc_final: 0.8007 (tp-100)
REVERT: C   21 MET cc_start: 0.8855 (tpp) cc_final: 0.8139 (ttt)
REVERT: R  116 GLN cc_start: 0.6280 (OUTLIER) cc_final: 0.5725 (mp10)
REVERT: R  134 ASN cc_start: 0.6270 (t0) cc_final: 0.6029 (t0)
REVERT: R  353 ILE cc_start: 0.8006 (tp) cc_final: 0.7718 (tp)
REVERT: S   34 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6810 (ttt)
REVERT: S   70 ILE cc_start: 0.7264 (OUTLIER) cc_final: 0.5960 (tt)
REVERT: S   90 ASP cc_start: 0.7815 (m-30) cc_final: 0.7464 (m-30)
REVERT: S  151 LYS cc_start: 0.6781 (mmtm) cc_final: 0.5574 (pttt)
REVERT: S  222 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6608 (tt0)
  outliers start: 30
  outliers final: 15
  residues processed: 124
  average time/residue: 0.2015
  time to fit residues: 34.8873
Evaluate side-chains
  113 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain R residue  116 GLN
Chi-restraints excluded: chain R residue  123 SER
Chi-restraints excluded: chain R residue  403 ASP
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   70 ILE
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  218 MET
Chi-restraints excluded: chain S residue  225 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 63 optimal weight:    8.9990
   chunk 79 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 54 optimal weight:    7.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.177726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.142018 restraints weight = 12182.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 2.23
r_work: 0.3530 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3402 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8568  Z= 0.128
  Angle     :  0.528   6.662  11605  Z= 0.275
  Chirality :  0.041   0.162   1347
  Planarity :  0.003   0.052   1447
  Dihedral  :  4.476  24.544   1186
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.80 %
    Favored  : 80.61 %
  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: -0.19 (0.26), residues: 1057
  helix:  1.39 (0.28), residues: 378
  sheet: -0.32 (0.32), residues: 271
  loop : -1.41 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP S  36 
 HIS   0.010   0.001   HIS R 154 
 PHE   0.019   0.001   PHE B 199 
 TYR   0.010   0.001   TYR R 296 
 ARG   0.004   0.000   ARG A 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03538 (  369)
  hydrogen bonds       : angle       4.11101 ( 1059)
  covalent geometry    : bond        0.00301 ( 8568)
  covalent geometry    : angle       0.52834 (11605)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.970 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8175 (tm-30)
REVERT: C   18 GLN cc_start: 0.8513 (tp-100) cc_final: 0.7966 (tp-100)
REVERT: C   21 MET cc_start: 0.8843 (tpp) cc_final: 0.8127 (ttt)
REVERT: R  116 GLN cc_start: 0.6281 (OUTLIER) cc_final: 0.5818 (mp10)
REVERT: R  353 ILE cc_start: 0.7987 (tp) cc_final: 0.7706 (tp)
REVERT: S   70 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.5735 (tt)
REVERT: S   90 ASP cc_start: 0.7760 (m-30) cc_final: 0.7376 (m-30)
REVERT: S  151 LYS cc_start: 0.6787 (mmtm) cc_final: 0.5664 (pttt)
  outliers start: 23
  outliers final: 16
  residues processed: 115
  average time/residue: 0.2121
  time to fit residues: 33.4941
Evaluate side-chains
  116 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain R residue  116 GLN
Chi-restraints excluded: chain R residue  123 SER
Chi-restraints excluded: chain R residue  403 ASP
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   70 ILE
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  218 MET
Chi-restraints excluded: chain S residue  225 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 77 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 99 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.177770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.142390 restraints weight = 12115.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3771 rms_B_bonded: 2.29
r_work: 0.3530 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3401 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8568  Z= 0.127
  Angle     :  0.527   7.036  11605  Z= 0.273
  Chirality :  0.041   0.194   1347
  Planarity :  0.003   0.050   1447
  Dihedral  :  4.347  24.208   1186
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 17.14 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.27), residues: 1057
  helix:  1.37 (0.28), residues: 382
  sheet: -0.48 (0.31), residues: 277
  loop : -1.36 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP S  36 
 HIS   0.010   0.001   HIS R 154 
 PHE   0.019   0.001   PHE B 199 
 TYR   0.010   0.001   TYR R 296 
 ARG   0.003   0.000   ARG A 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03432 (  369)
  hydrogen bonds       : angle       4.02678 ( 1059)
  covalent geometry    : bond        0.00298 ( 8568)
  covalent geometry    : angle       0.52699 (11605)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.985 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8177 (tm-30)
REVERT: B  234 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8282 (m-80)
REVERT: B  283 ARG cc_start: 0.8172 (tpt-90) cc_final: 0.7700 (tpt170)
REVERT: C   18 GLN cc_start: 0.8547 (tp-100) cc_final: 0.7982 (tp-100)
REVERT: C   21 MET cc_start: 0.8847 (tpp) cc_final: 0.8111 (ttt)
REVERT: R  116 GLN cc_start: 0.6214 (OUTLIER) cc_final: 0.5678 (mp10)
REVERT: R  353 ILE cc_start: 0.7993 (tp) cc_final: 0.7701 (tp)
REVERT: S   34 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6662 (ttt)
REVERT: S   70 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.5694 (tt)
REVERT: S   90 ASP cc_start: 0.7790 (m-30) cc_final: 0.7478 (m-30)
REVERT: S  151 LYS cc_start: 0.6831 (mmtm) cc_final: 0.5762 (pttt)
  outliers start: 26
  outliers final: 16
  residues processed: 123
  average time/residue: 0.2182
  time to fit residues: 36.5022
Evaluate side-chains
  124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain R residue  116 GLN
Chi-restraints excluded: chain R residue  346 VAL
Chi-restraints excluded: chain R residue  403 ASP
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   70 ILE
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  218 MET
Chi-restraints excluded: chain S residue  225 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 88 optimal weight:    6.9990
   chunk 15 optimal weight:    8.9990
   chunk 106 optimal weight:    7.9990
   chunk 56 optimal weight:    8.9990
   chunk 103 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 256 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.173404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.138073 restraints weight = 12242.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 2.30
r_work: 0.3480 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8568  Z= 0.203
  Angle     :  0.618   7.510  11605  Z= 0.319
  Chirality :  0.044   0.218   1347
  Planarity :  0.004   0.050   1447
  Dihedral  :  4.753  25.695   1186
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 18.15 %
    Favored  : 78.69 %
  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: -0.44 (0.26), residues: 1057
  helix:  1.20 (0.28), residues: 381
  sheet: -0.56 (0.31), residues: 275
  loop : -1.50 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP S  36 
 HIS   0.012   0.002   HIS R 154 
 PHE   0.024   0.002   PHE B 199 
 TYR   0.013   0.002   TYR B 264 
 ARG   0.004   0.000   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04300 (  369)
  hydrogen bonds       : angle       4.32164 ( 1059)
  covalent geometry    : bond        0.00491 ( 8568)
  covalent geometry    : angle       0.61848 (11605)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.880 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8148 (tm-30)
REVERT: B  234 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8342 (m-80)
REVERT: B  283 ARG cc_start: 0.8282 (tpt-90) cc_final: 0.7809 (tpt170)
REVERT: B  289 TYR cc_start: 0.8280 (m-80) cc_final: 0.7991 (m-80)
REVERT: C   18 GLN cc_start: 0.8558 (tp-100) cc_final: 0.8010 (tp-100)
REVERT: C   21 MET cc_start: 0.8860 (tpp) cc_final: 0.8107 (ttt)
REVERT: R  116 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.5829 (mp10)
REVERT: R  353 ILE cc_start: 0.8151 (tp) cc_final: 0.7795 (tp)
REVERT: S   34 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6734 (ttt)
REVERT: S   70 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.5808 (tt)
REVERT: S   90 ASP cc_start: 0.7842 (m-30) cc_final: 0.7489 (m-30)
REVERT: S  151 LYS cc_start: 0.7077 (mmtm) cc_final: 0.6110 (pttt)
REVERT: S  211 ASP cc_start: 0.6792 (t0) cc_final: 0.6501 (t0)
  outliers start: 28
  outliers final: 21
  residues processed: 120
  average time/residue: 0.2152
  time to fit residues: 35.8718
Evaluate side-chains
  127 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain R residue  116 GLN
Chi-restraints excluded: chain R residue  123 SER
Chi-restraints excluded: chain R residue  249 VAL
Chi-restraints excluded: chain R residue  346 VAL
Chi-restraints excluded: chain R residue  354 ILE
Chi-restraints excluded: chain R residue  403 ASP
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   70 ILE
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  218 MET
Chi-restraints excluded: chain S residue  225 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 79 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   chunk 71 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 99 optimal weight:    2.9990
   chunk 95 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
B 142 HIS
** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.177409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.142208 restraints weight = 12288.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3762 rms_B_bonded: 2.34
r_work: 0.3532 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3403 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.3086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8568  Z= 0.107
  Angle     :  0.523   8.059  11605  Z= 0.269
  Chirality :  0.040   0.186   1347
  Planarity :  0.003   0.052   1447
  Dihedral  :  4.290  24.682   1186
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.83 %
    Favored  : 78.69 %
  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: -0.18 (0.27), residues: 1057
  helix:  1.43 (0.28), residues: 381
  sheet: -0.42 (0.31), residues: 275
  loop : -1.38 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP S  36 
 HIS   0.009   0.001   HIS R 154 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.010   0.001   TYR R 296 
 ARG   0.003   0.000   ARG A 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03215 (  369)
  hydrogen bonds       : angle       3.95673 ( 1059)
  covalent geometry    : bond        0.00246 ( 8568)
  covalent geometry    : angle       0.52283 (11605)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.883 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8149 (tm-30)
REVERT: B  234 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8141 (m-80)
REVERT: B  283 ARG cc_start: 0.8214 (tpt-90) cc_final: 0.7750 (tpt170)
REVERT: C   18 GLN cc_start: 0.8530 (tp-100) cc_final: 0.7978 (tp-100)
REVERT: C   21 MET cc_start: 0.8879 (tpp) cc_final: 0.8105 (ttt)
REVERT: R  116 GLN cc_start: 0.6165 (OUTLIER) cc_final: 0.5670 (mp10)
REVERT: R  353 ILE cc_start: 0.8057 (tp) cc_final: 0.7731 (tp)
REVERT: S   34 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6590 (ttt)
REVERT: S   90 ASP cc_start: 0.7804 (m-30) cc_final: 0.7452 (m-30)
REVERT: S  151 LYS cc_start: 0.7108 (mmtm) cc_final: 0.5976 (pttt)
  outliers start: 22
  outliers final: 14
  residues processed: 122
  average time/residue: 0.2107
  time to fit residues: 35.3591
Evaluate side-chains
  121 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain R residue  116 GLN
Chi-restraints excluded: chain R residue  249 VAL
Chi-restraints excluded: chain R residue  346 VAL
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  218 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 85 optimal weight:    9.9990
   chunk 94 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.175025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.140722 restraints weight = 12364.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 2.42
r_work: 0.3501 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8568  Z= 0.161
  Angle     :  0.582   8.388  11605  Z= 0.300
  Chirality :  0.042   0.211   1347
  Planarity :  0.003   0.050   1447
  Dihedral  :  4.547  28.371   1186
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 18.71 %
    Favored  : 78.69 %
  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: -0.33 (0.26), residues: 1057
  helix:  1.36 (0.28), residues: 381
  sheet: -0.50 (0.31), residues: 270
  loop : -1.52 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP S  36 
 HIS   0.018   0.002   HIS S 220 
 PHE   0.021   0.002   PHE B 199 
 TYR   0.011   0.001   TYR R 296 
 ARG   0.003   0.000   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03855 (  369)
  hydrogen bonds       : angle       4.10239 ( 1059)
  covalent geometry    : bond        0.00386 ( 8568)
  covalent geometry    : angle       0.58240 (11605)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.991 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8179 (tm-30)
REVERT: B   70 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8002 (mp)
REVERT: B  234 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8269 (m-80)
REVERT: B  283 ARG cc_start: 0.8328 (tpt-90) cc_final: 0.7644 (mmm160)
REVERT: B  289 TYR cc_start: 0.8206 (m-80) cc_final: 0.7902 (m-80)
REVERT: C   18 GLN cc_start: 0.8554 (tp-100) cc_final: 0.7997 (tp-100)
REVERT: C   21 MET cc_start: 0.8897 (tpp) cc_final: 0.8125 (ttt)
REVERT: R  116 GLN cc_start: 0.6205 (OUTLIER) cc_final: 0.5534 (mp10)
REVERT: R  353 ILE cc_start: 0.8174 (tp) cc_final: 0.7821 (tp)
REVERT: S   34 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6671 (ttt)
REVERT: S   70 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.6041 (tt)
REVERT: S   90 ASP cc_start: 0.7899 (m-30) cc_final: 0.7642 (m-30)
REVERT: S  151 LYS cc_start: 0.7383 (mmtm) cc_final: 0.6446 (pttt)
REVERT: S  211 ASP cc_start: 0.6984 (t0) cc_final: 0.6684 (t0)
  outliers start: 23
  outliers final: 15
  residues processed: 121
  average time/residue: 0.2151
  time to fit residues: 35.8212
Evaluate side-chains
  124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain R residue  116 GLN
Chi-restraints excluded: chain R residue  249 VAL
Chi-restraints excluded: chain R residue  346 VAL
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   70 ILE
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue   97 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 33 optimal weight:    0.3980
   chunk 9 optimal weight:    5.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.178179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.144217 restraints weight = 12194.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3787 rms_B_bonded: 2.31
r_work: 0.3556 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3427 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8568  Z= 0.105
  Angle     :  0.525   8.468  11605  Z= 0.269
  Chirality :  0.040   0.198   1347
  Planarity :  0.003   0.051   1447
  Dihedral  :  4.209  28.221   1186
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 19.39 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.27), residues: 1057
  helix:  1.56 (0.28), residues: 378
  sheet: -0.51 (0.31), residues: 275
  loop : -1.37 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP S  36 
 HIS   0.014   0.001   HIS S 220 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.009   0.001   TYR R 296 
 ARG   0.002   0.000   ARG A 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03064 (  369)
  hydrogen bonds       : angle       3.85506 ( 1059)
  covalent geometry    : bond        0.00243 ( 8568)
  covalent geometry    : angle       0.52534 (11605)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.895 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8154 (tm-30)
REVERT: B   70 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8037 (mp)
REVERT: B  234 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8134 (m-80)
REVERT: B  283 ARG cc_start: 0.8186 (tpt-90) cc_final: 0.7709 (tpt170)
REVERT: C   18 GLN cc_start: 0.8503 (tp-100) cc_final: 0.7961 (tp-100)
REVERT: C   21 MET cc_start: 0.8894 (tpp) cc_final: 0.8120 (ttt)
REVERT: R  116 GLN cc_start: 0.6175 (OUTLIER) cc_final: 0.5761 (mp10)
REVERT: R  353 ILE cc_start: 0.8044 (tp) cc_final: 0.7741 (tp)
REVERT: S   34 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6533 (ttt)
REVERT: S   70 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.5905 (tt)
REVERT: S   90 ASP cc_start: 0.7848 (m-30) cc_final: 0.7583 (m-30)
REVERT: S  151 LYS cc_start: 0.7378 (mmtm) cc_final: 0.6288 (pttt)
REVERT: S  222 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6117 (mp0)
  outliers start: 20
  outliers final: 15
  residues processed: 117
  average time/residue: 0.2128
  time to fit residues: 34.0306
Evaluate side-chains
  124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain R residue  116 GLN
Chi-restraints excluded: chain R residue  249 VAL
Chi-restraints excluded: chain R residue  346 VAL
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   70 ILE
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue   97 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0000
   chunk 24 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 106 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    2.7992

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.173048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.138695 restraints weight = 12426.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 2.43
r_work: 0.3464 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.3580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   8568  Z= 0.228
  Angle     :  0.653   8.201  11605  Z= 0.336
  Chirality :  0.044   0.233   1347
  Planarity :  0.004   0.049   1447
  Dihedral  :  4.816  28.689   1186
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 19.17 %
    Favored  : 78.13 %
  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: -0.48 (0.26), residues: 1057
  helix:  1.23 (0.28), residues: 382
  sheet: -0.58 (0.31), residues: 268
  loop : -1.61 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP S  36 
 HIS   0.016   0.002   HIS S 220 
 PHE   0.023   0.002   PHE B 199 
 TYR   0.013   0.002   TYR B 264 
 ARG   0.006   0.000   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04481 (  369)
  hydrogen bonds       : angle       4.29874 ( 1059)
  covalent geometry    : bond        0.00551 ( 8568)
  covalent geometry    : angle       0.65300 (11605)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5319.61 seconds
wall clock time: 92 minutes 19.87 seconds (5539.87 seconds total)