Starting phenix.real_space_refine
on Tue May 13 20:12:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iy5_35814/05_2025/8iy5_35814.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iy5_35814/05_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_35814/05_2025/8iy5_35814.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iy5_35814/05_2025/8iy5_35814.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iy5_35814/05_2025/8iy5_35814.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iy5_35814/05_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-5687/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: 2.37
  Conformation dependent library (CDL) restraints added in 1.5 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: 1.15
  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: 2.64

  Time building geometry restraints manager: 2.73 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:             0.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.430
  Find NCS groups from input model:        0.120
  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:10.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.320
-------------------------------------------------------------------------------
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  : 0.973 
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: 0.9782
  time to fit residues: 172.8877
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  : 1.063 
-------------------------------------------------------------------------------
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 = 0.245182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.192301 restraints weight = 11903.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.4105 rms_B_bonded: 2.70
r_work: 0.3936 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3955 r_free = 0.3955    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3955 r_free = 0.3955    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3955
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6397
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  : 1.029 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6872 (tt0)
REVERT: A  314 LYS cc_start: 0.6493 (mptp) cc_final: 0.6133 (mptm)
REVERT: A  333 GLN cc_start: 0.6504 (OUTLIER) cc_final: 0.6254 (mp10)
REVERT: C   21 MET cc_start: 0.5285 (mmm) cc_final: 0.4897 (mmp)
REVERT: C   38 MET cc_start: 0.6346 (mmm) cc_final: 0.5566 (mmt)
REVERT: R  363 PHE cc_start: 0.7244 (t80) cc_final: 0.6943 (t80)
  outliers start: 24
  outliers final: 11
  residues processed: 144
  average time/residue: 0.9920
  time to fit residues: 155.0857
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  : 1.054 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 33 optimal weight:    0.5980
   chunk 85 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   chunk 21 optimal weight:   20.0000
   chunk 28 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 72 optimal weight:    7.9990
   chunk 64 optimal weight:    4.9990
   chunk 61 optimal weight:   20.0000
   chunk 49 optimal weight:    0.8980
   overall best weight:    3.8986

-------------------------------------------------------------------------------
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 220 GLN
B 295 ASN
B 340 ASN
E 220 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.241882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.191005 restraints weight = 16015.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.4075 rms_B_bonded: 3.13
r_work: 0.3884 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3874
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3874 r_free = 0.3874    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3874 r_free = 0.3874    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3874
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6544
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   9374  Z= 0.224
  Angle     :  0.724   9.120  12708  Z= 0.385
  Chirality :  0.048   0.219   1450
  Planarity :  0.005   0.051   1600
  Dihedral  :  5.630  28.542   1266
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.35 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 14.00 %
    Favored  : 82.82 %
  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: -0.61 (0.25), residues: 1160
  helix:  0.92 (0.26), residues: 399
  sheet: -0.56 (0.30), residues: 282
  loop : -1.39 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 332 
 HIS   0.008   0.002   HIS A 213 
 PHE   0.031   0.003   PHE A 250 
 TYR   0.021   0.002   TYR E 178 
 ARG   0.012   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04443 (  445)
  hydrogen bonds       : angle       5.21478 ( 1268)
  SS BOND              : bond        0.00676 (    7)
  SS BOND              : angle       1.85737 (   14)
  covalent geometry    : bond        0.00510 ( 9367)
  covalent geometry    : angle       0.72219 (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
  164 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 132
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6868 (tt0)
REVERT: A  302 TYR cc_start: 0.5385 (t80) cc_final: 0.5153 (t80)
REVERT: A  333 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6564 (mp10)
REVERT: B  211 TRP cc_start: 0.5363 (OUTLIER) cc_final: 0.3569 (m-10)
REVERT: B  237 ASN cc_start: 0.8037 (p0) cc_final: 0.7800 (p0)
REVERT: C   21 MET cc_start: 0.5489 (mmm) cc_final: 0.5134 (mmp)
REVERT: E  174 GLN cc_start: 0.6784 (mt0) cc_final: 0.5904 (pt0)
REVERT: E  208 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6650 (pp20)
REVERT: R  192 LEU cc_start: 0.7296 (mt) cc_final: 0.7064 (mm)
  outliers start: 32
  outliers final: 17
  residues processed: 150
  average time/residue: 1.0264
  time to fit residues: 166.4896
Evaluate side-chains
  138 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
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   71 VAL
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  172 GLU
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 B residue  336 LEU
Chi-restraints excluded: chain E residue   86 LEU
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 87 optimal weight:    5.9990
   chunk 114 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 105 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 101 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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
B 220 GLN
B 293 ASN
R 104 ASN
R 373 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.242796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.187377 restraints weight = 11562.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.4087 rms_B_bonded: 2.51
r_work: 0.3904 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3887
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3887 r_free = 0.3887    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3887 r_free = 0.3887    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3887
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6441
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9374  Z= 0.153
  Angle     :  0.693  23.759  12708  Z= 0.360
  Chirality :  0.045   0.347   1450
  Planarity :  0.004   0.045   1600
  Dihedral  :  5.310  28.204   1266
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.14 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 15.19 %
    Favored  : 81.23 %
  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: -0.39 (0.25), residues: 1160
  helix:  1.13 (0.26), residues: 398
  sheet: -0.47 (0.31), residues: 271
  loop : -1.25 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 332 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.027   0.002   PHE R 363 
 TYR   0.017   0.001   TYR E 178 
 ARG   0.005   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03774 (  445)
  hydrogen bonds       : angle       5.02251 ( 1268)
  SS BOND              : bond        0.00952 (    7)
  SS BOND              : angle       4.44130 (   14)
  covalent geometry    : bond        0.00344 ( 9367)
  covalent geometry    : angle       0.67746 (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
  172 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 136
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6922 (tt0)
REVERT: A  211 TRP cc_start: 0.6367 (p-90) cc_final: 0.5978 (p-90)
REVERT: A  302 TYR cc_start: 0.5206 (t80) cc_final: 0.4932 (t80)
REVERT: B  211 TRP cc_start: 0.5469 (OUTLIER) cc_final: 0.3494 (m-10)
REVERT: B  237 ASN cc_start: 0.8031 (p0) cc_final: 0.7766 (p0)
REVERT: C   21 MET cc_start: 0.5611 (mmm) cc_final: 0.5127 (mmp)
REVERT: E  120 SER cc_start: 0.6834 (t) cc_final: 0.6356 (m)
REVERT: E  174 GLN cc_start: 0.6796 (mt0) cc_final: 0.5817 (pt0)
REVERT: E  208 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6658 (pp20)
  outliers start: 36
  outliers final: 23
  residues processed: 157
  average time/residue: 0.9385
  time to fit residues: 160.0137
Evaluate side-chains
  149 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
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  128 THR
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  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 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
Chi-restraints excluded: chain R residue  373 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 2 optimal weight:    8.9990
   chunk 84 optimal weight:    1.9990
   chunk 65 optimal weight:    8.9990
   chunk 74 optimal weight:   10.0000
   chunk 86 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 102 optimal weight:    5.9990
   chunk 10 optimal weight:    0.5980
   chunk 89 optimal weight:    9.9990
   chunk 99 optimal weight:   20.0000
   overall best weight:    2.3188

-------------------------------------------------------------------------------
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 331 ASN
A 333 GLN
B  44 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4868 r_free = 0.4868 target = 0.267557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.215581 restraints weight = 13099.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.4075 rms_B_bonded: 2.83
r_work: 0.3901 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3891
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3891 r_free = 0.3891    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3891 r_free = 0.3891    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3891
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6480
moved from start:          0.2433

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= 0.162
  Angle     :  0.700  23.100  12708  Z= 0.363
  Chirality :  0.046   0.350   1450
  Planarity :  0.004   0.043   1600
  Dihedral  :  5.296  29.273   1266
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.57 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 15.89 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.15 (0.26), residues: 397
  sheet: -0.42 (0.31), residues: 271
  loop : -1.21 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 276 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.027   0.002   PHE R 363 
 TYR   0.016   0.002   TYR E 178 
 ARG   0.007   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03776 (  445)
  hydrogen bonds       : angle       5.00384 ( 1268)
  SS BOND              : bond        0.00858 (    7)
  SS BOND              : angle       4.30983 (   14)
  covalent geometry    : bond        0.00369 ( 9367)
  covalent geometry    : angle       0.68561 (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
  182 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 133
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6877 (tt0)
REVERT: A  333 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6434 (mm110)
REVERT: B    7 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6571 (pp)
REVERT: B   96 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6906 (mmp-170)
REVERT: B  211 TRP cc_start: 0.5299 (OUTLIER) cc_final: 0.3468 (m-10)
REVERT: B  237 ASN cc_start: 0.8018 (p0) cc_final: 0.7765 (p0)
REVERT: B  336 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7745 (mt)
REVERT: C   21 MET cc_start: 0.5354 (mmm) cc_final: 0.4956 (mmp)
REVERT: E  120 SER cc_start: 0.7029 (t) cc_final: 0.6516 (m)
REVERT: E  174 GLN cc_start: 0.6802 (mt0) cc_final: 0.5865 (pt0)
REVERT: E  208 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6582 (pp20)
REVERT: R  192 LEU cc_start: 0.7239 (mt) cc_final: 0.7018 (mm)
  outliers start: 49
  outliers final: 28
  residues processed: 164
  average time/residue: 0.9350
  time to fit residues: 167.2218
Evaluate side-chains
  161 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 128
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
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  284 THR
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   47 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  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  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   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  198 ASP
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:    0.9990
   chunk 93 optimal weight:    4.9990
   chunk 96 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9990
   chunk 85 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0870
   chunk 50 optimal weight:    1.9990
   chunk 101 optimal weight:    9.9990
   overall best weight:    1.0164

-------------------------------------------------------------------------------
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 333 GLN
B 295 ASN
R 314 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.244634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.191954 restraints weight = 12015.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.4131 rms_B_bonded: 3.17
r_work: 0.3944 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3925
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3925 r_free = 0.3925    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3925 r_free = 0.3925    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3925
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6367
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9374  Z= 0.125
  Angle     :  0.665  22.332  12708  Z= 0.344
  Chirality :  0.044   0.343   1450
  Planarity :  0.004   0.046   1600
  Dihedral  :  5.031  31.447   1266
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.97 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 18.17 %
    Favored  : 78.95 %
  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: -0.09 (0.25), residues: 1160
  helix:  1.37 (0.26), residues: 395
  sheet: -0.16 (0.31), residues: 263
  loop : -1.16 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 339 
 HIS   0.003   0.001   HIS R 150 
 PHE   0.025   0.002   PHE A 250 
 TYR   0.017   0.001   TYR E 178 
 ARG   0.007   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03462 (  445)
  hydrogen bonds       : angle       4.87068 ( 1268)
  SS BOND              : bond        0.00780 (    7)
  SS BOND              : angle       4.33482 (   14)
  covalent geometry    : bond        0.00274 ( 9367)
  covalent geometry    : angle       0.65012 (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
  165 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 136
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7377 (tm-30) cc_final: 0.6879 (tt0)
REVERT: A  263 SER cc_start: 0.8146 (p) cc_final: 0.7862 (m)
REVERT: A  333 GLN cc_start: 0.6299 (OUTLIER) cc_final: 0.6000 (mm110)
REVERT: B    7 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6549 (pp)
REVERT: B  237 ASN cc_start: 0.7959 (p0) cc_final: 0.7693 (p0)
REVERT: B  336 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7460 (mm)
REVERT: C   21 MET cc_start: 0.5450 (mmm) cc_final: 0.5046 (mmp)
REVERT: E  174 GLN cc_start: 0.6746 (mt0) cc_final: 0.5753 (pt0)
REVERT: E  208 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6850 (tm-30)
REVERT: R  192 LEU cc_start: 0.7231 (mt) cc_final: 0.7026 (mm)
REVERT: L   20 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7602 (pp)
  outliers start: 29
  outliers final: 13
  residues processed: 154
  average time/residue: 0.9316
  time to fit residues: 156.2317
Evaluate side-chains
  142 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  135 VAL
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  263 THR
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 R residue  173 MET
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain L residue   20 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    6.9990
   chunk 82 optimal weight:    0.7980
   chunk 79 optimal weight:   20.0000
   chunk 8 optimal weight:    0.3980
   chunk 111 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 4 optimal weight:    0.0970
   chunk 22 optimal weight:    6.9990
   chunk 49 optimal weight:    6.9990
   chunk 75 optimal weight:    6.9990
   chunk 92 optimal weight:    0.9990
   overall best weight:    1.8582

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.243680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.191006 restraints weight = 11725.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.4127 rms_B_bonded: 2.51
r_work: 0.3940 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3907
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3907 r_free = 0.3907    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3907 r_free = 0.3907    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3907
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6398
moved from start:          0.2644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9374  Z= 0.147
  Angle     :  0.697  23.037  12708  Z= 0.358
  Chirality :  0.045   0.360   1450
  Planarity :  0.004   0.045   1600
  Dihedral  :  5.094  32.073   1266
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.66 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 18.07 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.14 (0.25), residues: 1160
  helix:  1.32 (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   0.010   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.037   0.002   PHE A 307 
 TYR   0.016   0.001   TYR E 223 
 ARG   0.007   0.000   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03540 (  445)
  hydrogen bonds       : angle       4.89069 ( 1268)
  SS BOND              : bond        0.00742 (    7)
  SS BOND              : angle       4.40520 (   14)
  covalent geometry    : bond        0.00333 ( 9367)
  covalent geometry    : angle       0.68170 (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
  167 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 129
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6877 (tt0)
REVERT: A   46 LYS cc_start: 0.6198 (OUTLIER) cc_final: 0.5929 (mptt)
REVERT: A  263 SER cc_start: 0.8234 (p) cc_final: 0.7968 (m)
REVERT: B    7 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6466 (pp)
REVERT: B   96 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6899 (mmp-170)
REVERT: B  237 ASN cc_start: 0.7760 (p0) cc_final: 0.7505 (p0)
REVERT: B  336 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7802 (mt)
REVERT: C   21 MET cc_start: 0.5418 (mmm) cc_final: 0.5061 (mmp)
REVERT: E  174 GLN cc_start: 0.6763 (mt0) cc_final: 0.5780 (pt0)
REVERT: R  192 LEU cc_start: 0.7254 (mt) cc_final: 0.7042 (mm)
REVERT: L   20 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7597 (pp)
  outliers start: 38
  outliers final: 22
  residues processed: 152
  average time/residue: 0.9096
  time to fit residues: 150.5073
Evaluate side-chains
  152 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 125
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  284 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   71 VAL
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  154 ASP
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  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   86 LEU
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain R residue  173 MET
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain L residue   20 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 1 optimal weight:    0.1980
   chunk 76 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 100 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 68 optimal weight:    6.9990
   chunk 114 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    2.0386

-------------------------------------------------------------------------------
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**
L  16 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4873 r_free = 0.4873 target = 0.267304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.216549 restraints weight = 12728.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.4098 rms_B_bonded: 2.58
r_work: 0.3940 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3928
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3928 r_free = 0.3928    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3928 r_free = 0.3928    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3928
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6464
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   9374  Z= 0.153
  Angle     :  0.712  22.837  12708  Z= 0.365
  Chirality :  0.046   0.383   1450
  Planarity :  0.004   0.045   1600
  Dihedral  :  5.131  32.270   1266
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.31 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 18.57 %
    Favored  : 77.66 %
  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: -0.10 (0.25), residues: 1160
  helix:  1.32 (0.26), residues: 397
  sheet: -0.18 (0.32), residues: 258
  loop : -1.10 (0.28), residues: 505

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   0.038   0.002   PHE A 307 
 TYR   0.015   0.001   TYR E 178 
 ARG   0.012   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03604 (  445)
  hydrogen bonds       : angle       4.89272 ( 1268)
  SS BOND              : bond        0.00984 (    7)
  SS BOND              : angle       4.46306 (   14)
  covalent geometry    : bond        0.00347 ( 9367)
  covalent geometry    : angle       0.69674 (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
  167 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 129
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6864 (tt0)
REVERT: A  260 THR cc_start: 0.6137 (OUTLIER) cc_final: 0.5932 (m)
REVERT: A  284 THR cc_start: 0.2263 (OUTLIER) cc_final: 0.2060 (m)
REVERT: B    7 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6434 (pp)
REVERT: B   96 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6875 (mmp-170)
REVERT: B  221 THR cc_start: 0.7387 (m) cc_final: 0.7117 (t)
REVERT: B  237 ASN cc_start: 0.7765 (p0) cc_final: 0.7550 (p0)
REVERT: B  336 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7787 (mt)
REVERT: C   21 MET cc_start: 0.5421 (mmm) cc_final: 0.5091 (mmt)
REVERT: E  174 GLN cc_start: 0.6789 (mt0) cc_final: 0.5815 (pt0)
REVERT: R  192 LEU cc_start: 0.7392 (mt) cc_final: 0.7186 (mm)
REVERT: L   20 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7617 (pp)
  outliers start: 38
  outliers final: 22
  residues processed: 156
  average time/residue: 0.8875
  time to fit residues: 151.1797
Evaluate side-chains
  152 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  284 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   71 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  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   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  311 LEU
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain L residue   20 ILE
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:   30.0000
   chunk 38 optimal weight:    9.9990
   chunk 64 optimal weight:    0.7980
   chunk 96 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 101 optimal weight:    6.9990
   chunk 113 optimal weight:   30.0000
   overall best weight:    5.1588

-------------------------------------------------------------------------------
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**
E 157 ASN
L  16 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4823 r_free = 0.4823 target = 0.261950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.210059 restraints weight = 15248.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.4006 rms_B_bonded: 3.04
r_work: 0.3819 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3813
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3813 r_free = 0.3813    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3813 r_free = 0.3813    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3813
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6617
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.099   9374  Z= 0.275
  Angle     :  0.870  24.362  12708  Z= 0.450
  Chirality :  0.051   0.401   1450
  Planarity :  0.005   0.057   1600
  Dihedral  :  5.924  34.213   1266
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.95 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 17.87 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.62 (0.24), residues: 1160
  helix:  0.74 (0.26), residues: 396
  sheet: -0.56 (0.31), residues: 269
  loop : -1.21 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP B 297 
 HIS   0.009   0.002   HIS A 213 
 PHE   0.055   0.003   PHE A 307 
 TYR   0.026   0.003   TYR E 163 
 ARG   0.015   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04713 (  445)
  hydrogen bonds       : angle       5.33149 ( 1268)
  SS BOND              : bond        0.01198 (    7)
  SS BOND              : angle       4.53053 (   14)
  covalent geometry    : bond        0.00636 ( 9367)
  covalent geometry    : angle       0.85768 (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
  165 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 120
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6912 (tt0)
REVERT: A  245 GLU cc_start: 0.4101 (OUTLIER) cc_final: 0.3517 (pm20)
REVERT: A  284 THR cc_start: 0.2468 (OUTLIER) cc_final: 0.2243 (m)
REVERT: B    7 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6769 (pp)
REVERT: B   96 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6933 (mmp-170)
REVERT: B  211 TRP cc_start: 0.5406 (OUTLIER) cc_final: 0.4174 (m-90)
REVERT: B  237 ASN cc_start: 0.7825 (p0) cc_final: 0.7555 (p0)
REVERT: B  301 LYS cc_start: 0.7288 (mtpp) cc_final: 0.7076 (mtpt)
REVERT: B  336 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7805 (mt)
REVERT: C   21 MET cc_start: 0.5663 (mmm) cc_final: 0.5126 (ptm)
REVERT: E  174 GLN cc_start: 0.6880 (mt0) cc_final: 0.5820 (pt0)
REVERT: E  203 THR cc_start: 0.6068 (OUTLIER) cc_final: 0.5706 (p)
REVERT: R  192 LEU cc_start: 0.7474 (mt) cc_final: 0.7226 (mm)
  outliers start: 45
  outliers final: 25
  residues processed: 152
  average time/residue: 0.9032
  time to fit residues: 149.6978
Evaluate side-chains
  147 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  245 GLU
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 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   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  164 THR
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  205 ASP
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  263 THR
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   30 SER
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  203 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 54 optimal weight:   20.0000
   chunk 33 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0060
   chunk 76 optimal weight:    8.9990
   chunk 104 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   chunk 91 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   overall best weight:    1.2600

-------------------------------------------------------------------------------
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**
B 293 ASN
R 373 ASN
L  16 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4867 r_free = 0.4867 target = 0.266589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.214753 restraints weight = 12630.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.4096 rms_B_bonded: 2.70
r_work: 0.3921 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3945
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3945 r_free = 0.3945    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3945 r_free = 0.3945    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3945
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6459
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9374  Z= 0.139
  Angle     :  0.730  24.001  12708  Z= 0.372
  Chirality :  0.046   0.386   1450
  Planarity :  0.005   0.072   1600
  Dihedral  :  5.312  33.573   1266
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.06 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.86 %
    Favored  : 77.26 %
  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: -0.21 (0.25), residues: 1160
  helix:  1.13 (0.26), residues: 396
  sheet: -0.28 (0.31), residues: 272
  loop : -1.07 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 332 
 HIS   0.003   0.001   HIS R 150 
 PHE   0.048   0.002   PHE A 307 
 TYR   0.016   0.001   TYR E 223 
 ARG   0.013   0.001   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03674 (  445)
  hydrogen bonds       : angle       5.00710 ( 1268)
  SS BOND              : bond        0.00824 (    7)
  SS BOND              : angle       4.59860 (   14)
  covalent geometry    : bond        0.00313 ( 9367)
  covalent geometry    : angle       0.71450 (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
  154 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6903 (tt0)
REVERT: A  248 LYS cc_start: 0.4576 (mmmm) cc_final: 0.3993 (mmmt)
REVERT: A  284 THR cc_start: 0.2260 (OUTLIER) cc_final: 0.2022 (m)
REVERT: B    7 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6647 (pp)
REVERT: B   96 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6855 (mmp-170)
REVERT: B  237 ASN cc_start: 0.7714 (p0) cc_final: 0.7484 (p0)
REVERT: B  336 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7556 (mm)
REVERT: C   21 MET cc_start: 0.5619 (mmm) cc_final: 0.5131 (mmp)
REVERT: E  174 GLN cc_start: 0.6912 (mt0) cc_final: 0.5826 (pt0)
REVERT: E  203 THR cc_start: 0.5995 (OUTLIER) cc_final: 0.5629 (p)
REVERT: R  192 LEU cc_start: 0.7366 (mt) cc_final: 0.7158 (mm)
  outliers start: 29
  outliers final: 16
  residues processed: 144
  average time/residue: 0.9347
  time to fit residues: 146.5246
Evaluate side-chains
  146 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  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  336 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain R residue  173 MET
Chi-restraints excluded: chain R residue  311 LEU
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain R residue  373 ASN
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:    0.7980
   chunk 108 optimal weight:    0.0060
   chunk 89 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 102 optimal weight:    6.9990
   chunk 70 optimal weight:    7.9990
   chunk 103 optimal weight:    0.0060
   chunk 77 optimal weight:    0.4980
   chunk 10 optimal weight:    8.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    0.8614

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

Flipped N/Q/H residues before XYZ refinement:
** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 373 ASN
L  16 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4598 r_free = 0.4598 target = 0.241795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.188880 restraints weight = 11672.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.4089 rms_B_bonded: 2.57
r_work: 0.3939 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3937
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3937 r_free = 0.3937    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3937 r_free = 0.3937    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3937
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6432
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.193   9374  Z= 0.249
  Angle     :  1.012  59.169  12708  Z= 0.585
  Chirality :  0.048   0.620   1450
  Planarity :  0.005   0.070   1600
  Dihedral  :  5.432  42.733   1266
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.23 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 20.46 %
    Favored  : 77.06 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.21 (0.25), residues: 1160
  helix:  1.13 (0.26), residues: 396
  sheet: -0.28 (0.31), residues: 272
  loop : -1.05 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 332 
 HIS   0.003   0.001   HIS R 150 
 PHE   0.043   0.002   PHE A 307 
 TYR   0.014   0.001   TYR E 178 
 ARG   0.037   0.001   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03939 (  445)
  hydrogen bonds       : angle       5.05238 ( 1268)
  SS BOND              : bond        0.00764 (    7)
  SS BOND              : angle       4.52414 (   14)
  covalent geometry    : bond        0.00474 ( 9367)
  covalent geometry    : angle       1.00126 (12694)

===============================================================================
Job complete
usr+sys time: 8424.69 seconds
wall clock time: 145 minutes 19.04 seconds (8719.04 seconds total)