Starting phenix.real_space_refine
on Tue Jul 29 03:05:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iy5_35814/07_2025/8iy5_35814.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iy5_35814/07_2025/8iy5_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iy5_35814/07_2025/8iy5_35814.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iy5_35814/07_2025/8iy5_35814.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iy5_35814/07_2025/8iy5_35814.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iy5_35814/07_2025/8iy5_35814.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.00, per 1000 atoms: 0.65
  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: 2.18
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 0.93
  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: 2.59

  Time building geometry restraints manager: 2.60 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:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.620
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5518
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 : 11.68
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (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
 TRP   0.027   0.001   TRP B 332 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.030   0.002   PHE A 250 
 TYR   0.022   0.001   TYR E 178 
 ARG   0.009   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12519 (  445)
  hydrogen bonds       : angle       5.83658 ( 1268)
  SS BOND              : bond        0.00807 (    7)
  SS BOND              : angle       2.85949 (   14)
  covalent geometry    : bond        0.00290 ( 9367)
  covalent geometry    : angle       0.68362 (12694)

*********************** 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  : 1.038 
Fit side-chains
REVERT: B   76 ASP cc_start: 0.6166 (p0) cc_final: 0.5740 (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: 1.0373
  time to fit residues: 183.2177
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  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:   10.0000
   chunk 87 optimal weight:    7.9990
   chunk 48 optimal weight:    9.9990
   chunk 29 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0050
   chunk 46 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 54 optimal weight:   20.0000
   chunk 67 optimal weight:   10.0000
   chunk 104 optimal weight:    0.0020
   overall best weight:    3.0008

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 256 ASN
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B  88 ASN
** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.245202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.191063 restraints weight = 11903.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.4103 rms_B_bonded: 2.79
r_work: 0.3913 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3904
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3904 r_free = 0.3904    target_work(ls_wunit_k1) = 0.168         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3903 r_free = 0.3903    target_work(ls_wunit_k1) = 0.168         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3903
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6407
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   9374  Z= 0.194
  Angle     :  0.698   9.521  12708  Z= 0.368
  Chirality :  0.047   0.218   1450
  Planarity :  0.005   0.051   1600
  Dihedral  :  5.312  28.732   1266
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.83 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 10.82 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.25), residues: 1160
  helix:  1.29 (0.26), residues: 390
  sheet: -0.69 (0.30), residues: 285
  loop : -1.18 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 332 
 HIS   0.009   0.002   HIS B  62 
 PHE   0.028   0.003   PHE R 112 
 TYR   0.017   0.002   TYR E 178 
 ARG   0.007   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04235 (  445)
  hydrogen bonds       : angle       5.07954 ( 1268)
  SS BOND              : bond        0.00818 (    7)
  SS BOND              : angle       2.08671 (   14)
  covalent geometry    : bond        0.00442 ( 9367)
  covalent geometry    : angle       0.69461 (12694)

*********************** 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
  159 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6896 (tt0)
REVERT: A  314 LYS cc_start: 0.6493 (mptp) cc_final: 0.6118 (mptm)
REVERT: A  333 GLN cc_start: 0.6462 (OUTLIER) cc_final: 0.6208 (mp10)
REVERT: C   21 MET cc_start: 0.5345 (mmm) cc_final: 0.4934 (mmp)
REVERT: C   38 MET cc_start: 0.6338 (mmm) cc_final: 0.5534 (mmt)
REVERT: R  363 PHE cc_start: 0.7233 (t80) cc_final: 0.6936 (t80)
  outliers start: 24
  outliers final: 11
  residues processed: 144
  average time/residue: 0.9635
  time to fit residues: 150.4536
Evaluate side-chains
  133 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  128 THR
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  221 LEU
Chi-restraints excluded: chain R residue  296 MET
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 33 optimal weight:    0.5980
   chunk 85 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 21 optimal weight:   20.0000
   chunk 28 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 61 optimal weight:   20.0000
   chunk 49 optimal weight:    0.7980
   overall best weight:    2.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B 295 ASN
B 340 ASN
E 220 HIS
R 104 ASN
R 314 HIS
R 373 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.243989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.187766 restraints weight = 16068.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 3.19
r_work: 0.3912 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3877
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3877 r_free = 0.3877    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3877 r_free = 0.3877    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3877
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6473
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9374  Z= 0.182
  Angle     :  0.670   8.884  12708  Z= 0.355
  Chirality :  0.046   0.206   1450
  Planarity :  0.005   0.048   1600
  Dihedral  :  5.365  27.325   1266
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.66 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 14.10 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.25), residues: 1160
  helix:  1.13 (0.26), residues: 396
  sheet: -0.55 (0.30), residues: 284
  loop : -1.33 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 332 
 HIS   0.006   0.001   HIS A 213 
 PHE   0.024   0.003   PHE R 112 
 TYR   0.020   0.002   TYR E 178 
 ARG   0.011   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04071 (  445)
  hydrogen bonds       : angle       5.05549 ( 1268)
  SS BOND              : bond        0.00693 (    7)
  SS BOND              : angle       1.81749 (   14)
  covalent geometry    : bond        0.00412 ( 9367)
  covalent geometry    : angle       0.66773 (12694)

*********************** 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: 28
    poor density    : 133
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6861 (tt0)
REVERT: A  302 TYR cc_start: 0.5426 (t80) cc_final: 0.5217 (t80)
REVERT: A  333 GLN cc_start: 0.6638 (OUTLIER) cc_final: 0.6259 (mp10)
REVERT: B  237 ASN cc_start: 0.8057 (p0) cc_final: 0.7804 (p0)
REVERT: C   21 MET cc_start: 0.5457 (mmm) cc_final: 0.5058 (mmp)
REVERT: E  208 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6431 (pp20)
REVERT: R  256 LEU cc_start: 0.6449 (pt) cc_final: 0.6192 (pt)
REVERT: R  363 PHE cc_start: 0.7250 (t80) cc_final: 0.6982 (t80)
REVERT: R  392 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6928 (mtm180)
  outliers start: 28
  outliers final: 17
  residues processed: 148
  average time/residue: 1.0180
  time to fit residues: 163.3543
Evaluate side-chains
  144 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
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  128 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  263 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain R residue  296 MET
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain R residue  373 ASN
Chi-restraints excluded: chain R residue  392 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 87 optimal weight:    6.9990
   chunk 114 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 57 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   chunk 105 optimal weight:   10.0000
   chunk 75 optimal weight:    4.9990
   chunk 68 optimal weight:    7.9990
   chunk 101 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B  44 GLN
B 220 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4887 r_free = 0.4887 target = 0.269978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.232272 restraints weight = 11041.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.4271 rms_B_bonded: 2.63
r_work: 0.3908 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3924
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3924 r_free = 0.3924    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3924 r_free = 0.3924    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3924
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6499
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9374  Z= 0.151
  Angle     :  0.687  23.668  12708  Z= 0.355
  Chirality :  0.045   0.330   1450
  Planarity :  0.004   0.043   1600
  Dihedral  :  5.225  27.949   1266
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.49 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 15.00 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.25), residues: 1160
  helix:  1.20 (0.26), residues: 398
  sheet: -0.41 (0.31), residues: 271
  loop : -1.24 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.023   0.002   PHE R 112 
 TYR   0.019   0.001   TYR E 178 
 ARG   0.006   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03743 (  445)
  hydrogen bonds       : angle       4.95686 ( 1268)
  SS BOND              : bond        0.00891 (    7)
  SS BOND              : angle       4.47778 (   14)
  covalent geometry    : bond        0.00337 ( 9367)
  covalent geometry    : angle       0.67113 (12694)

*********************** 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
  174 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 135
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7446 (tm-30) cc_final: 0.6991 (tt0)
REVERT: A  333 GLN cc_start: 0.6805 (OUTLIER) cc_final: 0.6524 (mm110)
REVERT: B  211 TRP cc_start: 0.5446 (OUTLIER) cc_final: 0.3514 (m-10)
REVERT: B  237 ASN cc_start: 0.8065 (p0) cc_final: 0.7827 (p0)
REVERT: C   21 MET cc_start: 0.5576 (mmm) cc_final: 0.5059 (mmp)
REVERT: E  120 SER cc_start: 0.6979 (t) cc_final: 0.6484 (m)
REVERT: E  174 GLN cc_start: 0.6821 (mt0) cc_final: 0.5987 (pt0)
REVERT: E  208 GLU cc_start: 0.7260 (tm-30) cc_final: 0.6725 (pp20)
REVERT: R  363 PHE cc_start: 0.7303 (t80) cc_final: 0.7041 (t80)
  outliers start: 39
  outliers final: 18
  residues processed: 158
  average time/residue: 1.0444
  time to fit residues: 178.1121
Evaluate side-chains
  147 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
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  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  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   30 SER
Chi-restraints excluded: chain E residue   86 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 2 optimal weight:    8.9990
   chunk 84 optimal weight:   10.0000
   chunk 65 optimal weight:    0.5980
   chunk 74 optimal weight:    0.5980
   chunk 86 optimal weight:   30.0000
   chunk 12 optimal weight:    4.9990
   chunk 102 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 89 optimal weight:   20.0000
   chunk 99 optimal weight:    2.9990
   overall best weight:    2.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B  44 GLN
B  91 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.243176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.190882 restraints weight = 13731.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.4091 rms_B_bonded: 2.81
r_work: 0.3937 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3942 r_free = 0.3942    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3942 r_free = 0.3942    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6446
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9374  Z= 0.150
  Angle     :  0.681  22.156  12708  Z= 0.353
  Chirality :  0.045   0.352   1450
  Planarity :  0.004   0.042   1600
  Dihedral  :  5.189  28.938   1266
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.40 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 15.49 %
    Favored  : 80.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.25), residues: 1160
  helix:  1.25 (0.26), residues: 398
  sheet: -0.37 (0.31), residues: 271
  loop : -1.21 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 332 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.021   0.002   PHE R 112 
 TYR   0.017   0.002   TYR E 178 
 ARG   0.008   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03673 (  445)
  hydrogen bonds       : angle       4.92372 ( 1268)
  SS BOND              : bond        0.00840 (    7)
  SS BOND              : angle       4.36965 (   14)
  covalent geometry    : bond        0.00338 ( 9367)
  covalent geometry    : angle       0.66554 (12694)

*********************** 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
  180 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 139
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6887 (tt0)
REVERT: A  211 TRP cc_start: 0.6434 (p-90) cc_final: 0.6068 (p-90)
REVERT: A  333 GLN cc_start: 0.6654 (OUTLIER) cc_final: 0.6188 (mp-120)
REVERT: B   46 ARG cc_start: 0.7606 (ttp-170) cc_final: 0.7346 (tpm170)
REVERT: B   68 ARG cc_start: 0.8054 (ttt90) cc_final: 0.7851 (ttt180)
REVERT: B  211 TRP cc_start: 0.5361 (OUTLIER) cc_final: 0.3442 (m-10)
REVERT: B  237 ASN cc_start: 0.8007 (p0) cc_final: 0.7749 (p0)
REVERT: B  262 MET cc_start: 0.6819 (ptm) cc_final: 0.6593 (ptm)
REVERT: C   21 MET cc_start: 0.5398 (mmm) cc_final: 0.4999 (mmp)
REVERT: E  120 SER cc_start: 0.6880 (t) cc_final: 0.6360 (m)
REVERT: E  174 GLN cc_start: 0.6817 (mt0) cc_final: 0.5880 (pt0)
REVERT: E  208 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6699 (tm-30)
REVERT: R  192 LEU cc_start: 0.7226 (mt) cc_final: 0.7015 (mm)
REVERT: R  363 PHE cc_start: 0.7440 (t80) cc_final: 0.7125 (t80)
  outliers start: 41
  outliers final: 24
  residues processed: 164
  average time/residue: 0.9658
  time to fit residues: 171.8830
Evaluate side-chains
  155 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
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  135 VAL
Chi-restraints excluded: chain B residue  147 SER
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  318 LEU
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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 96 optimal weight:    7.9990
   chunk 5 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   chunk 88 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 76 optimal weight:    0.3980
   chunk 50 optimal weight:    1.9990
   chunk 101 optimal weight:    3.9990
   overall best weight:    2.6788

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 ASN
A 333 GLN
B  44 GLN
B 220 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4608 r_free = 0.4608 target = 0.242729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.191276 restraints weight = 11906.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.4101 rms_B_bonded: 2.61
r_work: 0.3952 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3827 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3831 r_free = 0.3831    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3831 r_free = 0.3831    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3831
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6585
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9374  Z= 0.174
  Angle     :  0.717  23.123  12708  Z= 0.372
  Chirality :  0.046   0.375   1450
  Planarity :  0.004   0.043   1600
  Dihedral  :  5.269  30.981   1266
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.75 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 15.99 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.25), residues: 1160
  helix:  1.17 (0.26), residues: 398
  sheet: -0.29 (0.31), residues: 269
  loop : -1.23 (0.29), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP R 276 
 HIS   0.006   0.001   HIS A 213 
 PHE   0.022   0.002   PHE A 307 
 TYR   0.017   0.002   TYR E 178 
 ARG   0.010   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03827 (  445)
  hydrogen bonds       : angle       4.96998 ( 1268)
  SS BOND              : bond        0.00963 (    7)
  SS BOND              : angle       4.34046 (   14)
  covalent geometry    : bond        0.00394 ( 9367)
  covalent geometry    : angle       0.70256 (12694)

*********************** 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
  183 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 137
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7037 (tt0)
REVERT: A  263 SER cc_start: 0.8157 (p) cc_final: 0.7837 (m)
REVERT: A  333 GLN cc_start: 0.6576 (OUTLIER) cc_final: 0.6229 (mp10)
REVERT: B    7 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6565 (pp)
REVERT: B   96 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7143 (mmp-170)
REVERT: B  237 ASN cc_start: 0.8037 (p0) cc_final: 0.7773 (p0)
REVERT: C   21 MET cc_start: 0.5501 (mmm) cc_final: 0.5055 (mmp)
REVERT: E  120 SER cc_start: 0.6957 (t) cc_final: 0.6419 (m)
REVERT: E  174 GLN cc_start: 0.6923 (mt0) cc_final: 0.5969 (pt0)
REVERT: R  192 LEU cc_start: 0.7398 (mt) cc_final: 0.7188 (mm)
  outliers start: 46
  outliers final: 29
  residues processed: 165
  average time/residue: 0.9801
  time to fit residues: 176.3235
Evaluate side-chains
  162 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
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  314 LYS
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain B residue    7 LEU
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  147 SER
Chi-restraints excluded: chain B residue  154 ASP
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  318 LEU
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 R residue  173 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 97 optimal weight:    8.9990
   chunk 82 optimal weight:    3.9990
   chunk 79 optimal weight:   30.0000
   chunk 8 optimal weight:    5.9990
   chunk 111 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 4 optimal weight:    9.9990
   chunk 22 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 75 optimal weight:    9.9990
   chunk 92 optimal weight:    0.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B 295 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.238719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.186784 restraints weight = 11632.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.4040 rms_B_bonded: 2.65
r_work: 0.3892 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3770 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3772
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3772 r_free = 0.3772    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3772 r_free = 0.3772    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3772
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6671
moved from start:          0.2977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072   9374  Z= 0.252
  Angle     :  0.824  24.363  12708  Z= 0.429
  Chirality :  0.050   0.393   1450
  Planarity :  0.005   0.044   1600
  Dihedral  :  5.772  32.164   1266
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 13.32
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.78 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 16.09 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.24), residues: 1160
  helix:  0.80 (0.26), residues: 397
  sheet: -0.48 (0.31), residues: 268
  loop : -1.32 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP R 217 
 HIS   0.008   0.002   HIS A 213 
 PHE   0.041   0.003   PHE A 307 
 TYR   0.019   0.002   TYR E 163 
 ARG   0.009   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04502 (  445)
  hydrogen bonds       : angle       5.26852 ( 1268)
  SS BOND              : bond        0.01224 (    7)
  SS BOND              : angle       4.50337 (   14)
  covalent geometry    : bond        0.00577 ( 9367)
  covalent geometry    : angle       0.81119 (12694)

*********************** 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
  177 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 126
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7038 (tt0)
REVERT: A  263 SER cc_start: 0.8238 (p) cc_final: 0.7907 (m)
REVERT: A  333 GLN cc_start: 0.6678 (OUTLIER) cc_final: 0.6400 (mp10)
REVERT: B    7 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6711 (pp)
REVERT: B   96 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7100 (mmp-170)
REVERT: B  138 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.6130 (mt-10)
REVERT: B  211 TRP cc_start: 0.5658 (OUTLIER) cc_final: 0.4271 (m-90)
REVERT: B  237 ASN cc_start: 0.7928 (p0) cc_final: 0.7674 (p0)
REVERT: C   21 MET cc_start: 0.5710 (mmm) cc_final: 0.5295 (mmp)
REVERT: E  174 GLN cc_start: 0.6964 (mt0) cc_final: 0.5966 (pt0)
REVERT: R  192 LEU cc_start: 0.7534 (mt) cc_final: 0.7292 (mm)
REVERT: R  256 LEU cc_start: 0.6824 (pt) cc_final: 0.6566 (pt)
  outliers start: 51
  outliers final: 31
  residues processed: 161
  average time/residue: 0.9320
  time to fit residues: 163.6413
Evaluate side-chains
  159 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 123
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
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  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  138 GLU
Chi-restraints excluded: chain B residue  147 SER
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  318 LEU
Chi-restraints excluded: chain B residue  331 SER
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   96 CYS
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  151 LYS
Chi-restraints excluded: chain R residue  173 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 1 optimal weight:    1.9990
   chunk 76 optimal weight:    0.4980
   chunk 21 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 7 optimal weight:    0.0770
   chunk 100 optimal weight:    8.9990
   chunk 46 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 68 optimal weight:    6.9990
   chunk 114 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.3144

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.243220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.193146 restraints weight = 13259.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.4122 rms_B_bonded: 2.65
r_work: 0.3962 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3958
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3958 r_free = 0.3958    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3958 r_free = 0.3958    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3958
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6465
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9374  Z= 0.135
  Angle     :  0.696  23.034  12708  Z= 0.360
  Chirality :  0.045   0.372   1450
  Planarity :  0.004   0.046   1600
  Dihedral  :  5.192  31.037   1266
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.06 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 18.27 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.25), residues: 1160
  helix:  1.18 (0.26), residues: 397
  sheet: -0.25 (0.31), residues: 271
  loop : -1.19 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 339 
 HIS   0.003   0.001   HIS R 150 
 PHE   0.030   0.002   PHE R 363 
 TYR   0.015   0.001   TYR E 178 
 ARG   0.010   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03614 (  445)
  hydrogen bonds       : angle       4.99160 ( 1268)
  SS BOND              : bond        0.01039 (    7)
  SS BOND              : angle       4.53289 (   14)
  covalent geometry    : bond        0.00298 ( 9367)
  covalent geometry    : angle       0.68023 (12694)

*********************** 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
  163 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 130
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6896 (tt0)
REVERT: A  248 LYS cc_start: 0.5011 (mmmm) cc_final: 0.4390 (mmmt)
REVERT: A  333 GLN cc_start: 0.6501 (OUTLIER) cc_final: 0.6291 (mp10)
REVERT: B    7 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6686 (pp)
REVERT: B   96 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6878 (mmp-170)
REVERT: B  101 MET cc_start: 0.7693 (mpp) cc_final: 0.7396 (mpt)
REVERT: B  237 ASN cc_start: 0.7781 (p0) cc_final: 0.7535 (p0)
REVERT: C   21 MET cc_start: 0.5430 (mmm) cc_final: 0.5096 (mmp)
REVERT: E  174 GLN cc_start: 0.6873 (mt0) cc_final: 0.5845 (pt0)
REVERT: R  192 LEU cc_start: 0.7367 (mt) cc_final: 0.7155 (mm)
  outliers start: 33
  outliers final: 17
  residues processed: 151
  average time/residue: 1.0707
  time to fit residues: 175.4290
Evaluate side-chains
  146 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 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   74 SER
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  147 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  195 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  116 THR
Chi-restraints excluded: chain R residue  198 ASP
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 72 optimal weight:   40.0000
   chunk 79 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   chunk 64 optimal weight:    2.9990
   chunk 96 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   chunk 60 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0980
   chunk 101 optimal weight:    8.9990
   chunk 113 optimal weight:    0.6980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B 176 GLN
L  16 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.243052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.191010 restraints weight = 16213.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.4100 rms_B_bonded: 3.21
r_work: 0.3923 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3903
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3903 r_free = 0.3903    target_work(ls_wunit_k1) = 0.168         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3903 r_free = 0.3903    target_work(ls_wunit_k1) = 0.168         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3903
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6480
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9374  Z= 0.142
  Angle     :  0.708  23.379  12708  Z= 0.364
  Chirality :  0.045   0.380   1450
  Planarity :  0.005   0.067   1600
  Dihedral  :  5.158  31.553   1266
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.49 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 19.36 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.25), residues: 1160
  helix:  1.23 (0.26), residues: 397
  sheet: -0.24 (0.32), residues: 263
  loop : -1.14 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.048   0.002   PHE A 307 
 TYR   0.015   0.001   TYR E 223 
 ARG   0.014   0.001   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03566 (  445)
  hydrogen bonds       : angle       4.92789 ( 1268)
  SS BOND              : bond        0.00879 (    7)
  SS BOND              : angle       4.49130 (   14)
  covalent geometry    : bond        0.00321 ( 9367)
  covalent geometry    : angle       0.69281 (12694)

*********************** 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
  160 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 132
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6930 (tt0)
REVERT: A  248 LYS cc_start: 0.4702 (mmmm) cc_final: 0.4099 (mmmt)
REVERT: A  263 SER cc_start: 0.8166 (p) cc_final: 0.7914 (m)
REVERT: B    7 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6711 (pp)
REVERT: B   96 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6909 (mmp-170)
REVERT: B  237 ASN cc_start: 0.7814 (p0) cc_final: 0.7563 (p0)
REVERT: C   21 MET cc_start: 0.5581 (mmm) cc_final: 0.5161 (mmt)
REVERT: E  174 GLN cc_start: 0.6802 (mt0) cc_final: 0.5779 (pt0)
REVERT: E  220 HIS cc_start: 0.6662 (OUTLIER) cc_final: 0.5885 (t70)
REVERT: R  381 ILE cc_start: 0.6939 (tp) cc_final: 0.6632 (tp)
  outliers start: 28
  outliers final: 21
  residues processed: 151
  average time/residue: 0.9436
  time to fit residues: 154.9986
Evaluate side-chains
  151 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   65 THR
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  147 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
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  116 THR
Chi-restraints excluded: chain E residue  220 HIS
Chi-restraints excluded: chain R residue  198 ASP
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 54 optimal weight:   20.0000
   chunk 33 optimal weight:    5.9990
   chunk 58 optimal weight:    0.0060
   chunk 76 optimal weight:    1.9990
   chunk 104 optimal weight:    5.9990
   chunk 34 optimal weight:    7.9990
   chunk 91 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 49 optimal weight:    0.4980
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
L  16 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.246883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.197555 restraints weight = 13313.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.4158 rms_B_bonded: 2.73
r_work: 0.4006 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3981
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3981 r_free = 0.3981    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3981 r_free = 0.3981    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3981
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6375
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9374  Z= 0.120
  Angle     :  0.698  22.886  12708  Z= 0.355
  Chirality :  0.045   0.380   1450
  Planarity :  0.004   0.065   1600
  Dihedral  :  4.940  31.294   1266
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.06 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 20.06 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.25), residues: 1160
  helix:  1.48 (0.26), residues: 395
  sheet: -0.00 (0.32), residues: 266
  loop : -1.11 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 339 
 HIS   0.003   0.001   HIS A 322 
 PHE   0.033   0.002   PHE A 307 
 TYR   0.015   0.001   TYR E 223 
 ARG   0.014   0.001   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03358 (  445)
  hydrogen bonds       : angle       4.80058 ( 1268)
  SS BOND              : bond        0.00793 (    7)
  SS BOND              : angle       4.52179 (   14)
  covalent geometry    : bond        0.00265 ( 9367)
  covalent geometry    : angle       0.68197 (12694)

********************** 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
  157 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6923 (tt0)
REVERT: B    7 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6605 (pp)
REVERT: B   96 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6863 (mmp-170)
REVERT: C   21 MET cc_start: 0.5421 (mmm) cc_final: 0.4993 (mmp)
REVERT: E  174 GLN cc_start: 0.6692 (mt0) cc_final: 0.5743 (pt0)
REVERT: R  363 PHE cc_start: 0.6817 (t80) cc_final: 0.6557 (t80)
  outliers start: 21
  outliers final: 14
  residues processed: 150
  average time/residue: 0.8946
  time to fit residues: 147.1866
Evaluate side-chains
  146 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  103 CYS
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain R residue  198 ASP
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 96 optimal weight:   10.0000
   chunk 76 optimal weight:    9.9990
   chunk 108 optimal weight:    0.0980
   chunk 89 optimal weight:   10.0000
   chunk 88 optimal weight:    4.9990
   chunk 102 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0570
   chunk 77 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   overall best weight:    0.9700

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B 220 GLN
L  16 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.246329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.194243 restraints weight = 11729.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.4177 rms_B_bonded: 2.62
r_work: 0.4011 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.4011
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3967
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3967 r_free = 0.3967    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3967 r_free = 0.3967    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3967
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6380
moved from start:          0.3082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9374  Z= 0.126
  Angle     :  0.698  23.365  12708  Z= 0.355
  Chirality :  0.045   0.376   1450
  Planarity :  0.004   0.057   1600
  Dihedral  :  4.930  32.733   1266
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.14 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 20.56 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.25), residues: 1160
  helix:  1.50 (0.26), residues: 395
  sheet: -0.06 (0.31), residues: 280
  loop : -1.02 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 339 
 HIS   0.003   0.001   HIS A 322 
 PHE   0.032   0.002   PHE A 307 
 TYR   0.015   0.001   TYR E 223 
 ARG   0.013   0.001   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03352 (  445)
  hydrogen bonds       : angle       4.75482 ( 1268)
  SS BOND              : bond        0.00839 (    7)
  SS BOND              : angle       4.55866 (   14)
  covalent geometry    : bond        0.00279 ( 9367)
  covalent geometry    : angle       0.68144 (12694)

===============================================================================
Job complete
usr+sys time: 9311.21 seconds
wall clock time: 162 minutes 45.55 seconds (9765.55 seconds total)