Starting phenix.real_space_refine
on Fri Jun  6 22:48:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d4z_46571/06_2025/9d4z_46571.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d4z_46571/06_2025/9d4z_46571.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d4z_46571/06_2025/9d4z_46571.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d4z_46571/06_2025/9d4z_46571.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d4z_46571/06_2025/9d4z_46571.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d4z_46571/06_2025/9d4z_46571.cif"
  }
  resolution = 2.74
  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=   0.001 sd=   0.024
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      53      5.16       5
     C    5296      2.51       5
     N    1371      2.21       5
     O    1547      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8267
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2300
          Classifications: {'peptide': 303}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 5, 'TRANS': 297}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "G"
      Number of atoms: 174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 174
          Classifications: {'peptide': 24}
          Link IDs: {'PTRANS': 3, 'TRANS': 20}
    Chain: "R"
      Number of atoms: 2327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2327
          Classifications: {'peptide': 297}
          Link IDs: {'PTRANS': 10, 'TRANS': 286}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1765
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1765
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "A"
      Number of atoms: 1701
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1701
          Classifications: {'peptide': 212}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 5, 'TRANS': 206}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 32
  Time building chain proxies: 5.24, per 1000 atoms: 0.63
  Number of scatterers: 8267
  At special positions: 0
  Unit cell: (85.905, 119.025, 130.41, 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      53     16.00
     O    1547      8.00
     N    1371      7.00
     C    5296      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 175 " - pdb=" SG  CYS R 254 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.05
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1996

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 15 sheets defined
      39.2% alpha, 23.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'B' and resid 256 through 258
      No H-bonds generated for 'chain 'B' and resid 256 through 258'
    Processing helix  chain 'G' and resid 35 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.922A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'R' and resid 89 through 97
    Processing helix  chain 'R' and resid 98 through 130
      removed outlier: 4.748A  pdb=" N   VAL R 105 " --> pdb=" O   LEU R 101 " (cutoff:3.500A)
      Proline residue:  R 106  - end of helix
      Proline residue:  R 118  - end of helix
    Processing helix  chain 'R' and resid 135 through 154
      removed outlier: 3.506A  pdb=" N   VAL R 139 " --> pdb=" O   LYS R 135 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   VAL R 154 " --> pdb=" O   LEU R 150 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 154 through 164
      removed outlier: 3.913A  pdb=" N   LYS R 158 " --> pdb=" O   VAL R 154 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 206
      removed outlier: 3.976A  pdb=" N   ARG R 176 " --> pdb=" O   SER R 172 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   PHE R 177 " --> pdb=" O   GLU R 173 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   MET R 186 " --> pdb=" O   PHE R 182 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   TYR R 187 " --> pdb=" O   TYR R 183 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE R 190 " --> pdb=" O   MET R 186 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 206 through 214
      removed outlier: 3.821A  pdb=" N   LEU R 211 " --> pdb=" O   PRO R 207 " (cutoff:3.500A)
      removed outlier: 5.513A  pdb=" N   SER R 212 " --> pdb=" O   MET R 208 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   TRP R 213 " --> pdb=" O   GLN R 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 215 through 234
      removed outlier: 3.555A  pdb=" N   VAL R 234 " --> pdb=" O   ALA R 230 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 234 through 240
      removed outlier: 3.701A  pdb=" N   LYS R 240 " --> pdb=" O   PRO R 236 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 260 through 265
    Processing helix  chain 'R' and resid 265 through 279
    Processing helix  chain 'R' and resid 279 through 299
    Processing helix  chain 'R' and resid 299 through 304
      removed outlier: 4.053A  pdb=" N   ASN R 304 " --> pdb=" O   SER R 300 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 308 through 339
      Proline residue:  R 328  - end of helix
      removed outlier: 3.619A  pdb=" N   PHE R 339 " --> pdb=" O   ALA R 335 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 342 through 360
      removed outlier: 3.818A  pdb=" N   GLU R 347 " --> pdb=" O   THR R 343 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   ALA R 348 " --> pdb=" O   SER R 344 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 362 through 372
      Proline residue:  R 368  - end of helix
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 4.227A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 74 through 76
      No H-bonds generated for 'chain 'E' and resid 74 through 76'
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'A' and resid 7 through 38
      removed outlier: 3.656A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 55
      removed outlier: 3.669A  pdb=" N   PHE A  55 " --> pdb=" O   LYS A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 221
      removed outlier: 3.840A  pdb=" N   GLN A 218 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 250
      removed outlier: 3.571A  pdb=" N   GLN A 239 " --> pdb=" O   TYR A 235 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   GLU A 240 " --> pdb=" O   ASN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 255
      removed outlier: 3.833A  pdb=" N   ARG A 255 " --> pdb=" O   ARG A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 276
    Processing helix  chain 'A' and resid 279 through 284
      removed outlier: 4.141A  pdb=" N   TYR A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 290
    Processing helix  chain 'A' and resid 303 through 325
      removed outlier: 3.728A  pdb=" N   PHE A 317 " --> pdb=" O   ILE A 313 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   SER A 324 " --> pdb=" O   ILE A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 363
      removed outlier: 3.681A  pdb=" N   ILE A 347 " --> pdb=" O   ASN A 343 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.778A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63
      removed outlier: 6.388A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.698A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.011A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.823A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.763A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.521A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.028A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'R' and resid 43 through 45
      removed outlier: 5.683A  pdb=" N   PHE R  43 " --> pdb=" O   LEU R 258 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'R' and resid 244 through 245
    Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.537A  pdb=" N   ALA E  49 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 155 through 160
      removed outlier: 3.791A  pdb=" N   ALA E 211 " --> pdb=" O   SER E 208 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195
      removed outlier: 4.054A  pdb=" N   ASN E 194 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 5.652A  pdb=" N   LEU E 187 " --> pdb=" O   LEU E 178 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   LEU E 178 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 189 through 191
    Processing sheet with id=AB6, first strand: chain 'A' and resid 189 through 191
      removed outlier: 5.007A  pdb=" N   VAL A 206 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   GLY A  46 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   LYS A  41 " --> pdb=" O   ALA A 225 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   ILE A 227 " --> pdb=" O   LYS A  41 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   LEU A  43 " --> pdb=" O   ILE A 227 " (cutoff:3.500A)
      removed outlier: 7.381A  pdb=" N   VAL A 229 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 229 " (cutoff:3.500A)
      removed outlier: 8.612A  pdb=" N   ASP A 231 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   ILE A 226 " --> pdb=" O   ILE A 260 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   PHE A 262 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   PHE A 228 " --> pdb=" O   PHE A 262 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ASN A 264 " --> pdb=" O   PHE A 228 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   VAL A 230 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   VAL A 259 " --> pdb=" O   TYR A 332 " (cutoff:3.500A)

    397 hydrogen bonds defined for protein.
    1104 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: 2.41

  Time building geometry restraints manager: 2.43 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2626
        1.34 -     1.46: 2186
        1.46 -     1.58: 3567
        1.58 -     1.70: 0
        1.70 -     1.82: 76
  Bond restraints: 8455
  Sorted by residual:
  bond pdb=" N   ASP B  38 "
       pdb=" CA  ASP B  38 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.99e+00
  bond pdb=" N   SER R  42 "
       pdb=" CA  SER R  42 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.94e+00
  bond pdb=" N   ASP E   1 "
       pdb=" CA  ASP E   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.93e+00
  bond pdb=" N   ALA G  34 "
       pdb=" CA  ALA G  34 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.81e+00
  bond pdb=" N   SER A   6 "
       pdb=" CA  SER A   6 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.64e+00
  ... (remaining 8450 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 11168
        1.50 -     3.00: 259
        3.00 -     4.49: 49
        4.49 -     5.99: 8
        5.99 -     7.49: 3
  Bond angle restraints: 11487
  Sorted by residual:
  angle pdb=" CB  ARG A  38 "
        pdb=" CG  ARG A  38 "
        pdb=" CD  ARG A  38 "
      ideal   model   delta    sigma   weight residual
     111.30  117.39   -6.09 2.30e+00 1.89e-01 7.01e+00
  angle pdb=" CG  ARG A  38 "
        pdb=" CD  ARG A  38 "
        pdb=" NE  ARG A  38 "
      ideal   model   delta    sigma   weight residual
     112.00  117.74   -5.74 2.20e+00 2.07e-01 6.82e+00
  angle pdb=" CB  GLU B 172 "
        pdb=" CG  GLU B 172 "
        pdb=" CD  GLU B 172 "
      ideal   model   delta    sigma   weight residual
     112.60  116.87   -4.27 1.70e+00 3.46e-01 6.31e+00
  angle pdb=" CB  ILE A 330 "
        pdb=" CG1 ILE A 330 "
        pdb=" CD1 ILE A 330 "
      ideal   model   delta    sigma   weight residual
     113.80  119.01   -5.21 2.10e+00 2.27e-01 6.16e+00
  angle pdb=" CA  ILE A 330 "
        pdb=" CB  ILE A 330 "
        pdb=" CG1 ILE A 330 "
      ideal   model   delta    sigma   weight residual
     110.40  114.30   -3.90 1.70e+00 3.46e-01 5.26e+00
  ... (remaining 11482 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 4453
       17.86 -    35.73: 385
       35.73 -    53.59: 97
       53.59 -    71.45: 15
       71.45 -    89.31: 3
  Dihedral angle restraints: 4953
    sinusoidal: 1851
      harmonic: 3102
  Sorted by residual:
  dihedral pdb=" CA  ASP B 153 "
           pdb=" C   ASP B 153 "
           pdb=" N   ASP B 154 "
           pdb=" CA  ASP B 154 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.15   26.85     0      5.00e+00 4.00e-02 2.88e+01
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  96 "
           pdb=" CB  CYS E  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   61.14   31.86     1      1.00e+01 1.00e-02 1.45e+01
  dihedral pdb=" CB  CYS E 159 "
           pdb=" SG  CYS E 159 "
           pdb=" SG  CYS E 229 "
           pdb=" CB  CYS E 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   64.14   28.86     1      1.00e+01 1.00e-02 1.19e+01
  ... (remaining 4950 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1025
       0.047 -    0.095: 221
       0.095 -    0.142: 65
       0.142 -    0.190: 1
       0.190 -    0.237: 1
  Chirality restraints: 1313
  Sorted by residual:
  chirality pdb=" CB  VAL R 291 "
            pdb=" CA  VAL R 291 "
            pdb=" CG1 VAL R 291 "
            pdb=" CG2 VAL R 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CA  ILE B 232 "
            pdb=" N   ILE B 232 "
            pdb=" C   ILE B 232 "
            pdb=" CB  ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.54e-01
  chirality pdb=" CG  LEU R 354 "
            pdb=" CB  LEU R 354 "
            pdb=" CD1 LEU R 354 "
            pdb=" CD2 LEU R 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.87e-01
  ... (remaining 1310 not shown)

  Planarity restraints: 1444
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 281 "    0.033 5.00e-02 4.00e+02   5.00e-02 4.00e+00
        pdb=" N   PRO R 282 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO R 282 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO R 282 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER R 315 "    0.009 2.00e-02 2.50e+03   1.77e-02 3.14e+00
        pdb=" C   SER R 315 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   SER R 315 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ALA R 316 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP R 367 "   -0.028 5.00e-02 4.00e+02   4.29e-02 2.95e+00
        pdb=" N   PRO R 368 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO R 368 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO R 368 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1441 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 699
        2.74 -     3.28: 8642
        3.28 -     3.82: 13621
        3.82 -     4.36: 16989
        4.36 -     4.90: 29009
  Nonbonded interactions: 68960
  Sorted by model distance:
  nonbonded pdb=" NE1 TRP R 168 "
            pdb=" O   GLY R 171 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" OE2 GLU A  28 "
            pdb=" NH2 ARG A  38 "
     model   vdw
     2.350 3.120
  nonbonded pdb=" O   THR B 263 "
            pdb=" OG1 THR B 263 "
     model   vdw
     2.371 3.040
  nonbonded pdb=" O   ALA B 302 "
            pdb=" OD1 ASP B 303 "
     model   vdw
     2.376 3.040
  nonbonded pdb=" O   ASP B 163 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.404 3.040
  ... (remaining 68955 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:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.750
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:12.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
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   0.037   8458  Z= 0.177
  Angle     :  0.586   7.491  11493  Z= 0.313
  Chirality :  0.042   0.237   1313
  Planarity :  0.004   0.050   1444
  Dihedral  : 14.509  89.315   2948
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 18.57 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.24 (0.26), residues: 1047
  helix:  0.45 (0.29), residues: 326
  sheet: -0.31 (0.30), residues: 286
  loop : -0.34 (0.32), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 168 
 HIS   0.009   0.002   HIS R 336 
 PHE   0.019   0.002   PHE R 274 
 TYR   0.016   0.002   TYR A 235 
 ARG   0.007   0.001   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18439 (  395)
  hydrogen bonds       : angle       7.83631 ( 1104)
  SS BOND              : bond        0.00690 (    3)
  SS BOND              : angle       1.52231 (    6)
  covalent geometry    : bond        0.00390 ( 8455)
  covalent geometry    : angle       0.58472 (11487)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.953 
Fit side-chains
REVERT: B   55 LEU cc_start: 0.8395 (mt) cc_final: 0.8120 (mp)
REVERT: B   72 SER cc_start: 0.8022 (t) cc_final: 0.7774 (p)
REVERT: B   96 ARG cc_start: 0.7625 (mtm110) cc_final: 0.7338 (mtm110)
REVERT: B  190 LEU cc_start: 0.7660 (tp) cc_final: 0.7422 (tp)
REVERT: B  334 SER cc_start: 0.7720 (m) cc_final: 0.7221 (t)
REVERT: E  172 THR cc_start: 0.8132 (m) cc_final: 0.7733 (p)
REVERT: E  230 MET cc_start: 0.7097 (ptm) cc_final: 0.6599 (ptt)
REVERT: A   52 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8116 (mtmt)
REVERT: A  280 ILE cc_start: 0.8539 (mt) cc_final: 0.8332 (mp)
REVERT: A  345 ARG cc_start: 0.7904 (mmm160) cc_final: 0.7133 (tpt170)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 1.0136
  time to fit residues: 255.1977
Evaluate side-chains
  226 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0770
   chunk 44 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B  88 ASN
B 110 ASN
B 125 ASN
B 220 GLN
R 255 HIS
E  82 GLN
E 171 ASN
E 186 GLN
A 200 ASN
A 250 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.148649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.134259 restraints weight = 11983.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3878 rms_B_bonded: 2.03
r_work: 0.3774 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3627 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.1252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8458  Z= 0.159
  Angle     :  0.596  10.912  11493  Z= 0.315
  Chirality :  0.044   0.168   1313
  Planarity :  0.005   0.042   1444
  Dihedral  :  4.790  26.194   1158
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 15.77 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.30 (0.26), residues: 1047
  helix:  1.20 (0.29), residues: 329
  sheet:  0.01 (0.31), residues: 277
  loop : -0.33 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 169 
 HIS   0.007   0.002   HIS E  35 
 PHE   0.020   0.002   PHE R 274 
 TYR   0.018   0.002   TYR E 190 
 ARG   0.008   0.001   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04588 (  395)
  hydrogen bonds       : angle       5.29452 ( 1104)
  SS BOND              : bond        0.00763 (    3)
  SS BOND              : angle       1.52485 (    6)
  covalent geometry    : bond        0.00359 ( 8455)
  covalent geometry    : angle       0.59538 (11487)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 218
  time to evaluate  : 0.949 
Fit side-chains
REVERT: B   49 ARG cc_start: 0.8264 (mmt-90) cc_final: 0.8039 (mpt180)
REVERT: B   72 SER cc_start: 0.8023 (t) cc_final: 0.7760 (p)
REVERT: B   75 GLN cc_start: 0.7544 (mt0) cc_final: 0.7316 (mt0)
REVERT: B  119 ASN cc_start: 0.8021 (m-40) cc_final: 0.7772 (m-40)
REVERT: B  273 ILE cc_start: 0.7643 (mt) cc_final: 0.7309 (mt)
REVERT: B  334 SER cc_start: 0.7380 (m) cc_final: 0.6844 (t)
REVERT: R  109 TYR cc_start: 0.7186 (m-80) cc_final: 0.6940 (m-80)
REVERT: R  140 TYR cc_start: 0.8018 (m-80) cc_final: 0.7774 (m-80)
REVERT: E  140 MET cc_start: 0.7263 (mmt) cc_final: 0.6739 (mmt)
REVERT: A   17 LYS cc_start: 0.8167 (mtpp) cc_final: 0.7860 (mtpp)
REVERT: A  251 ASN cc_start: 0.8557 (t0) cc_final: 0.8329 (t160)
  outliers start: 28
  outliers final: 13
  residues processed: 230
  average time/residue: 1.0455
  time to fit residues: 257.8204
Evaluate side-chains
  219 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 206
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain R residue  235 VAL
Chi-restraints excluded: chain R residue  263 LEU
Chi-restraints excluded: chain R residue  320 CYS
Chi-restraints excluded: chain R residue  323 ILE
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 90 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 110 ASN
B 125 ASN
B 237 ASN
E  82 GLN
E 186 GLN
A 200 ASN
A 250 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.148349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.133797 restraints weight = 12266.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 2.07
r_work: 0.3761 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3611 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8458  Z= 0.175
  Angle     :  0.581  12.587  11493  Z= 0.303
  Chirality :  0.043   0.178   1313
  Planarity :  0.004   0.037   1444
  Dihedral  :  4.707  26.665   1158
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 16.67 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.45 (0.26), residues: 1047
  helix:  1.46 (0.29), residues: 324
  sheet:  0.17 (0.31), residues: 268
  loop : -0.38 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.006   0.001   HIS E  35 
 PHE   0.020   0.002   PHE R 274 
 TYR   0.015   0.002   TYR E 190 
 ARG   0.009   0.001   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04245 (  395)
  hydrogen bonds       : angle       5.02730 ( 1104)
  SS BOND              : bond        0.00872 (    3)
  SS BOND              : angle       1.55632 (    6)
  covalent geometry    : bond        0.00398 ( 8455)
  covalent geometry    : angle       0.58043 (11487)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 204
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
REVERT: B   61 MET cc_start: 0.8516 (ppp) cc_final: 0.8293 (ppp)
REVERT: B   72 SER cc_start: 0.8068 (t) cc_final: 0.7795 (p)
REVERT: B   75 GLN cc_start: 0.7627 (mt0) cc_final: 0.7375 (mt0)
REVERT: B  273 ILE cc_start: 0.7715 (mt) cc_final: 0.7396 (mt)
REVERT: B  334 SER cc_start: 0.7387 (m) cc_final: 0.6852 (t)
REVERT: R  140 TYR cc_start: 0.8092 (m-80) cc_final: 0.7808 (m-80)
REVERT: E  140 MET cc_start: 0.7419 (mmt) cc_final: 0.6858 (mmt)
REVERT: E  212 PHE cc_start: 0.6364 (m-80) cc_final: 0.6138 (m-80)
  outliers start: 36
  outliers final: 20
  residues processed: 221
  average time/residue: 1.0640
  time to fit residues: 251.2107
Evaluate side-chains
  219 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 199
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  212 ASP
Chi-restraints excluded: chain R residue  210 SER
Chi-restraints excluded: chain R residue  235 VAL
Chi-restraints excluded: chain R residue  263 LEU
Chi-restraints excluded: chain R residue  294 ILE
Chi-restraints excluded: chain R residue  323 ILE
Chi-restraints excluded: chain R residue  363 SER
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 83 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
E  82 GLN
E 186 GLN
A 250 ASN
A 364 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.147472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.133103 restraints weight = 12144.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3863 rms_B_bonded: 2.05
r_work: 0.3759 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3609 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8458  Z= 0.172
  Angle     :  0.574  13.222  11493  Z= 0.297
  Chirality :  0.043   0.186   1313
  Planarity :  0.004   0.036   1444
  Dihedral  :  4.637  27.300   1158
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 18.34 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.26), residues: 1047
  helix:  1.47 (0.29), residues: 324
  sheet:  0.15 (0.31), residues: 269
  loop : -0.42 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.006   0.001   HIS E  35 
 PHE   0.017   0.002   PHE R 274 
 TYR   0.014   0.002   TYR E 102 
 ARG   0.010   0.001   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03950 (  395)
  hydrogen bonds       : angle       4.91143 ( 1104)
  SS BOND              : bond        0.00855 (    3)
  SS BOND              : angle       1.56091 (    6)
  covalent geometry    : bond        0.00392 ( 8455)
  covalent geometry    : angle       0.57311 (11487)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 201
  time to evaluate  : 0.814 
Fit side-chains
REVERT: B   61 MET cc_start: 0.8502 (ppp) cc_final: 0.7671 (ppp)
REVERT: B   72 SER cc_start: 0.8019 (t) cc_final: 0.7680 (p)
REVERT: B  234 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6065 (t80)
REVERT: B  314 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7261 (ttt90)
REVERT: B  334 SER cc_start: 0.7341 (m) cc_final: 0.6814 (t)
REVERT: R  140 TYR cc_start: 0.8106 (m-80) cc_final: 0.7713 (m-80)
REVERT: E  116 THR cc_start: 0.8604 (t) cc_final: 0.8385 (p)
REVERT: E  140 MET cc_start: 0.7400 (mmt) cc_final: 0.6782 (mmt)
REVERT: E  178 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7300 (tt)
REVERT: A   41 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8110 (mtmm)
  outliers start: 32
  outliers final: 19
  residues processed: 217
  average time/residue: 1.0292
  time to fit residues: 238.8469
Evaluate side-chains
  217 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 194
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  212 ASP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain R residue  235 VAL
Chi-restraints excluded: chain R residue  263 LEU
Chi-restraints excluded: chain R residue  294 ILE
Chi-restraints excluded: chain R residue  323 ILE
Chi-restraints excluded: chain R residue  363 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 103 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 95 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 69 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   chunk 80 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
E  82 GLN
E 186 GLN
A 221 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.148146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.133941 restraints weight = 12047.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3866 rms_B_bonded: 2.03
r_work: 0.3762 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3615 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8458  Z= 0.166
  Angle     :  0.567   8.223  11493  Z= 0.295
  Chirality :  0.043   0.193   1313
  Planarity :  0.004   0.044   1444
  Dihedral  :  4.607  27.172   1158
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.13 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: 1047
  helix:  1.51 (0.29), residues: 325
  sheet:  0.23 (0.31), residues: 265
  loop : -0.43 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.006   0.001   HIS E  35 
 PHE   0.016   0.001   PHE R 274 
 TYR   0.014   0.002   TYR E 102 
 ARG   0.017   0.001   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03791 (  395)
  hydrogen bonds       : angle       4.85240 ( 1104)
  SS BOND              : bond        0.00902 (    3)
  SS BOND              : angle       1.60265 (    6)
  covalent geometry    : bond        0.00380 ( 8455)
  covalent geometry    : angle       0.56564 (11487)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 209
  time to evaluate  : 0.847 
Fit side-chains
REVERT: B   61 MET cc_start: 0.8438 (ppp) cc_final: 0.7568 (ppp)
REVERT: B   72 SER cc_start: 0.8033 (t) cc_final: 0.7660 (p)
REVERT: B  119 ASN cc_start: 0.7995 (m-40) cc_final: 0.7730 (m-40)
REVERT: B  212 ASP cc_start: 0.7572 (m-30) cc_final: 0.7008 (m-30)
REVERT: B  334 SER cc_start: 0.7438 (m) cc_final: 0.6916 (t)
REVERT: R  140 TYR cc_start: 0.8065 (m-80) cc_final: 0.7674 (m-80)
REVERT: R  196 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7515 (mt)
REVERT: E  172 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7852 (p)
REVERT: E  192 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7267 (mmp)
  outliers start: 34
  outliers final: 19
  residues processed: 229
  average time/residue: 0.9882
  time to fit residues: 243.0611
Evaluate side-chains
  228 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 206
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  210 SER
Chi-restraints excluded: chain R residue  216 LEU
Chi-restraints excluded: chain R residue  263 LEU
Chi-restraints excluded: chain R residue  294 ILE
Chi-restraints excluded: chain R residue  323 ILE
Chi-restraints excluded: chain R residue  363 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  192 MET
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 80 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 89 optimal weight:    0.4980
   chunk 87 optimal weight:    1.9990
   chunk 44 optimal weight:    0.4980
   chunk 20 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
E  82 GLN
E 186 GLN
A 221 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.147784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.133679 restraints weight = 12147.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 2.03
r_work: 0.3765 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3617 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8458  Z= 0.161
  Angle     :  0.573   8.843  11493  Z= 0.296
  Chirality :  0.043   0.203   1313
  Planarity :  0.004   0.040   1444
  Dihedral  :  4.567  27.409   1158
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 21.14 %
    Favored  : 74.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.52 (0.26), residues: 1047
  helix:  1.54 (0.29), residues: 325
  sheet:  0.26 (0.31), residues: 265
  loop : -0.40 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.006   0.001   HIS E  35 
 PHE   0.014   0.001   PHE R 274 
 TYR   0.013   0.002   TYR E 102 
 ARG   0.010   0.001   ARG B 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03674 (  395)
  hydrogen bonds       : angle       4.85377 ( 1104)
  SS BOND              : bond        0.00889 (    3)
  SS BOND              : angle       1.51412 (    6)
  covalent geometry    : bond        0.00371 ( 8455)
  covalent geometry    : angle       0.57202 (11487)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 206
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
REVERT: B   61 MET cc_start: 0.8387 (ppp) cc_final: 0.7471 (ppp)
REVERT: B   72 SER cc_start: 0.8020 (t) cc_final: 0.7702 (p)
REVERT: B  111 TYR cc_start: 0.8549 (m-80) cc_final: 0.8298 (m-80)
REVERT: B  119 ASN cc_start: 0.8001 (m-40) cc_final: 0.7726 (m-40)
REVERT: B  169 TRP cc_start: 0.8472 (OUTLIER) cc_final: 0.8108 (m-10)
REVERT: B  334 SER cc_start: 0.7420 (m) cc_final: 0.6899 (t)
REVERT: R  140 TYR cc_start: 0.8067 (m-80) cc_final: 0.7690 (m-80)
REVERT: R  168 TRP cc_start: 0.6305 (t-100) cc_final: 0.5356 (t-100)
REVERT: R  196 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7538 (mt)
REVERT: E  140 MET cc_start: 0.7481 (mmt) cc_final: 0.7150 (mmt)
REVERT: E  172 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.7870 (p)
REVERT: E  192 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7275 (mmp)
REVERT: A   17 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7976 (mtpp)
  outliers start: 39
  outliers final: 23
  residues processed: 229
  average time/residue: 1.0012
  time to fit residues: 246.4881
Evaluate side-chains
  231 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 204
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  166 SER
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  210 SER
Chi-restraints excluded: chain R residue  216 LEU
Chi-restraints excluded: chain R residue  263 LEU
Chi-restraints excluded: chain R residue  294 ILE
Chi-restraints excluded: chain R residue  320 CYS
Chi-restraints excluded: chain R residue  323 ILE
Chi-restraints excluded: chain R residue  363 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  192 MET
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain A residue  234 ASP
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 102 optimal weight:    0.0040
   chunk 66 optimal weight:    0.9980
   chunk 103 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
E  82 GLN
E 186 GLN
E 194 ASN
A 200 ASN
A 221 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.147727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.133684 restraints weight = 12263.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 2.04
r_work: 0.3767 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3619 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8458  Z= 0.152
  Angle     :  0.569   7.657  11493  Z= 0.294
  Chirality :  0.043   0.211   1313
  Planarity :  0.004   0.034   1444
  Dihedral  :  4.529  27.166   1158
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 21.70 %
    Favored  : 74.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.54 (0.26), residues: 1047
  helix:  1.58 (0.29), residues: 325
  sheet:  0.24 (0.31), residues: 266
  loop : -0.39 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.005   0.001   HIS E  35 
 PHE   0.014   0.002   PHE R 326 
 TYR   0.013   0.001   TYR E 102 
 ARG   0.009   0.001   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03638 (  395)
  hydrogen bonds       : angle       4.84302 ( 1104)
  SS BOND              : bond        0.00712 (    3)
  SS BOND              : angle       1.26688 (    6)
  covalent geometry    : bond        0.00347 ( 8455)
  covalent geometry    : angle       0.56859 (11487)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 208
  time to evaluate  : 0.953 
Fit side-chains
REVERT: B   61 MET cc_start: 0.8336 (ppp) cc_final: 0.7479 (ppp)
REVERT: B   72 SER cc_start: 0.7993 (t) cc_final: 0.7681 (p)
REVERT: B  111 TYR cc_start: 0.8562 (m-80) cc_final: 0.8314 (m-80)
REVERT: B  119 ASN cc_start: 0.7994 (m-40) cc_final: 0.7722 (m-40)
REVERT: B  169 TRP cc_start: 0.8467 (OUTLIER) cc_final: 0.8092 (m-10)
REVERT: B  334 SER cc_start: 0.7422 (m) cc_final: 0.6889 (t)
REVERT: R  140 TYR cc_start: 0.8063 (m-80) cc_final: 0.7664 (m-80)
REVERT: R  168 TRP cc_start: 0.6307 (t-100) cc_final: 0.5375 (t-100)
REVERT: E  140 MET cc_start: 0.7508 (mmt) cc_final: 0.7235 (mmt)
REVERT: E  172 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7876 (p)
REVERT: E  192 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7277 (mmp)
REVERT: A   17 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7990 (mtpp)
  outliers start: 37
  outliers final: 23
  residues processed: 227
  average time/residue: 1.0640
  time to fit residues: 258.7608
Evaluate side-chains
  231 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 205
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  210 SER
Chi-restraints excluded: chain R residue  216 LEU
Chi-restraints excluded: chain R residue  263 LEU
Chi-restraints excluded: chain R residue  294 ILE
Chi-restraints excluded: chain R residue  320 CYS
Chi-restraints excluded: chain R residue  363 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  192 MET
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain A residue  234 ASP
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 13 optimal weight:    0.0170
   chunk 100 optimal weight:    0.9990
   chunk 66 optimal weight:    0.2980
   chunk 76 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 60 optimal weight:    0.3980
   chunk 44 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 54 optimal weight:   10.0000
   overall best weight:    0.5420

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  82 GLN
E 186 GLN
A 200 ASN
A 250 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.148420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.134345 restraints weight = 12316.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 2.05
r_work: 0.3772 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3625 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8458  Z= 0.136
  Angle     :  0.569   7.573  11493  Z= 0.292
  Chirality :  0.043   0.214   1313
  Planarity :  0.004   0.032   1444
  Dihedral  :  4.473  27.161   1158
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 21.92 %
    Favored  : 74.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.52 (0.26), residues: 1047
  helix:  1.55 (0.29), residues: 328
  sheet:  0.16 (0.31), residues: 261
  loop : -0.35 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.005   0.001   HIS E  35 
 PHE   0.018   0.001   PHE A 312 
 TYR   0.012   0.001   TYR B 289 
 ARG   0.007   0.001   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03518 (  395)
  hydrogen bonds       : angle       4.83986 ( 1104)
  SS BOND              : bond        0.00791 (    3)
  SS BOND              : angle       1.37842 (    6)
  covalent geometry    : bond        0.00310 ( 8455)
  covalent geometry    : angle       0.56854 (11487)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 209
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
REVERT: B   61 MET cc_start: 0.8283 (ppp) cc_final: 0.7578 (ppp)
REVERT: B   72 SER cc_start: 0.7973 (t) cc_final: 0.7667 (p)
REVERT: B  111 TYR cc_start: 0.8553 (m-80) cc_final: 0.8322 (m-80)
REVERT: B  119 ASN cc_start: 0.7984 (m-40) cc_final: 0.7729 (m-40)
REVERT: B  169 TRP cc_start: 0.8464 (OUTLIER) cc_final: 0.8090 (m-10)
REVERT: B  217 MET cc_start: 0.7189 (mmt) cc_final: 0.6941 (mmt)
REVERT: B  234 PHE cc_start: 0.7000 (OUTLIER) cc_final: 0.6023 (t80)
REVERT: B  334 SER cc_start: 0.7389 (m) cc_final: 0.6874 (t)
REVERT: R  140 TYR cc_start: 0.8044 (m-80) cc_final: 0.7713 (m-80)
REVERT: R  167 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7408 (m-30)
REVERT: R  168 TRP cc_start: 0.6311 (t-100) cc_final: 0.5386 (t-100)
REVERT: E   18 ARG cc_start: 0.8074 (ptm160) cc_final: 0.7773 (ptm160)
REVERT: E  140 MET cc_start: 0.7474 (mmt) cc_final: 0.7175 (mmt)
REVERT: E  172 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7879 (p)
REVERT: E  192 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7273 (mmp)
REVERT: A   17 LYS cc_start: 0.8197 (mtpp) cc_final: 0.7984 (mtpp)
  outliers start: 35
  outliers final: 22
  residues processed: 229
  average time/residue: 0.9997
  time to fit residues: 246.2915
Evaluate side-chains
  229 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 202
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  167 ASP
Chi-restraints excluded: chain R residue  210 SER
Chi-restraints excluded: chain R residue  216 LEU
Chi-restraints excluded: chain R residue  263 LEU
Chi-restraints excluded: chain R residue  294 ILE
Chi-restraints excluded: chain R residue  363 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain E residue  192 MET
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain A residue  234 ASP
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0670
   chunk 94 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 220 GLN
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  47 ASN
E 186 GLN
A 221 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.148100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.133831 restraints weight = 12357.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 2.06
r_work: 0.3762 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3613 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8458  Z= 0.157
  Angle     :  0.584   8.189  11493  Z= 0.300
  Chirality :  0.044   0.220   1313
  Planarity :  0.004   0.032   1444
  Dihedral  :  4.523  27.190   1158
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 22.82 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.54 (0.26), residues: 1047
  helix:  1.56 (0.29), residues: 327
  sheet:  0.20 (0.31), residues: 258
  loop : -0.35 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 211 
 HIS   0.006   0.001   HIS E  35 
 PHE   0.017   0.002   PHE A 312 
 TYR   0.015   0.002   TYR B 289 
 ARG   0.007   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03646 (  395)
  hydrogen bonds       : angle       4.85805 ( 1104)
  SS BOND              : bond        0.00818 (    3)
  SS BOND              : angle       1.45772 (    6)
  covalent geometry    : bond        0.00360 ( 8455)
  covalent geometry    : angle       0.58296 (11487)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 205
  time to evaluate  : 0.867 
Fit side-chains
REVERT: B   61 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7694 (ppp)
REVERT: B   72 SER cc_start: 0.7965 (t) cc_final: 0.7661 (p)
REVERT: B  111 TYR cc_start: 0.8572 (m-80) cc_final: 0.8314 (m-80)
REVERT: B  119 ASN cc_start: 0.8017 (m-40) cc_final: 0.7802 (m-40)
REVERT: B  169 TRP cc_start: 0.8485 (OUTLIER) cc_final: 0.8119 (m-10)
REVERT: B  217 MET cc_start: 0.7176 (mmt) cc_final: 0.6923 (mmt)
REVERT: B  334 SER cc_start: 0.7433 (m) cc_final: 0.6913 (t)
REVERT: R  140 TYR cc_start: 0.8051 (m-80) cc_final: 0.7725 (m-80)
REVERT: R  168 TRP cc_start: 0.6315 (t-100) cc_final: 0.5404 (t-100)
REVERT: E   18 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7765 (ptm160)
REVERT: E   38 ARG cc_start: 0.7952 (ptt90) cc_final: 0.7729 (ptm160)
REVERT: E  140 MET cc_start: 0.7493 (mmt) cc_final: 0.7178 (mmt)
REVERT: E  155 VAL cc_start: 0.8029 (p) cc_final: 0.7760 (t)
REVERT: E  192 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7285 (mmp)
REVERT: A   17 LYS cc_start: 0.8192 (mtpp) cc_final: 0.7991 (mtpp)
  outliers start: 33
  outliers final: 23
  residues processed: 222
  average time/residue: 0.9825
  time to fit residues: 234.0774
Evaluate side-chains
  231 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 204
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  210 SER
Chi-restraints excluded: chain R residue  216 LEU
Chi-restraints excluded: chain R residue  263 LEU
Chi-restraints excluded: chain R residue  294 ILE
Chi-restraints excluded: chain R residue  363 SER
Chi-restraints excluded: chain E residue   18 ARG
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  192 MET
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain A residue  234 ASP
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 92 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 73 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 100 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 103 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9990
   chunk 91 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  47 ASN
E 186 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.148018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.133835 restraints weight = 12220.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 2.05
r_work: 0.3768 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3621 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8458  Z= 0.162
  Angle     :  0.593   8.809  11493  Z= 0.304
  Chirality :  0.044   0.226   1313
  Planarity :  0.004   0.038   1444
  Dihedral  :  4.556  27.180   1158
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 23.27 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.52 (0.26), residues: 1047
  helix:  1.55 (0.29), residues: 327
  sheet:  0.14 (0.31), residues: 260
  loop : -0.34 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.006   0.001   HIS E  35 
 PHE   0.017   0.002   PHE A 312 
 TYR   0.024   0.002   TYR B  59 
 ARG   0.008   0.001   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03662 (  395)
  hydrogen bonds       : angle       4.87241 ( 1104)
  SS BOND              : bond        0.00866 (    3)
  SS BOND              : angle       1.54979 (    6)
  covalent geometry    : bond        0.00371 ( 8455)
  covalent geometry    : angle       0.59233 (11487)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 203
  time to evaluate  : 0.929 
Fit side-chains
REVERT: B   61 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7665 (ppp)
REVERT: B   72 SER cc_start: 0.7950 (t) cc_final: 0.7650 (p)
REVERT: B  111 TYR cc_start: 0.8572 (m-80) cc_final: 0.8308 (m-80)
REVERT: B  119 ASN cc_start: 0.8028 (m-40) cc_final: 0.7820 (m-40)
REVERT: B  169 TRP cc_start: 0.8474 (OUTLIER) cc_final: 0.8121 (m-10)
REVERT: B  217 MET cc_start: 0.7240 (mmt) cc_final: 0.6990 (mmt)
REVERT: B  234 PHE cc_start: 0.7050 (OUTLIER) cc_final: 0.6115 (t80)
REVERT: B  334 SER cc_start: 0.7455 (m) cc_final: 0.6946 (t)
REVERT: R  140 TYR cc_start: 0.8091 (m-80) cc_final: 0.7755 (m-80)
REVERT: R  168 TRP cc_start: 0.6319 (t-100) cc_final: 0.5408 (t-100)
REVERT: E   18 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7755 (ptm160)
REVERT: E  140 MET cc_start: 0.7455 (mmt) cc_final: 0.7134 (mmt)
REVERT: E  155 VAL cc_start: 0.8029 (p) cc_final: 0.7754 (t)
REVERT: E  192 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7300 (mmp)
REVERT: A   17 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7997 (mtpp)
  outliers start: 29
  outliers final: 21
  residues processed: 219
  average time/residue: 0.9674
  time to fit residues: 228.3074
Evaluate side-chains
  229 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 203
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  210 SER
Chi-restraints excluded: chain R residue  216 LEU
Chi-restraints excluded: chain R residue  263 LEU
Chi-restraints excluded: chain R residue  294 ILE
Chi-restraints excluded: chain R residue  363 SER
Chi-restraints excluded: chain E residue   18 ARG
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  192 MET
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain A residue  234 ASP
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0980
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 99 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 54 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 364 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.148001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.133721 restraints weight = 12439.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3867 rms_B_bonded: 2.08
r_work: 0.3763 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3615 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8458  Z= 0.166
  Angle     :  0.606   8.702  11493  Z= 0.309
  Chirality :  0.044   0.226   1313
  Planarity :  0.004   0.040   1444
  Dihedral  :  4.570  27.330   1158
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 23.49 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.26), residues: 1047
  helix:  1.51 (0.29), residues: 327
  sheet:  0.17 (0.32), residues: 248
  loop : -0.39 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 211 
 HIS   0.006   0.001   HIS E  35 
 PHE   0.016   0.002   PHE A 312 
 TYR   0.013   0.002   TYR E 102 
 ARG   0.011   0.001   ARG B 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03679 (  395)
  hydrogen bonds       : angle       4.92596 ( 1104)
  SS BOND              : bond        0.00923 (    3)
  SS BOND              : angle       1.60131 (    6)
  covalent geometry    : bond        0.00383 ( 8455)
  covalent geometry    : angle       0.60541 (11487)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8018.89 seconds
wall clock time: 138 minutes 47.68 seconds (8327.68 seconds total)