Starting phenix.real_space_refine
on Wed Aug  5 17:27:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iy5_35814/08_2026/8iy5_35814.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iy5_35814/08_2026/8iy5_35814.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iy5_35814/08_2026/8iy5_35814.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iy5_35814/08_2026/8iy5_35814.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iy5_35814/08_2026/8iy5_35814.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iy5_35814/08_2026/8iy5_35814.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.501
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2308 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      76      5.16       5
     C    5847      2.51       5
     N    1541      2.21       5
     O    1712      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9176
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1764
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 216}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2583
          Classifications: {'peptide': 336}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "C"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 407
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
    Chain: "E"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2468
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 316, 2465
          Classifications: {'peptide': 316}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 13, 'TRANS': 302}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 50
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
      Conformer: "B"
        Number of residues, atoms: 316, 2465
          Classifications: {'peptide': 316}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 13, 'TRANS': 302}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 50
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
          bond proxies already assigned to first conformer: 2521
    Chain: "L"
      Number of atoms: 171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 171
          Classifications: {'peptide': 21}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 20}
  Time building chain proxies: 1.74, per 1000 atoms: 0.19
  Number of scatterers: 9176
  At special positions: 0
  Unit cell: (88.312, 124.334, 139.44, 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      76     16.00
     O    1712      8.00
     N    1541      7.00
     C    5847      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 103 " - pdb=" SG  CYS B 114 " distance=2.05
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  90 " - pdb=" SG  CYS R 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 174 " - pdb=" SG  CYS R 255 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L   1 " - pdb=" SG  CYS L  15 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L   3 " - pdb=" SG  CYS L  11 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 337.3 milliseconds
  

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2208

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 13 sheets defined
      36.5% alpha, 22.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.908A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 216
      removed outlier: 3.523A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 232
      removed outlier: 4.572A  pdb=" N   TYR A 230 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LEU A 232 " --> pdb=" O   ASP A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 254
    Processing helix  chain 'A' and resid 277 through 281
      removed outlier: 3.732A  pdb=" N   LYS A 280 " --> pdb=" O   LYS A 277 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   SER A 281 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 277 through 281'
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.892A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 311
    Processing helix  chain 'A' and resid 329 through 351
      removed outlier: 3.758A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.606A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 22
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 4.353A  pdb=" N   ALA C  35 " --> pdb=" O   SER C  31 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   ASP C  36 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LEU C  37 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 3.913A  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 208 through 212
      removed outlier: 3.773A  pdb=" N   VAL E 212 " --> pdb=" O   ALA E 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 97 through 129
    Processing helix  chain 'R' and resid 134 through 165
      Proline residue:  R 156  - end of helix
    Processing helix  chain 'R' and resid 171 through 205
      Proline residue:  R 178  - end of helix
      removed outlier: 3.694A  pdb=" N   VAL R 203 " --> pdb=" O   ARG R 199 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 214 through 233
      removed outlier: 3.861A  pdb=" N   THR R 218 " --> pdb=" O   VAL R 214 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 235 through 239
    Processing helix  chain 'R' and resid 263 through 281
      removed outlier: 5.992A  pdb=" N   ASP R 274 " --> pdb=" O   LYS R 270 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   TRP R 275 " --> pdb=" O   THR R 271 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 282 through 301
    Processing helix  chain 'R' and resid 313 through 350
      removed outlier: 3.666A  pdb=" N   GLN R 317 " --> pdb=" O   ASP R 313 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   PHE R 332 " --> pdb=" O   LEU R 328 " (cutoff:3.500A)
      Proline residue:  R 338  - end of helix
      removed outlier: 3.678A  pdb=" N   TYR R 350 " --> pdb=" O   LYS R 346 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 357 through 390
      removed outlier: 3.754A  pdb=" N   VAL R 366 " --> pdb=" O   SER R 362 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   ASN R 382 " --> pdb=" O   ASN R 378 " (cutoff:3.500A)
      Proline residue:  R 383  - end of helix
    Processing helix  chain 'R' and resid 390 through 403
    Processing helix  chain 'L' and resid 8 through 18
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191
      removed outlier: 6.264A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 9.069A  pdb=" N   ALA A 220 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.867A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.858A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.851A  pdb=" N   ALA B 113 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 5.151A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   SER B 160 " --> pdb=" O   CYS B 148 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.009A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.655A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.643A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.167A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLY E  44 " --> pdb=" O   ALA E  40 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 130
    Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136
      removed outlier: 6.188A  pdb=" N   VAL E 135 " --> pdb=" O   GLU E 234 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 240 through 247

    445 hydrogen bonds defined for protein.
    1268 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.08

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2948
        1.34 -     1.46: 2274
        1.46 -     1.59: 4041
        1.59 -     1.71: 0
        1.71 -     1.83: 104
  Bond restraints: 9367
  Sorted by residual:
  bond pdb=" CA  ASP B 312 "
       pdb=" C   ASP B 312 "
    ideal  model  delta    sigma   weight residual
    1.523  1.545 -0.022 1.34e-02 5.57e+03 2.58e+00
  bond pdb=" C   VAL E  12 "
       pdb=" N   GLN E  13 "
    ideal  model  delta    sigma   weight residual
    1.330  1.352 -0.022 1.47e-02 4.63e+03 2.24e+00
  bond pdb=" C   CYS B 114 "
       pdb=" N   GLY B 115 "
    ideal  model  delta    sigma   weight residual
    1.326  1.340 -0.013 1.09e-02 8.42e+03 1.50e+00
  bond pdb=" CB  PRO A 288 "
       pdb=" CG  PRO A 288 "
    ideal  model  delta    sigma   weight residual
    1.492  1.552 -0.060 5.00e-02 4.00e+02 1.44e+00
  bond pdb=" CA  VAL R 177 "
       pdb=" CB  VAL R 177 "
    ideal  model  delta    sigma   weight residual
    1.539  1.533  0.006 5.40e-03 3.43e+04 1.16e+00
  ... (remaining 9362 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 12581
        2.75 -     5.51: 98
        5.51 -     8.26: 14
        8.26 -    11.02: 0
       11.02 -    13.77: 1
  Bond angle restraints: 12694
  Sorted by residual:
  angle pdb=" CA  CYS B 103 "
        pdb=" CB  CYS B 103 "
        pdb=" SG  CYS B 103 "
      ideal   model   delta    sigma   weight residual
     114.40  128.17  -13.77 2.30e+00 1.89e-01 3.59e+01
  angle pdb=" N   GLY R 239 "
        pdb=" CA  GLY R 239 "
        pdb=" C   GLY R 239 "
      ideal   model   delta    sigma   weight residual
     112.49  119.59   -7.10 1.21e+00 6.83e-01 3.45e+01
  angle pdb=" N   GLY B 115 "
        pdb=" CA  GLY B 115 "
        pdb=" C   GLY B 115 "
      ideal   model   delta    sigma   weight residual
     111.19  117.89   -6.70 1.45e+00 4.76e-01 2.14e+01
  angle pdb=" CA  CYS B 114 "
        pdb=" CB  CYS B 114 "
        pdb=" SG  CYS B 114 "
      ideal   model   delta    sigma   weight residual
     114.40  122.61   -8.21 2.30e+00 1.89e-01 1.27e+01
  angle pdb=" C   HIS E 220 "
        pdb=" N   LEU E 221 "
        pdb=" CA  LEU E 221 "
      ideal   model   delta    sigma   weight residual
     121.54  128.35   -6.81 1.91e+00 2.74e-01 1.27e+01
  ... (remaining 12689 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 5083
       17.75 -    35.50: 422
       35.50 -    53.25: 66
       53.25 -    71.00: 7
       71.00 -    88.74: 8
  Dihedral angle restraints: 5586
    sinusoidal: 2166
      harmonic: 3420
  Sorted by residual:
  dihedral pdb=" CB  CYS R  90 "
           pdb=" SG  CYS R  90 "
           pdb=" SG  CYS R 358 "
           pdb=" CB  CYS R 358 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   42.81   50.19     1      1.00e+01 1.00e-02 3.45e+01
  dihedral pdb=" CB  CYS B 103 "
           pdb=" SG  CYS B 103 "
           pdb=" SG  CYS B 114 "
           pdb=" CB  CYS B 114 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -36.60  -49.40     1      1.00e+01 1.00e-02 3.35e+01
  dihedral pdb=" CA  HIS E 220 "
           pdb=" C   HIS E 220 "
           pdb=" N   LEU E 221 "
           pdb=" CA  LEU E 221 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.63   24.37     0      5.00e+00 4.00e-02 2.37e+01
  ... (remaining 5583 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1139
       0.049 -    0.098: 247
       0.098 -    0.148: 61
       0.148 -    0.197: 2
       0.197 -    0.246: 1
  Chirality restraints: 1450
  Sorted by residual:
  chirality pdb=" CA  CYS B 103 "
            pdb=" N   CYS B 103 "
            pdb=" C   CYS B 103 "
            pdb=" CB  CYS B 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CA  TYR E 178 "
            pdb=" N   TYR E 178 "
            pdb=" C   TYR E 178 "
            pdb=" CB  TYR E 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.60e-01
  chirality pdb=" CA  ILE E 177 "
            pdb=" N   ILE E 177 "
            pdb=" C   ILE E 177 "
            pdb=" CB  ILE E 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.48e-01
  ... (remaining 1447 not shown)

  Planarity restraints: 1600
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E 221 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.73e+00
        pdb=" C   LEU E 221 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   LEU E 221 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLU E 222 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C  54 "    0.028 5.00e-02 4.00e+02   4.30e-02 2.96e+00
        pdb=" N   PRO C  55 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO C  55 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C  55 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 250 "   -0.012 2.00e-02 2.50e+03   1.27e-02 2.82e+00
        pdb=" CG  PHE A 250 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 250 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 250 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 250 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 250 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 250 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1597 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 324
        2.71 -     3.26: 9092
        3.26 -     3.81: 14927
        3.81 -     4.35: 18752
        4.35 -     4.90: 31786
  Nonbonded interactions: 74881
  Sorted by model distance:
  nonbonded pdb=" O   PHE E  32 "
            pdb=" NH2 ARG E  72 "
     model   vdw
     2.166 3.120
  nonbonded pdb=" OD1 ASP A 350 "
            pdb=" ND2 ASN R 134 "
     model   vdw
     2.178 3.120
  nonbonded pdb=" OD1 ASP B 290 "
            pdb=" NE  ARG B 314 "
     model   vdw
     2.193 3.120
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OG  SER R 342 "
            pdb=" OD1 ASP R 368 "
     model   vdw
     2.238 3.040
  ... (remaining 74876 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.30 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.760
  Find NCS groups from input model:        0.030
  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:5.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5702
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      :  0.003   0.060   9374  Z= 0.147
  Angle     :  0.690  13.775  12708  Z= 0.398
  Chirality :  0.044   0.246   1450
  Planarity :  0.004   0.054   1600
  Dihedral  : 13.175  88.745   3357
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.88 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.25), residues: 1160
  helix:  1.59 (0.27), residues: 381
  sheet: -0.66 (0.30), residues: 290
  loop : -1.40 (0.28), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  49 
 TYR   0.022   0.001   TYR E 178 
 PHE   0.030   0.002   PHE A 250 
 TRP   0.027   0.001   TRP B 332 
 HIS   0.004   0.001   HIS E  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.15 ( 9367)
  covalent geometry    : angle       0.68362 /  0.40 (12694)
  SS BOND              : bond        0.00807 /  0.42 (    7)
  SS BOND              : angle       2.85949 /  1.54 (   14)
  hydrogen bonds       : bond        0.12519 /  8.46 (  445)
  hydrogen bonds       : angle       5.83658 /  4.13 ( 1268)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.227 
Fit side-chains
REVERT: B   76 ASP cc_start: 0.6166 (p0) cc_final: 0.5739 (p0)
REVERT: C   38 MET cc_start: 0.5927 (mmm) cc_final: 0.5559 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.3864
  time to fit residues: 68.1952
Evaluate side-chains
  130 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    0.0020
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    9.9990
   overall best weight:    1.2992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  22 ASN
A 256 ASN
A 333 GLN
R 104 ASN
R 373 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.250752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.196106 restraints weight = 11726.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.4190 rms_B_bonded: 2.52
r_work: 0.3995 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3990
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3990 r_free = 0.3990    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3990 r_free = 0.3990    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (8 function evaluations)
r_final: 0.3990
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6439
moved from start:          0.1178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9374  Z= 0.137
  Angle     :  0.629   9.066  12708  Z= 0.331
  Chirality :  0.045   0.260   1450
  Planarity :  0.004   0.046   1600
  Dihedral  :  4.967  27.889   1266
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.06 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 10.63 %
    Favored  : 87.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.25), residues: 1160
  helix:  1.55 (0.27), residues: 389
  sheet: -0.52 (0.30), residues: 280
  loop : -1.22 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  49 
 TYR   0.016   0.001   TYR E 178 
 PHE   0.028   0.002   PHE R 112 
 TRP   0.015   0.001   TRP B 332 
 HIS   0.004   0.001   HIS B  62 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.14 ( 9367)
  covalent geometry    : angle       0.62577 /  0.33 (12694)
  SS BOND              : bond        0.00549 /  0.29 (    7)
  SS BOND              : angle       2.04245 /  1.06 (   14)
  hydrogen bonds       : bond        0.03709 /  2.46 (  445)
  hydrogen bonds       : angle       4.95086 /  3.45 ( 1268)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6839 (tt0)
REVERT: A  314 LYS cc_start: 0.6281 (mptp) cc_final: 0.6015 (mptm)
REVERT: A  333 GLN cc_start: 0.6346 (OUTLIER) cc_final: 0.6129 (mp10)
REVERT: B  336 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7196 (mt)
REVERT: C   38 MET cc_start: 0.6060 (mmm) cc_final: 0.5310 (mmt)
REVERT: R  126 ILE cc_start: 0.7251 (mm) cc_final: 0.6984 (mp)
REVERT: R  363 PHE cc_start: 0.7252 (t80) cc_final: 0.6957 (t80)
REVERT: L    7 MET cc_start: 0.1491 (pmm) cc_final: 0.0762 (pp-130)
  outliers start: 18
  outliers final: 9
  residues processed: 152
  average time/residue: 0.3538
  time to fit residues: 58.7357
Evaluate side-chains
  138 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  221 LEU
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain R residue  373 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 45 optimal weight:    0.2980
   chunk 91 optimal weight:    0.9990
   chunk 114 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 110 optimal weight:    3.9990
   chunk 98 optimal weight:   10.0000
   overall best weight:    1.8588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 333 GLN
E 220 HIS
R 314 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4642 r_free = 0.4642 target = 0.247626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.206192 restraints weight = 9952.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.4569 rms_B_bonded: 2.66
r_work: 0.4277 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.4277
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3976
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3976 r_free = 0.3976    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3976 r_free = 0.3976    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3976
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6493
moved from start:          0.1520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9374  Z= 0.146
  Angle     :  0.622   9.003  12708  Z= 0.329
  Chirality :  0.044   0.248   1450
  Planarity :  0.004   0.043   1600
  Dihedral  :  5.020  28.696   1266
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.31 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 13.11 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.25), residues: 1160
  helix:  1.51 (0.26), residues: 389
  sheet: -0.44 (0.30), residues: 274
  loop : -1.24 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  49 
 TYR   0.017   0.002   TYR E 178 
 PHE   0.025   0.002   PHE R 112 
 TRP   0.008   0.001   TRP B 339 
 HIS   0.005   0.001   HIS B  62 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.15 ( 9367)
  covalent geometry    : angle       0.61822 /  0.33 (12694)
  SS BOND              : bond        0.00751 /  0.39 (    7)
  SS BOND              : angle       2.21592 /  1.17 (   14)
  hydrogen bonds       : bond        0.03674 /  2.45 (  445)
  hydrogen bonds       : angle       4.84601 /  3.38 ( 1268)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6842 (tt0)
REVERT: A  248 LYS cc_start: 0.3964 (mmtm) cc_final: 0.3439 (mmmt)
REVERT: A  314 LYS cc_start: 0.6441 (mptp) cc_final: 0.6158 (mptm)
REVERT: E  208 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6346 (pp20)
REVERT: R  173 MET cc_start: 0.4742 (ppp) cc_final: 0.4407 (ptp)
REVERT: R  256 LEU cc_start: 0.6442 (pt) cc_final: 0.6180 (pt)
REVERT: R  363 PHE cc_start: 0.7230 (t80) cc_final: 0.6946 (t80)
  outliers start: 22
  outliers final: 15
  residues processed: 149
  average time/residue: 0.3661
  time to fit residues: 59.0534
Evaluate side-chains
  143 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  218 MET
Chi-restraints excluded: chain E residue  221 LEU
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 63 optimal weight:    9.9990
   chunk 76 optimal weight:    1.9990
   chunk 108 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 111 optimal weight:    0.2980
   chunk 11 optimal weight:    1.9990
   chunk 13 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.835 > 50:)
   chunk 89 optimal weight:   10.0000
   overall best weight:    1.4588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  22 ASN
A 304 GLN
A 333 GLN
B  44 GLN
B  88 ASN
B 295 ASN
R 373 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.272156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.233996 restraints weight = 11316.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.4308 rms_B_bonded: 2.78
r_work: 0.3923 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3887
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3887 r_free = 0.3887    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3887 r_free = 0.3887    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3887
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6589
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9374  Z= 0.131
  Angle     :  0.599   8.261  12708  Z= 0.316
  Chirality :  0.044   0.240   1450
  Planarity :  0.004   0.040   1600
  Dihedral  :  4.922  28.965   1266
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.31 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 14.10 %
    Favored  : 83.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.25), residues: 1160
  helix:  1.54 (0.26), residues: 390
  sheet: -0.29 (0.30), residues: 279
  loop : -1.23 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  49 
 TYR   0.018   0.001   TYR E 178 
 PHE   0.023   0.002   PHE R 112 
 TRP   0.010   0.001   TRP B 339 
 HIS   0.003   0.001   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.13 ( 9367)
  covalent geometry    : angle       0.59467 /  0.31 (12694)
  SS BOND              : bond        0.00359 /  0.19 (    7)
  SS BOND              : angle       2.18252 /  1.17 (   14)
  hydrogen bonds       : bond        0.03439 /  2.30 (  445)
  hydrogen bonds       : angle       4.79326 /  3.35 ( 1268)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 138
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7019 (tt0)
REVERT: A   32 ARG cc_start: 0.7504 (ttp80) cc_final: 0.7221 (ttp80)
REVERT: A  314 LYS cc_start: 0.6632 (mptp) cc_final: 0.5884 (mmtm)
REVERT: A  333 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6415 (mp-120)
REVERT: B  237 ASN cc_start: 0.7827 (p0) cc_final: 0.7617 (p0)
REVERT: E  174 GLN cc_start: 0.6981 (mt0) cc_final: 0.6075 (pt0)
REVERT: E  208 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6473 (pp20)
REVERT: R  173 MET cc_start: 0.4762 (ppp) cc_final: 0.4503 (ptp)
REVERT: R  256 LEU cc_start: 0.6461 (pt) cc_final: 0.6201 (pt)
REVERT: R  363 PHE cc_start: 0.7437 (t80) cc_final: 0.7117 (t80)
  outliers start: 26
  outliers final: 12
  residues processed: 151
  average time/residue: 0.3773
  time to fit residues: 61.9924
Evaluate side-chains
  144 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  218 MET
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain R residue  373 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 94 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   chunk 78 optimal weight:    5.9990
   chunk 86 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4624 r_free = 0.4624 target = 0.245355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.205295 restraints weight = 9909.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.4234 rms_B_bonded: 2.49
r_work: 0.3894 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3918
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3918 r_free = 0.3918    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3918 r_free = 0.3918    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3918
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6628
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   9374  Z= 0.162
  Angle     :  0.647  11.020  12708  Z= 0.340
  Chirality :  0.045   0.300   1450
  Planarity :  0.004   0.039   1600
  Dihedral  :  5.088  29.162   1266
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.49 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 15.00 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.25), residues: 1160
  helix:  1.44 (0.26), residues: 390
  sheet: -0.29 (0.30), residues: 280
  loop : -1.22 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  49 
 TYR   0.020   0.002   TYR E 223 
 PHE   0.022   0.002   PHE R 112 
 TRP   0.011   0.002   TRP B 332 
 HIS   0.006   0.001   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.16 ( 9367)
  covalent geometry    : angle       0.64024 /  0.34 (12694)
  SS BOND              : bond        0.00654 /  0.34 (    7)
  SS BOND              : angle       2.86575 /  1.54 (   14)
  hydrogen bonds       : bond        0.03650 /  2.47 (  445)
  hydrogen bonds       : angle       4.85421 /  3.38 ( 1268)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 144
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7396 (tm-30) cc_final: 0.6970 (tt0)
REVERT: A   32 ARG cc_start: 0.7422 (ttp80) cc_final: 0.7157 (ttp80)
REVERT: A  263 SER cc_start: 0.8132 (p) cc_final: 0.7856 (m)
REVERT: A  333 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6405 (mm110)
REVERT: B  237 ASN cc_start: 0.7819 (p0) cc_final: 0.7598 (p0)
REVERT: B  262 MET cc_start: 0.7255 (ptm) cc_final: 0.6936 (ptm)
REVERT: E  120 SER cc_start: 0.6748 (t) cc_final: 0.6217 (m)
REVERT: E  174 GLN cc_start: 0.6911 (mt0) cc_final: 0.6004 (pt0)
REVERT: E  208 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6742 (pp20)
REVERT: R  173 MET cc_start: 0.4669 (ppp) cc_final: 0.4420 (ptp)
REVERT: R  192 LEU cc_start: 0.7356 (mt) cc_final: 0.7149 (mm)
REVERT: R  256 LEU cc_start: 0.6376 (pt) cc_final: 0.6111 (pt)
REVERT: R  363 PHE cc_start: 0.7424 (t80) cc_final: 0.7127 (t80)
  outliers start: 34
  outliers final: 18
  residues processed: 165
  average time/residue: 0.3708
  time to fit residues: 66.5723
Evaluate side-chains
  150 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  218 MET
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    0.5980
   chunk 2 optimal weight:    8.9990
   chunk 64 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 21 optimal weight:    8.9990
   chunk 25 optimal weight:    7.9990
   chunk 43 optimal weight:    5.9990
   chunk 85 optimal weight:    6.9990
   chunk 55 optimal weight:    6.9990
   chunk 68 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    3.5186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4859 r_free = 0.4859 target = 0.266622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.222158 restraints weight = 11461.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.4168 rms_B_bonded: 3.84
r_work: 0.3824 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3779
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3779 r_free = 0.3779    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3779 r_free = 0.3779    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6689
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072   9374  Z= 0.208
  Angle     :  0.722  11.802  12708  Z= 0.381
  Chirality :  0.047   0.320   1450
  Planarity :  0.005   0.041   1600
  Dihedral  :  5.443  30.071   1266
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.83 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 15.09 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.25), residues: 1160
  helix:  1.10 (0.26), residues: 399
  sheet: -0.48 (0.30), residues: 285
  loop : -1.25 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  49 
 TYR   0.021   0.002   TYR E 223 
 PHE   0.026   0.003   PHE A 307 
 TRP   0.024   0.002   TRP B 332 
 HIS   0.007   0.002   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00476 /  0.21 ( 9367)
  covalent geometry    : angle       0.71438 /  0.38 (12694)
  SS BOND              : bond        0.01007 /  0.53 (    7)
  SS BOND              : angle       3.13188 /  1.70 (   14)
  hydrogen bonds       : bond        0.04026 /  2.74 (  445)
  hydrogen bonds       : angle       5.05400 /  3.52 ( 1268)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 140
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7019 (tt0)
REVERT: A   32 ARG cc_start: 0.7459 (ttp80) cc_final: 0.7146 (ttp80)
REVERT: A  211 TRP cc_start: 0.6441 (p-90) cc_final: 0.6095 (p-90)
REVERT: A  333 GLN cc_start: 0.6608 (OUTLIER) cc_final: 0.6403 (mp10)
REVERT: B    7 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6662 (pp)
REVERT: B   96 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7048 (mmp-170)
REVERT: B  217 MET cc_start: 0.6723 (ptp) cc_final: 0.6506 (pmm)
REVERT: B  237 ASN cc_start: 0.7923 (p0) cc_final: 0.7655 (p0)
REVERT: E  120 SER cc_start: 0.6918 (t) cc_final: 0.6371 (m)
REVERT: E  174 GLN cc_start: 0.7016 (mt0) cc_final: 0.5850 (pt0)
REVERT: E  208 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6398 (tm-30)
REVERT: R  192 LEU cc_start: 0.7360 (mt) cc_final: 0.7146 (mm)
  outliers start: 41
  outliers final: 26
  residues processed: 165
  average time/residue: 0.3679
  time to fit residues: 66.2762
Evaluate side-chains
  158 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  151 LYS
Chi-restraints excluded: chain E residue  218 MET
Chi-restraints excluded: chain R residue  296 MET
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 67 optimal weight:   20.0000
   chunk 91 optimal weight:    0.9990
   chunk 100 optimal weight:    9.9990
   chunk 105 optimal weight:    0.9990
   chunk 85 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 103 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B  91 HIS
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.243219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.187137 restraints weight = 11720.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.4043 rms_B_bonded: 2.75
r_work: 0.3881 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3868
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3868 r_free = 0.3868    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3868 r_free = 0.3868    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3868
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6559
moved from start:          0.2607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9374  Z= 0.154
  Angle     :  0.726  26.369  12708  Z= 0.373
  Chirality :  0.046   0.399   1450
  Planarity :  0.004   0.042   1600
  Dihedral  :  5.227  29.191   1266
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.57 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 17.08 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.25), residues: 1160
  helix:  1.20 (0.26), residues: 398
  sheet: -0.30 (0.31), residues: 268
  loop : -1.19 (0.29), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B  49 
 TYR   0.022   0.002   TYR E 223 
 PHE   0.020   0.002   PHE A 307 
 TRP   0.013   0.001   TRP B 332 
 HIS   0.005   0.001   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.15 ( 9367)
  covalent geometry    : angle       0.70857 /  0.37 (12694)
  SS BOND              : bond        0.01119 /  0.59 (    7)
  SS BOND              : angle       4.75990 /  2.67 (   14)
  hydrogen bonds       : bond        0.03655 /  2.48 (  445)
  hydrogen bonds       : angle       4.93056 /  3.42 ( 1268)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 137
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7385 (tm-30) cc_final: 0.6893 (tt0)
REVERT: A   32 ARG cc_start: 0.7311 (ttp80) cc_final: 0.7010 (ttp80)
REVERT: A  211 TRP cc_start: 0.6395 (p-90) cc_final: 0.5977 (p-90)
REVERT: A  263 SER cc_start: 0.8252 (p) cc_final: 0.7944 (m)
REVERT: A  284 THR cc_start: 0.2057 (OUTLIER) cc_final: 0.1849 (m)
REVERT: B    7 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6540 (pp)
REVERT: B   96 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6947 (mmp-170)
REVERT: B  217 MET cc_start: 0.6433 (ptp) cc_final: 0.6180 (pmm)
REVERT: B  237 ASN cc_start: 0.7787 (p0) cc_final: 0.7537 (p0)
REVERT: E  174 GLN cc_start: 0.6918 (mt0) cc_final: 0.5733 (pt0)
REVERT: E  208 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6832 (tm-30)
REVERT: R  192 LEU cc_start: 0.7151 (mt) cc_final: 0.6944 (mm)
REVERT: R  256 LEU cc_start: 0.6362 (pt) cc_final: 0.6103 (pt)
  outliers start: 37
  outliers final: 22
  residues processed: 157
  average time/residue: 0.3344
  time to fit residues: 57.6266
Evaluate side-chains
  155 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  151 LYS
Chi-restraints excluded: chain E residue  218 MET
Chi-restraints excluded: chain R residue  296 MET
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 98 optimal weight:    9.9990
   chunk 84 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 13 optimal weight:    6.9990
   chunk 112 optimal weight:    9.9990
   chunk 91 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 5 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   chunk 97 optimal weight:    8.9990
   overall best weight:    4.1388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  22 ASN
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.239909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.195305 restraints weight = 9910.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.4165 rms_B_bonded: 2.92
r_work: 0.3870 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3831 r_free = 0.3831    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3831 r_free = 0.3831    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3831
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6723
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.090   9374  Z= 0.234
  Angle     :  0.810  25.240  12708  Z= 0.420
  Chirality :  0.049   0.401   1450
  Planarity :  0.005   0.045   1600
  Dihedral  :  5.628  30.401   1266
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.69 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 16.29 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.25), residues: 1160
  helix:  0.90 (0.26), residues: 397
  sheet: -0.48 (0.31), residues: 269
  loop : -1.24 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  49 
 TYR   0.026   0.002   TYR E 223 
 PHE   0.031   0.003   PHE A 307 
 TRP   0.020   0.002   TRP B 332 
 HIS   0.008   0.002   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00540 /  0.23 ( 9367)
  covalent geometry    : angle       0.79577 /  0.41 (12694)
  SS BOND              : bond        0.01325 /  0.70 (    7)
  SS BOND              : angle       4.60196 /  2.59 (   14)
  hydrogen bonds       : bond        0.04312 /  2.92 (  445)
  hydrogen bonds       : angle       5.19686 /  3.60 ( 1268)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 129
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6926 (tt0)
REVERT: A  284 THR cc_start: 0.2347 (OUTLIER) cc_final: 0.2137 (m)
REVERT: A  333 GLN cc_start: 0.6758 (OUTLIER) cc_final: 0.6445 (mp10)
REVERT: B    7 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6650 (pp)
REVERT: B   68 ARG cc_start: 0.8248 (ttt90) cc_final: 0.7976 (ttt180)
REVERT: B   96 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6962 (mmp-170)
REVERT: B  217 MET cc_start: 0.6477 (ptp) cc_final: 0.6266 (pmm)
REVERT: B  237 ASN cc_start: 0.7860 (p0) cc_final: 0.7617 (p0)
REVERT: E  174 GLN cc_start: 0.6850 (mt0) cc_final: 0.5818 (pt0)
REVERT: R  192 LEU cc_start: 0.7361 (mt) cc_final: 0.7140 (mm)
REVERT: R  256 LEU cc_start: 0.6382 (pt) cc_final: 0.6119 (pt)
REVERT: R  363 PHE cc_start: 0.7211 (t80) cc_final: 0.6991 (t80)
  outliers start: 45
  outliers final: 26
  residues processed: 157
  average time/residue: 0.3643
  time to fit residues: 62.3732
Evaluate side-chains
  155 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  151 LYS
Chi-restraints excluded: chain E residue  218 MET
Chi-restraints excluded: chain R residue  296 MET
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 102 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 21 optimal weight:   20.0000
   chunk 85 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 30 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    1.3188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B 293 ASN
B 295 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.244037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.193150 restraints weight = 11641.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.4119 rms_B_bonded: 2.68
r_work: 0.3948 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3934
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3934 r_free = 0.3934    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3934 r_free = 0.3934    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3934
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6590
moved from start:          0.2884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9374  Z= 0.137
  Angle     :  0.710  24.917  12708  Z= 0.366
  Chirality :  0.046   0.371   1450
  Planarity :  0.004   0.045   1600
  Dihedral  :  5.193  29.197   1266
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.14 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.17 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.25), residues: 1160
  helix:  1.22 (0.26), residues: 395
  sheet: -0.23 (0.32), residues: 262
  loop : -1.16 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B  49 
 TYR   0.015   0.001   TYR E 178 
 PHE   0.054   0.002   PHE A 307 
 TRP   0.011   0.001   TRP B 339 
 HIS   0.004   0.001   HIS R 150 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.14 ( 9367)
  covalent geometry    : angle       0.69468 /  0.36 (12694)
  SS BOND              : bond        0.00771 /  0.40 (    7)
  SS BOND              : angle       4.53770 /  2.55 (   14)
  hydrogen bonds       : bond        0.03616 /  2.42 (  445)
  hydrogen bonds       : angle       4.95911 /  3.44 ( 1268)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 128
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6891 (tt0)
REVERT: A  284 THR cc_start: 0.2237 (OUTLIER) cc_final: 0.2002 (m)
REVERT: A  333 GLN cc_start: 0.6334 (OUTLIER) cc_final: 0.5921 (mp10)
REVERT: B    7 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6713 (pp)
REVERT: B   96 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6866 (mmp-170)
REVERT: B  262 MET cc_start: 0.6769 (ptm) cc_final: 0.6559 (ttm)
REVERT: E  174 GLN cc_start: 0.6780 (mt0) cc_final: 0.5775 (pt0)
REVERT: R  192 LEU cc_start: 0.7374 (mt) cc_final: 0.7164 (mm)
  outliers start: 31
  outliers final: 20
  residues processed: 147
  average time/residue: 0.3625
  time to fit residues: 58.0761
Evaluate side-chains
  148 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  218 MET
Chi-restraints excluded: chain R residue  296 MET
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain L residue   20 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 110 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0980
   chunk 8 optimal weight:    0.8980
   chunk 96 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   chunk 109 optimal weight:   10.0000
   chunk 95 optimal weight:    0.7980
   chunk 46 optimal weight:   10.0000
   chunk 81 optimal weight:    9.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 333 GLN
B 293 ASN
L  16 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4885 r_free = 0.4885 target = 0.269697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.229761 restraints weight = 12504.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.4245 rms_B_bonded: 3.35
r_work: 0.3870 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3823
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3823 r_free = 0.3823    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3823 r_free = 0.3823    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3823
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6668
moved from start:          0.2958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9374  Z= 0.142
  Angle     :  0.723  24.988  12708  Z= 0.368
  Chirality :  0.046   0.396   1450
  Planarity :  0.004   0.051   1600
  Dihedral  :  5.173  30.833   1266
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.75 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 18.37 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.25), residues: 1160
  helix:  1.26 (0.26), residues: 395
  sheet: -0.29 (0.31), residues: 273
  loop : -1.07 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  49 
 TYR   0.015   0.001   TYR E 223 
 PHE   0.039   0.002   PHE A 307 
 TRP   0.011   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.14 ( 9367)
  covalent geometry    : angle       0.70634 /  0.36 (12694)
  SS BOND              : bond        0.00993 /  0.52 (    7)
  SS BOND              : angle       4.65457 /  2.61 (   14)
  hydrogen bonds       : bond        0.03582 /  2.40 (  445)
  hydrogen bonds       : angle       4.91480 /  3.41 ( 1268)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7034 (tt0)
REVERT: A  263 SER cc_start: 0.8053 (p) cc_final: 0.7835 (m)
REVERT: A  284 THR cc_start: 0.2042 (OUTLIER) cc_final: 0.1797 (m)
REVERT: A  333 GLN cc_start: 0.6604 (OUTLIER) cc_final: 0.6267 (mm110)
REVERT: B    7 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6619 (pp)
REVERT: B   96 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7028 (mmp-170)
REVERT: E  174 GLN cc_start: 0.6870 (mt0) cc_final: 0.5908 (pt0)
  outliers start: 30
  outliers final: 21
  residues processed: 148
  average time/residue: 0.2972
  time to fit residues: 48.2394
Evaluate side-chains
  149 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  218 MET
Chi-restraints excluded: chain R residue  296 MET
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain L residue   20 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0970
   chunk 0 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0040
   chunk 113 optimal weight:    0.0980
   chunk 4 optimal weight:    8.9990
   chunk 41 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   chunk 60 optimal weight:    0.0970
   chunk 105 optimal weight:    0.9990
   overall best weight:    0.2588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 333 GLN
B 293 ASN
L  16 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.248216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.209835 restraints weight = 12048.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.4601 rms_B_bonded: 3.01
r_work: 0.4260 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.4260
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3988
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3988 r_free = 0.3988    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3988 r_free = 0.3988    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3988
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6500
moved from start:          0.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9374  Z= 0.116
  Angle     :  0.681  23.890  12708  Z= 0.347
  Chirality :  0.045   0.398   1450
  Planarity :  0.004   0.075   1600
  Dihedral  :  4.867  30.912   1266
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.88 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 19.56 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.25), residues: 1160
  helix:  1.53 (0.26), residues: 395
  sheet: -0.03 (0.31), residues: 279
  loop : -1.11 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A  32 
 TYR   0.016   0.001   TYR E 178 
 PHE   0.029   0.002   PHE R 363 
 TRP   0.017   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.12 ( 9367)
  covalent geometry    : angle       0.66441 /  0.34 (12694)
  SS BOND              : bond        0.00761 /  0.40 (    7)
  SS BOND              : angle       4.59819 /  2.57 (   14)
  hydrogen bonds       : bond        0.03304 /  2.21 (  445)
  hydrogen bonds       : angle       4.78734 /  3.33 ( 1268)

===============================================================================
Job complete
usr+sys time: 3282.15 seconds
wall clock time: 56 minutes 27.15 seconds (3387.15 seconds total)