Starting phenix.real_space_refine
on Mon May 12 05:35:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y01_38800/05_2025/8y01_38800_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y01_38800/05_2025/8y01_38800.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y01_38800/05_2025/8y01_38800.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y01_38800/05_2025/8y01_38800.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y01_38800/05_2025/8y01_38800_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y01_38800/05_2025/8y01_38800_neut.cif"
  }
  resolution = 2.48
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    5575      2.51       5
     N    1475      2.21       5
     O    1589      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 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: 8705
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1570
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1570
          Classifications: {'peptide': 205}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 2, 'TRANS': 202}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 92
          Unresolved non-hydrogen angles: 110
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 58
    Chain: "B"
      Number of atoms: 2599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2599
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "G"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 438
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "S"
      Number of atoms: 1751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1751
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 10, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 2327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2327
          Classifications: {'peptide': 298}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 18, 'TRANS': 279}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "R"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'RET': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   TRP R 177 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CH2 TRP R 177 " occ=0.50
    residue:
      pdb=" N   PHE R 329 " occ=0.50
      ... (9 atoms not shown)
      pdb=" CZ  PHE R 329 " occ=0.50
  Time building chain proxies: 5.27, per 1000 atoms: 0.61
  Number of scatterers: 8705
  At special positions: 0
  Unit cell: (89.64, 121.18, 126.99, 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      66     16.00
     O    1589      8.00
     N    1475      7.00
     C    5575      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 126 " - pdb=" SG  CYS R 203 " distance=1.59

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.38
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2116

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 15 sheets defined
      35.4% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.577A  pdb=" N   ASN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.860A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.785A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 275
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.646A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
    Processing helix  chain 'B' and resid 3 through 26
      removed outlier: 3.514A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.579A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.522A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'R' and resid 49 through 81
      removed outlier: 3.551A  pdb=" N   TYR R  53 " --> pdb=" O   PRO R  49 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 89 through 117
      removed outlier: 4.074A  pdb=" N   SER R 107 " --> pdb=" O   THR R 103 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE R 109 " --> pdb=" O   ILE R 105 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 122 through 157
    Processing helix  chain 'R' and resid 165 through 185
    Processing helix  chain 'R' and resid 214 through 228
      removed outlier: 4.445A  pdb=" N   SER R 218 " --> pdb=" O   PRO R 214 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ILE R 221 " --> pdb=" O   GLN R 217 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 228 through 253
    Processing helix  chain 'R' and resid 256 through 294
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 300 through 323
      removed outlier: 3.699A  pdb=" N   LEU R 306 " --> pdb=" O   LEU R 302 " (cutoff:3.500A)
      Proline residue:  R 307  - end of helix
      removed outlier: 3.784A  pdb=" N   ALA R 314 " --> pdb=" O   PHE R 310 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR R 315 " --> pdb=" O   ALA R 311 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ILE R 316 " --> pdb=" O   LYS R 312 " (cutoff:3.500A)
      Proline residue:  R 319  - end of helix
    Processing helix  chain 'R' and resid 326 through 335
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35
      removed outlier: 3.527A  pdb=" N   VAL A 185 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40
      removed outlier: 6.661A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.523A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.581A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.778A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.900A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.962A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.584A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.927A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.201A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.475A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.017A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASP B 298 " --> pdb=" O   ASP B 303 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.647A  pdb=" N   SER S  21 " --> pdb=" O   SER S   7 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 3.600A  pdb=" N   VAL S  97 " --> pdb=" O   HIS S  35 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12
      removed outlier: 4.286A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.807A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 155 through 160
      removed outlier: 3.505A  pdb=" N   ALA S 211 " --> pdb=" O   SER S 208 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR S 213 " --> pdb=" O   SER S 206 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'R' and resid 194 through 196

    431 hydrogen bonds defined for protein.
    1230 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: 2.67

  Time building geometry restraints manager: 2.74 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1548
        1.32 -     1.44: 2430
        1.44 -     1.57: 4839
        1.57 -     1.69: 0
        1.69 -     1.81: 94
  Bond restraints: 8911
  Sorted by residual:
  bond pdb=" C   LYS R 312 "
       pdb=" N   SER R 313 "
    ideal  model  delta    sigma   weight residual
    1.335  1.261  0.074 1.35e-02 5.49e+03 3.01e+01
  bond pdb=" N   LYS R 157 "
       pdb=" CA  LYS R 157 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.036 7.40e-03 1.83e+04 2.30e+01
  bond pdb=" C   GLY R 204 "
       pdb=" N   PRO R 205 "
    ideal  model  delta    sigma   weight residual
    1.332  1.391 -0.059 1.34e-02 5.57e+03 1.95e+01
  bond pdb=" N   PRO R 214 "
       pdb=" CD  PRO R 214 "
    ideal  model  delta    sigma   weight residual
    1.473  1.533 -0.060 1.40e-02 5.10e+03 1.84e+01
  bond pdb=" C   GLN R 114 "
       pdb=" N   VAL R 115 "
    ideal  model  delta    sigma   weight residual
    1.335  1.281  0.054 1.26e-02 6.30e+03 1.83e+01
  ... (remaining 8906 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.91: 12087
        6.91 -    13.82: 27
       13.82 -    20.73: 2
       20.73 -    27.64: 0
       27.64 -    34.55: 1
  Bond angle restraints: 12117
  Sorted by residual:
  angle pdb=" N   GLN S 231 "
        pdb=" CA  GLN S 231 "
        pdb=" C   GLN S 231 "
      ideal   model   delta    sigma   weight residual
     111.36  145.91  -34.55 1.09e+00 8.42e-01 1.00e+03
  angle pdb=" N   TYR R 194 "
        pdb=" CA  TYR R 194 "
        pdb=" C   TYR R 194 "
      ideal   model   delta    sigma   weight residual
     110.53   97.01   13.52 1.29e+00 6.01e-01 1.10e+02
  angle pdb=" N   ARG S 191 "
        pdb=" CA  ARG S 191 "
        pdb=" C   ARG S 191 "
      ideal   model   delta    sigma   weight residual
     108.38   98.07   10.31 1.35e+00 5.49e-01 5.83e+01
  angle pdb=" N   VAL R 320 "
        pdb=" CA  VAL R 320 "
        pdb=" C   VAL R 320 "
      ideal   model   delta    sigma   weight residual
     110.42  117.64   -7.22 9.60e-01 1.09e+00 5.65e+01
  angle pdb=" C   GLN S 231 "
        pdb=" CA  GLN S 231 "
        pdb=" CB  GLN S 231 "
      ideal   model   delta    sigma   weight residual
     110.85   98.66   12.19 1.70e+00 3.46e-01 5.14e+01
  ... (remaining 12112 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.88: 4629
       11.88 -    23.75: 397
       23.75 -    35.63: 121
       35.63 -    47.50: 47
       47.50 -    59.38: 17
  Dihedral angle restraints: 5211
    sinusoidal: 1928
      harmonic: 3283
  Sorted by residual:
  dihedral pdb=" N   HIS S 232 "
           pdb=" C   HIS S 232 "
           pdb=" CA  HIS S 232 "
           pdb=" CB  HIS S 232 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  156.47  -33.67     0      2.50e+00 1.60e-01 1.81e+02
  dihedral pdb=" C   HIS S 232 "
           pdb=" N   HIS S 232 "
           pdb=" CA  HIS S 232 "
           pdb=" CB  HIS S 232 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -153.77   31.17     0      2.50e+00 1.60e-01 1.55e+02
  dihedral pdb=" N   GLN S 231 "
           pdb=" C   GLN S 231 "
           pdb=" CA  GLN S 231 "
           pdb=" CB  GLN S 231 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  149.40  -26.60     0      2.50e+00 1.60e-01 1.13e+02
  ... (remaining 5208 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.311: 1366
       0.311 -    0.623: 3
       0.623 -    0.934: 0
       0.934 -    1.246: 1
       1.246 -    1.557: 2
  Chirality restraints: 1372
  Sorted by residual:
  chirality pdb=" CA  GLN S 231 "
            pdb=" N   GLN S 231 "
            pdb=" C   GLN S 231 "
            pdb=" CB  GLN S 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.95    1.56 2.00e-01 2.50e+01 6.06e+01
  chirality pdb=" CA  HIS S 232 "
            pdb=" N   HIS S 232 "
            pdb=" C   HIS S 232 "
            pdb=" CB  HIS S 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.05    1.46 2.00e-01 2.50e+01 5.31e+01
  chirality pdb=" CA  TYR S 235 "
            pdb=" N   TYR S 235 "
            pdb=" C   TYR S 235 "
            pdb=" CB  TYR S 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.57    0.94 2.00e-01 2.50e+01 2.21e+01
  ... (remaining 1369 not shown)

  Planarity restraints: 1529
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 RET R 401 "    0.181 2.00e-02 2.50e+03   1.18e-01 1.74e+02
        pdb=" C11 RET R 401 "   -0.143 2.00e-02 2.50e+03
        pdb=" C19 RET R 401 "    0.013 2.00e-02 2.50e+03
        pdb=" C8  RET R 401 "   -0.112 2.00e-02 2.50e+03
        pdb=" C9  RET R 401 "    0.061 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C12 RET R 401 "   -0.075 2.00e-02 2.50e+03   7.18e-02 6.45e+01
        pdb=" C13 RET R 401 "    0.055 2.00e-02 2.50e+03
        pdb=" C14 RET R 401 "    0.098 2.00e-02 2.50e+03
        pdb=" C15 RET R 401 "   -0.087 2.00e-02 2.50e+03
        pdb=" C20 RET R 401 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C6  RET R 401 "   -0.055 2.00e-02 2.50e+03   5.32e-02 2.83e+01
        pdb=" C7  RET R 401 "    0.062 2.00e-02 2.50e+03
        pdb=" C8  RET R 401 "    0.043 2.00e-02 2.50e+03
        pdb=" C9  RET R 401 "   -0.051 2.00e-02 2.50e+03
  ... (remaining 1526 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 65
        2.58 -     3.16: 7208
        3.16 -     3.74: 13465
        3.74 -     4.32: 19463
        4.32 -     4.90: 32200
  Nonbonded interactions: 72401
  Sorted by model distance:
  nonbonded pdb=" O   TYR S 173 "
            pdb=" O   GLN S 231 "
     model   vdw
     1.998 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 175 "
     model   vdw
     2.047 3.040
  nonbonded pdb=" OD2 ASP A   9 "
            pdb=" ND2 ASN S 169 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.282 3.040
  ... (remaining 72396 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=0.50 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:             3.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     22.830
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
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      :  0.013   0.443   8913  Z= 0.740
  Angle     :  1.362  34.552  12119  Z= 0.922
  Chirality :  0.102   1.557   1372
  Planarity :  0.007   0.118   1529
  Dihedral  : 11.411  59.378   3092
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.30 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  :  4.81 %
    Favored  : 92.56 %
  Cbeta Deviations :  0.66 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.24), residues: 1117
  helix:  0.85 (0.26), residues: 372
  sheet: -2.15 (0.29), residues: 270
  loop : -1.91 (0.26), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP S 111 
 HIS   0.022   0.003   HIS S  35 
 PHE   0.035   0.004   PHE S 177 
 TYR   0.041   0.004   TYR S  94 
 ARG   0.007   0.001   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19514 (  426)
  hydrogen bonds       : angle       7.11447 ( 1230)
  SS BOND              : bond        0.44298 (    1)
  SS BOND              : angle       4.57100 (    2)
  covalent geometry    : bond        0.01205 ( 8911)
  covalent geometry    : angle       1.36091 (12117)
  Misc. bond           : bond        0.12553 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 223
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LYS cc_start: 0.8931 (ttpp) cc_final: 0.8730 (ttmm)
REVERT: B   16 ASN cc_start: 0.8785 (m-40) cc_final: 0.7502 (m-40)
REVERT: B   19 ARG cc_start: 0.8888 (ttp80) cc_final: 0.8580 (tmm-80)
REVERT: B   20 ASP cc_start: 0.9427 (m-30) cc_final: 0.8387 (m-30)
REVERT: G   31 SER cc_start: 0.8347 (t) cc_final: 0.7994 (m)
REVERT: G   42 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7958 (pp20)
REVERT: S   82 GLN cc_start: 0.8522 (tp40) cc_final: 0.8192 (tp-100)
REVERT: S  186 GLN cc_start: 0.8402 (mt0) cc_final: 0.8107 (tt0)
REVERT: S  217 SER cc_start: 0.8889 (m) cc_final: 0.8638 (p)
REVERT: S  219 LEU cc_start: 0.9505 (mp) cc_final: 0.9260 (mm)
REVERT: S  232 HIS cc_start: 0.8921 (OUTLIER) cc_final: 0.7885 (t-90)
REVERT: S  235 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.7073 (t80)
REVERT: R   85 ARG cc_start: 0.8699 (mtm110) cc_final: 0.7782 (mtt-85)
REVERT: R  150 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7945 (mt-10)
REVERT: R  200 LYS cc_start: 0.8388 (mttt) cc_final: 0.8138 (mmtm)
REVERT: R  213 TYR cc_start: 0.6384 (OUTLIER) cc_final: 0.5122 (m-80)
REVERT: R  263 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7959 (tm-30)
REVERT: R  273 MET cc_start: 0.8182 (mtp) cc_final: 0.7868 (mtt)
REVERT: R  326 ASN cc_start: 0.8755 (t0) cc_final: 0.8004 (t0)
REVERT: R  328 GLN cc_start: 0.8472 (mt0) cc_final: 0.8152 (mp10)
  outliers start: 24
  outliers final: 5
  residues processed: 241
  average time/residue: 1.2459
  time to fit residues: 318.2019
Evaluate side-chains
  172 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 163
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  232 HIS
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain R residue   59 TRP
Chi-restraints excluded: chain R residue  114 GLN
Chi-restraints excluded: chain R residue  213 TYR
Chi-restraints excluded: chain R residue  263 GLU
Chi-restraints excluded: chain R residue  284 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 83 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 346 ASN
B  91 HIS
B 220 GLN
B 259 GLN
G   5 ASN
S 142 GLN
R 331 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.107210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.073980 restraints weight = 14437.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 2.96
r_work: 0.2837 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2847
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8913  Z= 0.159
  Angle     :  0.634   8.908  12119  Z= 0.330
  Chirality :  0.044   0.248   1372
  Planarity :  0.005   0.055   1529
  Dihedral  :  6.420  57.009   1245
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 12.36 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.25), residues: 1117
  helix:  1.81 (0.26), residues: 383
  sheet: -1.66 (0.29), residues: 278
  loop : -1.48 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP S 111 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.016   0.002   PHE R 208 
 TYR   0.021   0.002   TYR S 235 
 ARG   0.006   0.001   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04992 (  426)
  hydrogen bonds       : angle       5.07437 ( 1230)
  SS BOND              : bond        0.00561 (    1)
  SS BOND              : angle       0.57348 (    2)
  covalent geometry    : bond        0.00345 ( 8911)
  covalent geometry    : angle       0.63447 (12117)
  Misc. bond           : bond        0.00031 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 181
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8810 (mtp) cc_final: 0.8605 (ttm)
REVERT: A  298 GLU cc_start: 0.8873 (tt0) cc_final: 0.8634 (tt0)
REVERT: A  306 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8708 (mm110)
REVERT: A  354 PHE cc_start: 0.4920 (OUTLIER) cc_final: 0.4192 (m-10)
REVERT: B   16 ASN cc_start: 0.8706 (m-40) cc_final: 0.8282 (m-40)
REVERT: B   19 ARG cc_start: 0.9006 (ttp80) cc_final: 0.8719 (tmm-80)
REVERT: B   22 ARG cc_start: 0.8912 (mtt180) cc_final: 0.8673 (mtt180)
REVERT: B  215 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7180 (pt0)
REVERT: G   31 SER cc_start: 0.8069 (t) cc_final: 0.7670 (m)
REVERT: G   42 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8096 (pp20)
REVERT: S   82 GLN cc_start: 0.8298 (tp40) cc_final: 0.7892 (tp-100)
REVERT: S  186 GLN cc_start: 0.8522 (mt0) cc_final: 0.8133 (tt0)
REVERT: S  235 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.6760 (t80)
REVERT: S  244 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8516 (ttpp)
REVERT: R  113 ASN cc_start: 0.8927 (m-40) cc_final: 0.8471 (t0)
REVERT: R  157 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8278 (mtpt)
REVERT: R  258 SER cc_start: 0.7559 (OUTLIER) cc_final: 0.7241 (t)
REVERT: R  263 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7205 (tm-30)
REVERT: R  265 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7370 (tt0)
  outliers start: 46
  outliers final: 9
  residues processed: 207
  average time/residue: 1.2703
  time to fit residues: 278.6235
Evaluate side-chains
  174 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 158
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain S residue  244 LYS
Chi-restraints excluded: chain R residue  107 SER
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  258 SER
Chi-restraints excluded: chain R residue  263 GLU
Chi-restraints excluded: chain R residue  284 TYR
Chi-restraints excluded: chain R residue  313 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 64 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 81 optimal weight:    9.9990
   chunk 82 optimal weight:    5.9990
   chunk 90 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 94 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
B 239 ASN
B 259 GLN
S  39 GLN
** R  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  89 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.106516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.073642 restraints weight = 14786.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 2.96
r_work: 0.2833 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2844
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2844 r_free = 0.2844    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2844 r_free = 0.2844    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2844
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8913  Z= 0.139
  Angle     :  0.578   9.572  12119  Z= 0.296
  Chirality :  0.042   0.240   1372
  Planarity :  0.005   0.050   1529
  Dihedral  :  5.675  59.710   1235
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 16.52 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.25), residues: 1117
  helix:  2.25 (0.26), residues: 385
  sheet: -1.42 (0.29), residues: 277
  loop : -1.31 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP S 111 
 HIS   0.002   0.001   HIS S 232 
 PHE   0.019   0.001   PHE R 164 
 TYR   0.020   0.002   TYR S 235 
 ARG   0.010   0.001   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04250 (  426)
  hydrogen bonds       : angle       4.71555 ( 1230)
  SS BOND              : bond        0.00302 (    1)
  SS BOND              : angle       0.16832 (    2)
  covalent geometry    : bond        0.00309 ( 8911)
  covalent geometry    : angle       0.57782 (12117)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 171
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8784 (mtp) cc_final: 0.8546 (ttm)
REVERT: A  306 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8644 (mm110)
REVERT: A  354 PHE cc_start: 0.4993 (OUTLIER) cc_final: 0.4395 (m-10)
REVERT: B   16 ASN cc_start: 0.8658 (m-40) cc_final: 0.8101 (m-40)
REVERT: B   19 ARG cc_start: 0.9033 (ttp80) cc_final: 0.8745 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8252 (mpt90) cc_final: 0.7873 (mpp80)
REVERT: B  197 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7904 (mtp85)
REVERT: B  260 GLU cc_start: 0.8197 (pt0) cc_final: 0.7688 (tt0)
REVERT: G   31 SER cc_start: 0.8030 (t) cc_final: 0.7794 (m)
REVERT: G   42 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8167 (pp20)
REVERT: S   82 GLN cc_start: 0.8267 (tp40) cc_final: 0.7816 (tp-100)
REVERT: S   87 ARG cc_start: 0.8823 (ptp-170) cc_final: 0.8599 (pmm-80)
REVERT: S  186 GLN cc_start: 0.8548 (mt0) cc_final: 0.8217 (tt0)
REVERT: S  235 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.6835 (t80)
REVERT: S  244 LYS cc_start: 0.8849 (tttp) cc_final: 0.8561 (ttpp)
REVERT: R   85 ARG cc_start: 0.8502 (mtm110) cc_final: 0.7808 (mtm-85)
REVERT: R  113 ASN cc_start: 0.8898 (m-40) cc_final: 0.8417 (t0)
REVERT: R  150 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8085 (mt-10)
REVERT: R  157 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8286 (mtpt)
REVERT: R  200 LYS cc_start: 0.8208 (mmtp) cc_final: 0.7962 (mmtp)
REVERT: R  263 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7380 (tm-30)
REVERT: R  265 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7337 (tt0)
  outliers start: 37
  outliers final: 13
  residues processed: 190
  average time/residue: 1.3372
  time to fit residues: 268.6049
Evaluate side-chains
  175 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain R residue  107 SER
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  284 TYR
Chi-restraints excluded: chain R residue  315 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 99 optimal weight:    0.6980
   chunk 19 optimal weight:    0.4980
   chunk 108 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B  88 ASN
B 239 ASN
B 259 GLN
B 266 HIS
** R  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 335 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.106991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.074160 restraints weight = 14594.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 2.95
r_work: 0.2845 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.2930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8913  Z= 0.134
  Angle     :  0.571   8.433  12119  Z= 0.290
  Chirality :  0.042   0.226   1372
  Planarity :  0.004   0.048   1529
  Dihedral  :  5.404  59.969   1232
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 16.85 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.25), residues: 1117
  helix:  2.33 (0.26), residues: 386
  sheet: -1.32 (0.28), residues: 277
  loop : -1.15 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP R  59 
 HIS   0.003   0.001   HIS S 232 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.020   0.001   TYR S 235 
 ARG   0.008   0.001   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04036 (  426)
  hydrogen bonds       : angle       4.63168 ( 1230)
  SS BOND              : bond        0.00219 (    1)
  SS BOND              : angle       0.19565 (    2)
  covalent geometry    : bond        0.00298 ( 8911)
  covalent geometry    : angle       0.57070 (12117)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 172
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8858 (mtp) cc_final: 0.8441 (mtm)
REVERT: A  298 GLU cc_start: 0.8795 (tt0) cc_final: 0.8548 (tt0)
REVERT: A  306 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8592 (mm110)
REVERT: A  354 PHE cc_start: 0.5054 (OUTLIER) cc_final: 0.4449 (m-10)
REVERT: B   16 ASN cc_start: 0.8713 (m-40) cc_final: 0.7977 (m-40)
REVERT: B   19 ARG cc_start: 0.9038 (ttp80) cc_final: 0.8720 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8224 (mpt90) cc_final: 0.7757 (mpp80)
REVERT: B   96 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8797 (mtt180)
REVERT: B  197 ARG cc_start: 0.8286 (mtp85) cc_final: 0.8016 (mmm-85)
REVERT: B  217 MET cc_start: 0.9030 (ptp) cc_final: 0.8501 (pmt)
REVERT: B  260 GLU cc_start: 0.8227 (pt0) cc_final: 0.7819 (tt0)
REVERT: G   31 SER cc_start: 0.7973 (t) cc_final: 0.7754 (m)
REVERT: G   42 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8087 (pp20)
REVERT: S   43 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8363 (mtmm)
REVERT: S   82 GLN cc_start: 0.8259 (tp40) cc_final: 0.7774 (tp-100)
REVERT: S   87 ARG cc_start: 0.8810 (ptp-170) cc_final: 0.8600 (pmm-80)
REVERT: S  186 GLN cc_start: 0.8509 (mt0) cc_final: 0.8167 (tt0)
REVERT: S  244 LYS cc_start: 0.8843 (tttp) cc_final: 0.8555 (ttpp)
REVERT: R   85 ARG cc_start: 0.8455 (mtm110) cc_final: 0.7592 (mtt-85)
REVERT: R  113 ASN cc_start: 0.8796 (m-40) cc_final: 0.8315 (t0)
REVERT: R  150 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8155 (mt-10)
REVERT: R  157 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8278 (mtpt)
REVERT: R  200 LYS cc_start: 0.8293 (mmtp) cc_final: 0.8061 (mmtp)
REVERT: R  263 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7338 (tm-30)
REVERT: R  265 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7352 (tt0)
REVERT: R  303 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.7175 (ttp)
  outliers start: 39
  outliers final: 16
  residues processed: 192
  average time/residue: 1.3398
  time to fit residues: 271.9376
Evaluate side-chains
  183 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 162
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   43 LYS
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  223 ASP
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  284 TYR
Chi-restraints excluded: chain R residue  303 MET
Chi-restraints excluded: chain R residue  315 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 100 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 71 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
R  44 ASN
** R  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.106951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.073996 restraints weight = 14571.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 2.96
r_work: 0.2840 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2852
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8913  Z= 0.137
  Angle     :  0.560   9.243  12119  Z= 0.285
  Chirality :  0.042   0.205   1372
  Planarity :  0.004   0.051   1529
  Dihedral  :  4.928  59.562   1230
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 17.72 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.26), residues: 1117
  helix:  2.37 (0.26), residues: 389
  sheet: -1.23 (0.28), residues: 276
  loop : -1.06 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R  59 
 HIS   0.003   0.001   HIS S 232 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.025   0.001   TYR S 235 
 ARG   0.008   0.001   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03893 (  426)
  hydrogen bonds       : angle       4.57691 ( 1230)
  SS BOND              : bond        0.00201 (    1)
  SS BOND              : angle       0.05148 (    2)
  covalent geometry    : bond        0.00309 ( 8911)
  covalent geometry    : angle       0.56041 (12117)
  Misc. bond           : bond        0.00009 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 166
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.7701 (mtm110) cc_final: 0.7490 (ttm-80)
REVERT: A  247 MET cc_start: 0.8812 (mtp) cc_final: 0.8453 (mtm)
REVERT: A  298 GLU cc_start: 0.8807 (tt0) cc_final: 0.8499 (tt0)
REVERT: A  306 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8709 (mm110)
REVERT: B   16 ASN cc_start: 0.8720 (m-40) cc_final: 0.7919 (m-40)
REVERT: B   19 ARG cc_start: 0.9029 (ttp80) cc_final: 0.8700 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8208 (mpt90) cc_final: 0.7737 (mpp80)
REVERT: B   96 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8788 (mtt180)
REVERT: B  215 GLU cc_start: 0.7583 (pt0) cc_final: 0.7336 (pt0)
REVERT: B  217 MET cc_start: 0.9021 (ptp) cc_final: 0.8691 (ptp)
REVERT: B  260 GLU cc_start: 0.8292 (pt0) cc_final: 0.7801 (tt0)
REVERT: B  268 ASN cc_start: 0.8975 (m110) cc_final: 0.8767 (p0)
REVERT: G   31 SER cc_start: 0.7986 (t) cc_final: 0.7760 (m)
REVERT: G   42 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8097 (pp20)
REVERT: S   43 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8356 (mtmm)
REVERT: S   82 GLN cc_start: 0.8249 (tp40) cc_final: 0.7751 (tp-100)
REVERT: S   87 ARG cc_start: 0.8792 (ptp-170) cc_final: 0.8588 (pmm-80)
REVERT: S  160 ARG cc_start: 0.8033 (mtm-85) cc_final: 0.7386 (mtp85)
REVERT: S  186 GLN cc_start: 0.8518 (mt0) cc_final: 0.8177 (tt0)
REVERT: S  235 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6735 (t80)
REVERT: S  244 LYS cc_start: 0.8847 (tttp) cc_final: 0.8560 (ttpp)
REVERT: R   85 ARG cc_start: 0.8387 (mtm110) cc_final: 0.7580 (mtt-85)
REVERT: R  113 ASN cc_start: 0.8762 (m-40) cc_final: 0.8264 (t0)
REVERT: R  157 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8255 (mtpt)
REVERT: R  200 LYS cc_start: 0.8323 (mmtp) cc_final: 0.8109 (mmtp)
REVERT: R  263 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7319 (tm-30)
REVERT: R  303 MET cc_start: 0.7400 (tpp) cc_final: 0.7126 (ttp)
  outliers start: 43
  outliers final: 17
  residues processed: 189
  average time/residue: 1.2332
  time to fit residues: 247.4712
Evaluate side-chains
  181 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 160
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   43 LYS
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  223 ASP
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  315 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 92 optimal weight:    0.7980
   chunk 93 optimal weight:    0.0470
   chunk 86 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   chunk 33 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.1082

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B 239 ASN
B 259 GLN
** R  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.105712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.072823 restraints weight = 14522.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 2.94
r_work: 0.2819 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2827
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2827 r_free = 0.2827    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2827 r_free = 0.2827    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2827
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8913  Z= 0.158
  Angle     :  0.580   8.750  12119  Z= 0.294
  Chirality :  0.042   0.222   1372
  Planarity :  0.004   0.051   1529
  Dihedral  :  4.562  31.290   1228
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 19.47 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.26), residues: 1117
  helix:  2.42 (0.26), residues: 389
  sheet: -1.10 (0.28), residues: 276
  loop : -0.99 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R  59 
 HIS   0.003   0.001   HIS S 232 
 PHE   0.026   0.002   PHE R 208 
 TYR   0.025   0.001   TYR S 235 
 ARG   0.008   0.001   ARG A  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03944 (  426)
  hydrogen bonds       : angle       4.54125 ( 1230)
  SS BOND              : bond        0.00245 (    1)
  SS BOND              : angle       0.12265 (    2)
  covalent geometry    : bond        0.00365 ( 8911)
  covalent geometry    : angle       0.57988 (12117)
  Misc. bond           : bond        0.00011 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 166
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  298 GLU cc_start: 0.8837 (tt0) cc_final: 0.8444 (tt0)
REVERT: A  306 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8734 (mm110)
REVERT: B   16 ASN cc_start: 0.8731 (m-40) cc_final: 0.7933 (m-40)
REVERT: B   19 ARG cc_start: 0.9015 (ttp80) cc_final: 0.8690 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8197 (mpt90) cc_final: 0.7829 (mtm-85)
REVERT: B   96 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8728 (mtt-85)
REVERT: B  217 MET cc_start: 0.8991 (ptp) cc_final: 0.8611 (ptm)
REVERT: G   31 SER cc_start: 0.7997 (t) cc_final: 0.7766 (m)
REVERT: G   42 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8122 (pp20)
REVERT: S   43 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8391 (mtmm)
REVERT: S   82 GLN cc_start: 0.8239 (tp40) cc_final: 0.7746 (tp-100)
REVERT: S  160 ARG cc_start: 0.7983 (mtm-85) cc_final: 0.7398 (mtp85)
REVERT: S  186 GLN cc_start: 0.8552 (mt0) cc_final: 0.8184 (tt0)
REVERT: S  235 TYR cc_start: 0.6984 (OUTLIER) cc_final: 0.6675 (t80)
REVERT: S  244 LYS cc_start: 0.8849 (tttp) cc_final: 0.8564 (ttpp)
REVERT: R   85 ARG cc_start: 0.8391 (mtm110) cc_final: 0.7630 (mtt-85)
REVERT: R  157 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8266 (mtpt)
REVERT: R  200 LYS cc_start: 0.8358 (mmtp) cc_final: 0.8068 (mmtp)
REVERT: R  201 THR cc_start: 0.8628 (p) cc_final: 0.8344 (m)
REVERT: R  263 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7322 (tm-30)
REVERT: R  303 MET cc_start: 0.7146 (tpp) cc_final: 0.6918 (ttp)
  outliers start: 36
  outliers final: 21
  residues processed: 189
  average time/residue: 1.2437
  time to fit residues: 249.5709
Evaluate side-chains
  185 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 160
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   43 LYS
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  223 ASP
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  278 CYS
Chi-restraints excluded: chain R residue  313 SER
Chi-restraints excluded: chain R residue  315 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 53 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9980
   chunk 104 optimal weight:    1.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.104707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.071655 restraints weight = 14741.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 2.96
r_work: 0.2796 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2806
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2806 r_free = 0.2806    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2806 r_free = 0.2806    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2806
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8913  Z= 0.177
  Angle     :  0.588   9.792  12119  Z= 0.300
  Chirality :  0.043   0.224   1372
  Planarity :  0.004   0.054   1529
  Dihedral  :  4.623  33.752   1228
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 19.37 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.26), residues: 1117
  helix:  2.38 (0.26), residues: 391
  sheet: -1.04 (0.29), residues: 276
  loop : -0.92 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R  59 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.014   0.002   PHE B 199 
 TYR   0.023   0.001   TYR S 235 
 ARG   0.008   0.001   ARG A  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03998 (  426)
  hydrogen bonds       : angle       4.53484 ( 1230)
  SS BOND              : bond        0.00261 (    1)
  SS BOND              : angle       0.30609 (    2)
  covalent geometry    : bond        0.00412 ( 8911)
  covalent geometry    : angle       0.58791 (12117)
  Misc. bond           : bond        0.00010 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 160
  time to evaluate  : 1.106 
Fit side-chains
REVERT: A  247 MET cc_start: 0.8792 (mtp) cc_final: 0.8422 (mtt)
REVERT: A  275 GLU cc_start: 0.8942 (tt0) cc_final: 0.8591 (tt0)
REVERT: A  298 GLU cc_start: 0.8822 (tt0) cc_final: 0.8496 (tt0)
REVERT: A  306 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8708 (mm110)
REVERT: B   16 ASN cc_start: 0.8737 (m-40) cc_final: 0.7919 (m-40)
REVERT: B   19 ARG cc_start: 0.9006 (ttp80) cc_final: 0.8647 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8200 (mpt90) cc_final: 0.7868 (mtm-85)
REVERT: B   96 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8739 (mtt-85)
REVERT: B  214 ARG cc_start: 0.9077 (tpp80) cc_final: 0.8687 (mmt90)
REVERT: B  217 MET cc_start: 0.9074 (ptp) cc_final: 0.8486 (ptp)
REVERT: B  260 GLU cc_start: 0.8282 (pt0) cc_final: 0.7829 (tt0)
REVERT: B  268 ASN cc_start: 0.8978 (m110) cc_final: 0.8751 (p0)
REVERT: G   31 SER cc_start: 0.8022 (t) cc_final: 0.7777 (m)
REVERT: G   42 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8184 (pp20)
REVERT: S   43 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8392 (mtmm)
REVERT: S   82 GLN cc_start: 0.8212 (tp40) cc_final: 0.7736 (tp-100)
REVERT: S  160 ARG cc_start: 0.7959 (mtm-85) cc_final: 0.7355 (mtp85)
REVERT: S  186 GLN cc_start: 0.8555 (mt0) cc_final: 0.8156 (tt0)
REVERT: S  235 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.6762 (t80)
REVERT: S  244 LYS cc_start: 0.8846 (tttp) cc_final: 0.8555 (ttpp)
REVERT: R   85 ARG cc_start: 0.8426 (mtm110) cc_final: 0.7636 (mtt-85)
REVERT: R  113 ASN cc_start: 0.8673 (m-40) cc_final: 0.8071 (t0)
REVERT: R  157 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8273 (mtpt)
REVERT: R  200 LYS cc_start: 0.8395 (mmtp) cc_final: 0.8072 (mmtp)
REVERT: R  263 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7314 (tm-30)
REVERT: R  303 MET cc_start: 0.7084 (tpp) cc_final: 0.6701 (ttp)
  outliers start: 38
  outliers final: 19
  residues processed: 181
  average time/residue: 1.3858
  time to fit residues: 265.6715
Evaluate side-chains
  177 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 154
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   43 LYS
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  223 ASP
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  167 LYS
Chi-restraints excluded: chain R residue  278 CYS
Chi-restraints excluded: chain R residue  313 SER
Chi-restraints excluded: chain R residue  315 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 98 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9980
   chunk 57 optimal weight:    0.4980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.106289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.073403 restraints weight = 14647.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 2.96
r_work: 0.2830 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2839
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8913  Z= 0.135
  Angle     :  0.590  10.635  12119  Z= 0.297
  Chirality :  0.042   0.209   1372
  Planarity :  0.004   0.054   1529
  Dihedral  :  4.548  37.226   1228
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 21.12 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.26), residues: 1117
  helix:  2.48 (0.26), residues: 389
  sheet: -0.92 (0.29), residues: 276
  loop : -0.88 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R  59 
 HIS   0.002   0.001   HIS A 188 
 PHE   0.012   0.001   PHE R  69 
 TYR   0.025   0.001   TYR A 296 
 ARG   0.011   0.001   ARG R  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03754 (  426)
  hydrogen bonds       : angle       4.48652 ( 1230)
  SS BOND              : bond        0.00264 (    1)
  SS BOND              : angle       0.11556 (    2)
  covalent geometry    : bond        0.00307 ( 8911)
  covalent geometry    : angle       0.58970 (12117)
  Misc. bond           : bond        0.00146 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 163
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.7711 (mtm110) cc_final: 0.7226 (mtm-85)
REVERT: A  247 MET cc_start: 0.8774 (mtp) cc_final: 0.8447 (mtt)
REVERT: A  298 GLU cc_start: 0.8799 (tt0) cc_final: 0.8452 (tt0)
REVERT: A  306 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8619 (mm110)
REVERT: B   16 ASN cc_start: 0.8771 (m-40) cc_final: 0.8145 (m-40)
REVERT: B   19 ARG cc_start: 0.8971 (ttp80) cc_final: 0.8598 (tmm-80)
REVERT: B   44 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8182 (mp10)
REVERT: B   46 ARG cc_start: 0.8151 (mpt90) cc_final: 0.7825 (mtm-85)
REVERT: B  197 ARG cc_start: 0.8657 (mmm-85) cc_final: 0.8432 (mmm-85)
REVERT: B  214 ARG cc_start: 0.9071 (tpp80) cc_final: 0.8597 (mmt90)
REVERT: B  215 GLU cc_start: 0.7947 (pt0) cc_final: 0.7568 (pt0)
REVERT: B  260 GLU cc_start: 0.8177 (pt0) cc_final: 0.7804 (tt0)
REVERT: B  268 ASN cc_start: 0.8980 (m110) cc_final: 0.8761 (p0)
REVERT: G   31 SER cc_start: 0.7974 (t) cc_final: 0.7750 (m)
REVERT: G   42 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8163 (pp20)
REVERT: S   43 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8370 (mtmm)
REVERT: S   82 GLN cc_start: 0.8226 (tp40) cc_final: 0.7747 (tp-100)
REVERT: S   87 ARG cc_start: 0.8664 (pmm-80) cc_final: 0.8433 (pmm-80)
REVERT: S  160 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7417 (mtp85)
REVERT: S  186 GLN cc_start: 0.8537 (mt0) cc_final: 0.8130 (tt0)
REVERT: S  235 TYR cc_start: 0.7017 (OUTLIER) cc_final: 0.6706 (t80)
REVERT: S  244 LYS cc_start: 0.8858 (tttp) cc_final: 0.8570 (ttpp)
REVERT: R   85 ARG cc_start: 0.8416 (mtm110) cc_final: 0.7629 (mtt-85)
REVERT: R  113 ASN cc_start: 0.8583 (m-40) cc_final: 0.7955 (t0)
REVERT: R  157 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8271 (mtpt)
REVERT: R  200 LYS cc_start: 0.8425 (mmtp) cc_final: 0.8105 (mmtp)
REVERT: R  201 THR cc_start: 0.8640 (p) cc_final: 0.8351 (m)
REVERT: R  263 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7279 (tm-30)
REVERT: R  269 MET cc_start: 0.7557 (mmm) cc_final: 0.7335 (mmt)
REVERT: R  303 MET cc_start: 0.6972 (tpp) cc_final: 0.6638 (ttp)
  outliers start: 31
  outliers final: 16
  residues processed: 181
  average time/residue: 1.2933
  time to fit residues: 248.2121
Evaluate side-chains
  179 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 159
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   43 LYS
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  223 ASP
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  278 CYS
Chi-restraints excluded: chain R residue  315 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 3 optimal weight:    0.3980
   chunk 104 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0170
   chunk 21 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 54 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9980
   chunk 71 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   chunk 100 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
B 259 GLN
** R  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.107342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.074593 restraints weight = 14577.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 2.94
r_work: 0.2852 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2862
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2862
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8913  Z= 0.121
  Angle     :  0.581   9.414  12119  Z= 0.293
  Chirality :  0.042   0.191   1372
  Planarity :  0.004   0.055   1529
  Dihedral  :  4.424  32.467   1228
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 21.33 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.26), residues: 1117
  helix:  2.47 (0.26), residues: 392
  sheet: -0.79 (0.30), residues: 272
  loop : -0.78 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R  59 
 HIS   0.002   0.000   HIS A 188 
 PHE   0.012   0.001   PHE R  69 
 TYR   0.018   0.001   TYR S 235 
 ARG   0.011   0.001   ARG R  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03633 (  426)
  hydrogen bonds       : angle       4.40947 ( 1230)
  SS BOND              : bond        0.00268 (    1)
  SS BOND              : angle       0.03650 (    2)
  covalent geometry    : bond        0.00273 ( 8911)
  covalent geometry    : angle       0.58137 (12117)
  Misc. bond           : bond        0.00114 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 164
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.7688 (mtm110) cc_final: 0.7069 (mtm-85)
REVERT: A  247 MET cc_start: 0.8749 (mtp) cc_final: 0.8454 (mtt)
REVERT: A  275 GLU cc_start: 0.8956 (tt0) cc_final: 0.8660 (tt0)
REVERT: A  298 GLU cc_start: 0.8784 (tt0) cc_final: 0.8432 (tt0)
REVERT: A  306 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8635 (mm110)
REVERT: B   16 ASN cc_start: 0.8744 (m-40) cc_final: 0.8062 (m-40)
REVERT: B   19 ARG cc_start: 0.8962 (ttp80) cc_final: 0.8566 (tmm-80)
REVERT: B   44 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8191 (mp10)
REVERT: B   46 ARG cc_start: 0.8135 (mpt90) cc_final: 0.7810 (mtm-85)
REVERT: B  197 ARG cc_start: 0.8634 (mmm-85) cc_final: 0.8363 (mmm-85)
REVERT: B  214 ARG cc_start: 0.9097 (tpp80) cc_final: 0.8596 (mmt90)
REVERT: B  260 GLU cc_start: 0.8175 (pt0) cc_final: 0.7767 (tt0)
REVERT: B  268 ASN cc_start: 0.8957 (m110) cc_final: 0.8748 (p0)
REVERT: G   31 SER cc_start: 0.8010 (t) cc_final: 0.7779 (m)
REVERT: G   42 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8151 (pp20)
REVERT: S   43 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8373 (mtmm)
REVERT: S   82 GLN cc_start: 0.8238 (tp40) cc_final: 0.7725 (tp-100)
REVERT: S   87 ARG cc_start: 0.8719 (pmm-80) cc_final: 0.8476 (pmm-80)
REVERT: S  160 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7424 (mtp85)
REVERT: S  186 GLN cc_start: 0.8529 (mt0) cc_final: 0.8137 (tt0)
REVERT: S  235 TYR cc_start: 0.6975 (OUTLIER) cc_final: 0.6678 (t80)
REVERT: S  244 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8578 (ttpp)
REVERT: R   85 ARG cc_start: 0.8405 (mtm110) cc_final: 0.7657 (mtm180)
REVERT: R  113 ASN cc_start: 0.8446 (m-40) cc_final: 0.7958 (t0)
REVERT: R  157 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8256 (mtpt)
REVERT: R  200 LYS cc_start: 0.8444 (mmtp) cc_final: 0.8152 (mmtp)
REVERT: R  201 THR cc_start: 0.8591 (p) cc_final: 0.8356 (m)
REVERT: R  263 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7249 (tm-30)
REVERT: R  269 MET cc_start: 0.7564 (mmm) cc_final: 0.7331 (mmt)
REVERT: R  303 MET cc_start: 0.6751 (tpp) cc_final: 0.6507 (ttp)
  outliers start: 26
  outliers final: 16
  residues processed: 179
  average time/residue: 1.2969
  time to fit residues: 245.9411
Evaluate side-chains
  179 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 158
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   43 LYS
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain S residue  244 LYS
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  278 CYS
Chi-restraints excluded: chain R residue  315 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 12 optimal weight:    3.9990
   chunk 88 optimal weight:    7.9990
   chunk 63 optimal weight:    2.9990
   chunk 103 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 3 optimal weight:    0.1980
   chunk 101 optimal weight:    0.9990
   chunk 96 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B 259 GLN
R  44 ASN
** R  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.107185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.074823 restraints weight = 14652.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 2.94
r_work: 0.2855 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2864
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2864
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8913  Z= 0.123
  Angle     :  0.587  10.596  12119  Z= 0.295
  Chirality :  0.041   0.192   1372
  Planarity :  0.004   0.054   1529
  Dihedral  :  4.402  30.439   1228
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 22.21 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.26), residues: 1117
  helix:  2.48 (0.26), residues: 393
  sheet: -0.72 (0.30), residues: 277
  loop : -0.74 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R  59 
 HIS   0.002   0.000   HIS S  35 
 PHE   0.013   0.001   PHE R 208 
 TYR   0.024   0.001   TYR A 296 
 ARG   0.011   0.001   ARG R  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03623 (  426)
  hydrogen bonds       : angle       4.38813 ( 1230)
  SS BOND              : bond        0.00259 (    1)
  SS BOND              : angle       0.12188 (    2)
  covalent geometry    : bond        0.00279 ( 8911)
  covalent geometry    : angle       0.58711 (12117)
  Misc. bond           : bond        0.00106 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 162
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.7693 (mtm110) cc_final: 0.7207 (mtm-85)
REVERT: A  247 MET cc_start: 0.8745 (mtp) cc_final: 0.8444 (mtt)
REVERT: A  298 GLU cc_start: 0.8770 (tt0) cc_final: 0.8404 (tt0)
REVERT: A  306 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8652 (mm110)
REVERT: A  315 ASP cc_start: 0.9256 (OUTLIER) cc_final: 0.8901 (p0)
REVERT: B   16 ASN cc_start: 0.8785 (m-40) cc_final: 0.8103 (m-40)
REVERT: B   19 ARG cc_start: 0.8941 (ttp80) cc_final: 0.8544 (tmm-80)
REVERT: B   44 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8180 (mp10)
REVERT: B   46 ARG cc_start: 0.8123 (mpt90) cc_final: 0.7809 (mtm-85)
REVERT: B  197 ARG cc_start: 0.8601 (mmm-85) cc_final: 0.8354 (mmm-85)
REVERT: B  214 ARG cc_start: 0.9107 (tpp80) cc_final: 0.8640 (mmt90)
REVERT: B  215 GLU cc_start: 0.8026 (pt0) cc_final: 0.7712 (tm-30)
REVERT: B  217 MET cc_start: 0.9059 (ptp) cc_final: 0.8391 (ptt)
REVERT: B  260 GLU cc_start: 0.8169 (pt0) cc_final: 0.7818 (tt0)
REVERT: B  268 ASN cc_start: 0.8937 (m110) cc_final: 0.8731 (p0)
REVERT: G   31 SER cc_start: 0.7976 (t) cc_final: 0.7766 (m)
REVERT: G   42 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8111 (pp20)
REVERT: S   43 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8397 (mtmm)
REVERT: S   82 GLN cc_start: 0.8228 (tp40) cc_final: 0.7712 (tp-100)
REVERT: S   87 ARG cc_start: 0.8729 (pmm-80) cc_final: 0.8478 (pmm-80)
REVERT: S  160 ARG cc_start: 0.8039 (mtm-85) cc_final: 0.7469 (mtp85)
REVERT: S  186 GLN cc_start: 0.8527 (mt0) cc_final: 0.8148 (tt0)
REVERT: S  235 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.6690 (t80)
REVERT: S  244 LYS cc_start: 0.8876 (tttp) cc_final: 0.8590 (ttpp)
REVERT: R   85 ARG cc_start: 0.8390 (mtm110) cc_final: 0.7664 (mtm180)
REVERT: R  113 ASN cc_start: 0.8534 (m-40) cc_final: 0.7987 (t0)
REVERT: R  157 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8216 (mtpt)
REVERT: R  200 LYS cc_start: 0.8449 (mmtp) cc_final: 0.7589 (mmmm)
REVERT: R  201 THR cc_start: 0.8599 (p) cc_final: 0.8384 (m)
REVERT: R  263 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7232 (tm-30)
REVERT: R  269 MET cc_start: 0.7581 (mmm) cc_final: 0.7257 (mmt)
REVERT: R  300 HIS cc_start: 0.7481 (m90) cc_final: 0.7013 (m90)
REVERT: R  303 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6465 (ttp)
  outliers start: 27
  outliers final: 15
  residues processed: 175
  average time/residue: 1.3146
  time to fit residues: 243.6024
Evaluate side-chains
  180 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 159
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   43 LYS
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  223 ASP
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  278 CYS
Chi-restraints excluded: chain R residue  303 MET
Chi-restraints excluded: chain R residue  315 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 107 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 106 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.102303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.069441 restraints weight = 14791.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 2.93
r_work: 0.2752 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2762
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2762 r_free = 0.2762    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2762 r_free = 0.2762    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2762
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.3346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   8913  Z= 0.256
  Angle     :  0.658   9.061  12119  Z= 0.336
  Chirality :  0.045   0.248   1372
  Planarity :  0.005   0.058   1529
  Dihedral  :  4.863  37.790   1228
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 22.32 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.26), residues: 1117
  helix:  2.36 (0.26), residues: 393
  sheet: -0.96 (0.29), residues: 277
  loop : -0.83 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R  59 
 HIS   0.004   0.001   HIS S 232 
 PHE   0.016   0.002   PHE B 199 
 TYR   0.026   0.002   TYR S 235 
 ARG   0.010   0.001   ARG R  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04328 (  426)
  hydrogen bonds       : angle       4.63195 ( 1230)
  SS BOND              : bond        0.00218 (    1)
  SS BOND              : angle       0.21743 (    2)
  covalent geometry    : bond        0.00597 ( 8911)
  covalent geometry    : angle       0.65758 (12117)
  Misc. bond           : bond        0.00105 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8419.76 seconds
wall clock time: 145 minutes 36.45 seconds (8736.45 seconds total)